Contacts of the helix formed by residues 247 - 274 (chain A) in PDB entry 3W5D
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 THR 247 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A ASP 3.8 2.2 + - - +
246A LYS* 1.3 71.7 - - - +
248A PRO* 1.4 75.6 - - - +
249A LEU* 4.4 0.9 - - - +
250A GLN* 2.9 29.1 + - - +
251A GLN* 2.9 19.8 + - - +
337A PRO* 3.3 37.4 + - + +
338A SER* 5.1 0.9 - - - -
340A GLU* 2.9 20.3 + - - -
341A THR* 3.3 12.1 - - + +
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Residues in contact with PRO 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS 4.3 2.0 - - - +
247A THR* 1.4 83.2 - - - +
249A LEU* 1.3 53.7 + - - -
251A GLN* 3.4 13.0 + - + +
252A LYS* 2.9 42.4 + - - +
340A GLU* 3.0 21.1 - - - +
341A THR* 4.3 15.0 - - + +
344A CYS* 4.5 8.1 - - + -
697A ILE* 5.6 3.6 - - + -
822A ARG* 3.2 21.1 - - - +
824A PRO* 4.0 26.7 - - + +
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Residues in contact with LEU 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A THR* 5.5 0.7 - - - +
248A PRO* 1.3 74.1 - - - +
250A GLN* 1.3 57.2 + - + +
252A LYS* 4.2 7.4 - - - +
253A LEU* 2.7 67.5 + - + +
315A ILE* 4.6 11.4 - - + -
319A LEU* 6.0 2.0 - - + -
340A GLU* 3.0 27.0 + - + +
754A TYR* 4.6 9.0 - - + -
757A MET* 3.6 34.8 - - + -
761A ILE* 3.8 21.3 - - + -
828A LEU* 4.3 14.6 - - + -
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Residues in contact with GLN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LYS* 3.4 29.4 - - + +
247A THR* 2.9 40.1 + - - +
249A LEU* 1.3 79.7 - - + +
251A GLN* 1.3 61.6 + - - +
253A LEU* 3.5 6.4 + - + +
254A ASP* 2.8 34.7 + - - +
337A PRO* 3.4 28.9 - - + +
1002A PTY 6.0 4.0 - - - +
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Residues in contact with GLN 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ASP* 4.6 8.8 - - - +
246A LYS* 2.7 42.5 + - + +
247A THR 2.9 11.3 + - - +
248A PRO* 3.6 12.1 - - + +
250A GLN* 1.3 75.3 - - - +
252A LYS* 1.3 59.0 + - + +
254A ASP* 3.0 12.1 + - - +
255A GLU* 3.0 27.0 + - - +
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A PRO* 2.9 32.5 + - - +
249A LEU* 4.0 6.2 - - - +
251A GLN* 1.3 76.5 - - + +
253A LEU* 1.3 58.6 + - - +
255A GLU* 3.2 22.8 + