Contacts of the helix formed by residues 248 - 284 (chain A) in PDB entry 1Q90
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A TYR* 3.1 44.3 + - + -
247A GLN* 1.3 83.2 + - - +
249A PRO* 1.3 73.3 - - - +
250A ALA* 2.8 31.4 - - - +
251A ARG* 2.8 39.9 + - + +
252A ILE 3.9 0.9 + - - -
960B LFA 5.6 2.4 - - - +
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Residues in contact with PRO 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 3.5 40.3 - - + -
41A PRO* 4.8 4.9 - - + -
143A TYR* 5.3 0.7 - - + +
247A GLN 3.8 2.0 - - - +
248A ASN* 1.3 86.9 - - - +
250A ALA* 1.3 62.5 + - - +
252A ILE* 3.0 9.8 + - + +
253A GLN* 3.0 33.7 + - - +
72N ILE* 4.2 21.6 - - + +
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Residues in contact with ALA 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A ASN* 2.8 26.7 - - - +
249A PRO* 1.3 73.3 - - - +
251A ARG* 1.3 56.4 + - - +
253A GLN* 3.3 16.6 + - - +
254A GLY* 2.9 26.0 + - - -
960B LFA 4.0 25.4 - - + +
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Residues in contact with ARG 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A TYR* 3.6 48.4 + - - +
247A GLN* 4.4 9.3 - - - +
248A ASN* 2.8 33.4 + - + +
250A ALA* 1.3 76.3 - - + +
252A ILE* 1.3 57.5 + - - +
254A GLY 3.2 1.6 + - - -
255A LEU* 2.8 28.6 + - - +
73B MET 5.5 1.2 + - - -
80B TRP* 3.4 70.7 - - + +
960B LFA 3.6 21.1 - - + +
56D VAL* 3.9 18.2 - - + -
59D PRO* 5.1 8.3 - - - +
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Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A GLN* 4.2 20.2 - - + +
248A ASN 4.7 0.7 - - - +
249A PRO* 3.0 8.8 + - + +
251A ARG* 1.3 75.9 - - - +
253A GLN* 1.3 57.5 + - - +
255A LEU* 3.4 8.2 - - + +
256A LEU* 2.9 39.9 + - + +
56D VAL* 4.3 3.8 - - + -
57D LEU* 3.8 21.5 - - + -
72N ILE* 3.6 32.5 - - + +
73N VAL* 3.5 44.2 - - + +
76N GLY* 3.7 18.2 - - - -
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Residues in contact with GLN 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A PRO* 3.0 18.5 + - - +
250A ALA* 3.3 28.0 + - - +
252A ILE* 1.3 74.0 - - - +
254A GLY* 1.3 68.7 + - - +
256A LEU* 2.9 14.0 + - + +
257A VAL* 2.9 27.5 + - + +
72N ILE* 4.4 13.9 - - + +
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Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A ALA 2.9 14.4 + - - -
251A ARG 3.7 2.2 - - - -
253A GLN* 1.3 75.1 - - - +
255A LEU* 1.3 57.2 + - - +
257A VAL* 3.0 10.1 + - - +
258A PHE* 2.8 31.4 + - - +
960B LFA 3.9 20.3 - - - +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG 2.8 15.1 + - - +
252A ILE* 3.4 14.4 - - + +
253A GLN 3.1 0.2 - - - -
254A GLY* 1.3 74.3 - - - +
256A LEU* 1.3 58.8 + - + +
258A PHE* 3.3 7.4 + - + +
259A PHE* 2.9 75.1 + - + -
960B LFA 3.7 6.7 - - + +
52D ILE* 3.9 23.1 - - + +
53D GLY* 3.9 22.4 - - - +
56D VAL* 4.1 22.0 - - + -
57D LEU* 4.4 12.3 - - + -
76N GLY* 4.9 3.4 - - - +
80N THR* 4.1 6.3 - - - +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ILE* 2.9 32.8 + - + +
253A GLN* 2.9 11.5 + - + +
255A LEU* 1.3 76.3 - - + +
257A VAL* 1.3 66.9 + - + +
259A PHE* 3.1 19.4 + - + +
260A SER* 3.1 12.8 + - - -
10L LEU* 5.8 0.9 - - + -
72N ILE* 4.4 10.3 - - + -
75N ILE* 4.4 19.1 - - + -
76N GLY* 4.9 4.9 - - - -
79N ALA* 3.3 34.8 - - + -
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Residues in contact with VAL 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A GLN* 2.9 21.1 + - + +
254A GLY* 3.6 8.7 - - - +
256A LEU* 1.3 76.1 - - + +
258A PHE* 1.3 61.8 + - - +
260A SER* 2.4 26.5 + - - +
261A PHE* 3.2 36.0 + - + -
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Residues in contact with PHE 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A GLY 2.8 13.2 + - - +
255A LEU* 3.4 10.8 - - + +
257A VAL* 1.3 77.9 - - - +
259A PHE* 1.3 77.1 + + - +
261A PHE* 2.8 22.1 + + - +
262A VAL* 3.0 31.4 + - + +
960B LFA 3.8 20.0 - - + -
45D LEU* 5.7 0.4 - - + -
48D PHE* 5.1 4.0 - - + -
49D ALA* 4.6 12.6 - - - -
52D ILE* 3.6 20.0 - - + -
56R PRO* 3.9 31.9 - - + -
59R THR* 3.8 23.1 - - + -
60R LEU* 3.9 29.8 - - + -
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Residues in contact with PHE 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 2.9 50.2 + - + -
256A LEU* 3.1 14.1 + - + +
258A PHE* 1.3 83.4 - + - +
260A SER* 1.3 52.7 + - - +
262A VAL* 3.0 4.3 + - - +
263A LEU* 2.7 37.3 + - - +
49D ALA* 4.0 20.0 - - + -
53D GLY* 4.0 5.4 - - - -
79N ALA* 3.6 19.5 - - + -
80N THR* 3.4 46.0 - - + -
83N MET* 3.4 35.4 - - + +
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Residues in contact with SER 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A LEU 3.1 7.1 + - - -
257A VAL* 2.4 33.6 + - - +
259A PHE* 1.3 78.4 - - - +
261A PHE* 1.3 64.0 + - - +
263A LEU* 3.9 8.0 - - - +
264A LEU* 2.9 31.2 + - - +
17L PHE* 5.3 2.1 - - - -
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Residues in contact with PHE 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A VAL* 3.6 36.1 - - + -
258A PHE* 2.8 14.6 + - - +
260A SER* 1.3 87.0 + - - +
262A VAL* 1.3 60.6 + - - +
264A LEU* 3.5 6.4 - - + +
265A THR* 2.8 30.7 + - - -
55R LEU* 3.6 42.2 - - + -
56R PRO* 3.7 21.0 - - + +
59R THR* 3.6 25.1 - - + -
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A PHE* 3.0 50.5 + - + +
259A PHE 3.3 6.5 - - - +
261A PHE* 1.3 72.8 - - - +
263A LEU* 1.3 67.0 + - - +
265A THR* 3.0 9.1 + - - -
266A GLN* 2.8 46.5 + - - +
45D LEU* 3.8 30.7 - - + +
49D ALA* 4.6 3.1 - - + -
83N MET* 3.5 15.5 - - + -
56R PRO* 4.3 8.3 - - + -
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Residues in contact with LEU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A PHE 2.7 19.5 + - - +
260A SER* 3.9 8.3 - - - +
262A VAL* 1.3 73.4 - - - +
264A LEU* 1.3 67.0 + - - +
266A GLN* 3.3 10.5 + - - +
267A VAL* 3.1 22.2 + - + +
14L ALA* 4.0 24.0 - - + -
17L PHE* 4.2 23.3 - - + -
18L THR* 5.0 0.2 - - - +
82N VAL* 6.3 0.9 - - + -
83N MET* 4.0 13.7 - - + +
86N PHE* 3.4 35.4 - - + -
90N LEU* 4.2 7.9 - - + -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A SER 2.9 19.8 + - - +
261A PHE* 3.5 4.5 - - + +
263A LEU* 1.3 80.3 - - - +
265A THR* 1.3 62.8 + - - +
267A VAL* 3.0 10.0 + - - +
268A LEU* 3.0 37.1 + - + +
17L PHE* 3.9 19.7 - - + -
21L ILE* 4.1 18.8 - - + -
52R GLY* 4.4 14.4 - - - -
55R LEU* 3.7 29.4 - - + -
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Residues in contact with THR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261A PHE 2.8 15.5 + - - -
262A VAL 3.0 7.5 + - - -
264A LEU* 1.3 77.8 - - - +
266A GLN* 1.3 63.5 + - - +
268A LEU* 3.3 8.7 + - - +
269A LEU* 2.9 31.8 + - + +
45D LEU* 3.7 22.7 - - + -
49R LEU* 5.0 1.8 - - + -
52R GLY 3.4 9.4 + - - -
53R ALA* 3.6 29.6 - - + +
56R PRO* 3.2 23.0 - - + +
950R SQD 4.8 0.9 - - + -
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Residues in contact with GLN 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A VAL* 2.8 40.2 + - + +
263A LEU* 3.5 18.4 - - - +
265A THR* 1.3 72.3 - - - +
267A VAL* 1.3 61.3 + - - +
269A LEU* 3.2 10.7 + - - +
270A VAL* 2.9 29.2 + - - +
42D VAL* 3.3 43.6 + - + +
45D LEU* 4.3 6.5 - - + -
46D GLY* 3.6 6.7 - - - +
83N MET* 4.2 5.7 - - - +
87N SER* 3.1 30.1 + - - +
90N LEU* 3.4 18.8 - - + +
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Residues in contact with VAL 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A LEU* 3.1 19.2 + - + +
264A LEU* 3.0 9.4 + - - +
266A GLN* 1.3 74.1 - - - +
268A LEU* 1.3 57.8 + - + +
269A LEU 3.1 0.3 + - - -
270A VAL* 3.2 8.2 + - + +
271A LEU* 2.7 55.9 + - + +
17L PHE* 5.0 6.3 - - + -
18L THR* 3.7 41.5 - - + +
21L ILE* 4.6 14.1 - - + -
90N LEU* 4.0 17.9 - - + -
93N TRP* 5.2 0.9 - - + -
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Residues in contact with LEU 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A LEU* 3.0 38.7 + - + +
265A THR* 3.7 5.8 - - - +
267A VAL* 1.3 75.1 - - - +
269A LEU* 1.3 58.3 + - - +
271A LEU* 4.0 4.7 - - + +
272A LYS* 2.9 31.2 + - - +
21L ILE* 4.4 21.3 - - + -
25L LEU* 4.7 9.2 - - + -
45R MET* 4.8 5.7 - - + +
48R ILE* 3.5 46.4 - - + +
49R LEU* 3.7 22.2 - - + +
52R GLY* 4.0 13.9 - - - -
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A THR* 2.9 34.0 + - + +
266A GLN* 3.3 8.3 - - - +
268A LEU* 1.3 75.7 - - - +
270A VAL* 1.3 58.3 + - - +
272A LYS* 3.2 4.5 + - - +
273A LYS* 2.9 26.2 + - - +
37D LEU 4.2 9.0 - - - +
38D TYR* 3.9 22.6 - - + +
41D PRO* 3.5 27.4 - - + -
42D VAL* 3.7 23.1 - - + +
45D LEU* 4.2 1.6 - - + -
49R LEU* 3.7 29.2 - - + -
950R SQD 4.1 18.8 - - + -
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLN 2.9 19.3 - - - +
267A VAL* 3.3 15.5 - - - +
269A LEU* 1.3 73.0 - - - +
271A LEU* 1.3 63.6 + - - +
273A LYS* 3.2 8.2 + - - +
274A LYS* 3.0 37.9 + - - +
39D MET* 4.9 8.7 - - - -
42D VAL* 4.7 4.2 - - + +
90N LEU* 4.5 22.7 - - + +
93N TRP* 3.8 18.4 - - + -
94N GLY* 3.6 31.0 - - - +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A VAL* 2.7 36.9 + - + +
268A LEU* 4.0 5.4 - - - +
270A VAL* 1.3 72.5 - - - +
272A LYS* 1.3 52.2 + - - +
274A LYS* 3.2 10.1 + - + +
275A GLN* 2.8 34.8 + - - +
21L ILE* 3.9 12.1 - - + -
22L TYR* 3.6 44.2 - - + -
25L LEU* 3.9 17.5 - - + -
32L ILE* 3.7 27.7 - - + +
93N TRP* 3.9 21.1 - - + -
45R MET* 5.0 4.7 - - - -
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Residues in contact with LYS 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A LEU 2.9 20.3 + - - +
269A LEU 3.4 4.7 - - - +
271A LEU* 1.3 75.5 - - - +
273A LYS* 1.3 64.8 + - - +
275A GLN* 2.5 28.9 + - - +
276A PHE* 3.0 21.7 + - - +
38D TYR* 3.3 24.9 - - + +
42R ARG* 3.1 24.2 + - - +
45R MET* 3.9 19.9 - - + +
46R ASN* 3.1 20.7 + - - +
49R LEU* 3.8 20.2 - - + -
950R SQD 2.7 27.2 + - - -
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LEU 2.9 12.1 + - - +
270A VAL* 3.4 10.3 - - - +
271A LEU 3.2 0.4 - - - -
272A LYS* 1.3 79.2 - - - +
274A LYS* 1.3 65.0 + - + +
276A PHE* 3.1 2.8 + - - +
277A GLU* 2.9 52.5 + - + +
34D ASN* 3.5 37.3 + - - +
35D ASP* 4.1 7.9 + - - -
38D TYR* 3.4 28.4 - - + -
39D MET* 4.1 17.7 - - - +
94N GLY* 2.9 33.1 + - - +
95N ARG* 4.1 8.1 - - - +
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A VAL* 3.0 20.5 + - + +
271A LEU* 3.5 12.6 - - + +
273A LYS* 1.3 75.0 - - + +
275A GLN* 1.3 68.2 + - - +
277A GLU* 3.1 28.8 + - - +
278A LYS* 3.4 13.5 + - - +
22L TYR* 6.0 2.7 - - + -
32L ILE* 5.1 6.3 - - + -
88M LEU* 4.6 1.2 - - - +
91M GLU* 3.1 41.4 + - - +
93N TRP* 2.9 58.7 + - + +
94N GLY* 3.9 8.3 + - - +
96N SER* 4.4 8.1 + - - -
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Residues in contact with GLN 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A LEU 2.8 18.1 + - - +
272A LYS* 2.5 42.3 + - - +
274A LYS* 1.3 70.5 - - - +
276A PHE* 1.3 61.6 + - - +
278A LYS* 3.0 32.4 - - - +
279A VAL* 3.9 0.7 + - - +
31L LEU 3.2 16.5 + - - +
32L ILE* 4.1 21.4 - - + +
37R PRO* 3.7 19.7 - - + +
41R LYS 2.7 33.3 + - - -
42R ARG* 3.8 12.0 - - - +
45R MET* 3.4 16.0 - - + +
950R SQD 4.0 0.5 + - - -
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Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LYS 3.0 13.7 + - - +
273A LYS 3.7 3.6 - - - +
275A GLN* 1.3 77.2 - - - +
277A GLU* 1.3 61.6 + - + +
278A LYS 2.9 5.8 - - - -
279A VAL* 2.9 27.0 + - + +
280A GLN* 3.0 49.9 + - + +
283A GLU* 5.6 3.1 - - - -
33D PRO* 4.2 21.3 - - + -
34D ASN* 5.3 1.1 - - - -
38D TYR* 4.6 7.6 - + + -
42R ARG* 3.0 34.1 - - - +
950R SQD 3.4 50.5 - - + +
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LYS* 2.9 45.1 + - + +
274A LYS* 3.1 33.5 + - - +
276A PHE* 1.3 73.5 - - + +
278A LYS* 1.3 67.0 + - - +
280A GLN* 3.5 23.5 - - + +
281A LEU* 2.8 26.3 + - - +
34D ASN* 3.8 8.6 - - - +
94N GLY 4.9 0.5 - - - +
96N SER* 5.8 0.3 + - - -
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LYS 3.4 9.3 + - - +
275A GLN 3.0 20.7 + - - +
276A PHE 2.9 0.2 - - - -
277A GLU* 1.3 80.2 - - - +
279A VAL* 1.3 63.7 + - - +
281A LEU* 3.2 7.9 + - - +
282A ALA* 3.0 19.4 + - - +
26L LEU* 4.5 10.7 - - - +
32L ILE* 3.2 31.8 + - - +
34R SER* 3.5 24.2 + - - +
35R GLU 4.0 8.5 + - - +
36R VAL* 4.4 8.7 - - + +
37R PRO* 3.3 22.9 - - + -
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Residues in contact with VAL 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLN 4.4 2.5 - - - +
276A PHE* 3.2 20.4 - - + +
278A LYS* 1.3 75.6 - - - +
280A GLN* 1.3 66.0 + - - +
282A ALA* 2.9 11.7 + - + +
283A GLU* 3.1 41.8 + - + +
36R VAL* 3.8 16.2 - - + -
37R PRO* 4.0 15.9 - - + +
42R ARG* 3.5 48.5 - - - +
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PHE* 3.0 44.7 + - + +
277A GLU* 3.5 19.6 - - + +
279A VAL* 1.3 78.8 - - - +
281A LEU* 1.3 64.3 + - - +
283A GLU* 3.4 9.5 + - - +
284A MET* 3.2 28.3 + - + +
30D PRO* 3.8 13.0 - - - +
32D TRP 4.9 0.2 + - - -
33D PRO* 4.3 3.2 - - - +
34D ASN* 2.9 42.8 + - - +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A GLU 2.8 18.0 + - - +
278A LYS* 3.3 7.4 - - - +
280A GLN* 1.3 75.9 - - - +
282A ALA* 1.3 67.7 + - - +
284A MET* 3.2 23.2 + - + +
285A ASN* 3.7 5.0 + - + +
33R SER* 5.8 3.6 - - - +
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Residues in contact with ALA 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LYS 3.0 11.5 + - - +
279A VAL 2.9 10.4 + - - +
281A LEU* 1.3 81.0 - - - +
283A GLU* 1.3 61.2 + - + +
285A ASN* 2.8 32.5 + - - +
288A HIS* 4.1 11.0 - - + +
36R VAL* 3.8 28.3 - - + -
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Residues in contact with GLU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A PHE* 5.6 3.1 - - - -
279A VAL* 3.1 34.8 + - + +
280A GLN* 3.9 8.5 - - - +
282A ALA* 1.3 75.0 - - + +
284A MET* 1.3 64.4 + - + +
285A ASN 3.1 2.9 - - - -
288A HIS* 4.1 33.1 + - + +
289A HIS* 2.9 31.0 + - + +
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Residues in contact with MET 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A GLN* 3.2 15.9 + - + +
281A LEU* 3.2 18.8 + - + +
282A ALA 3.0 1.4 + - - -
283A GLU* 1.3 87.9 - - + +
285A ASN* 1.3 59.6 + - - +
286A PHE 3.7 2.3 + - - -
289A HIS* 5.2 3.1 - - - +
4D THR 4.1 27.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il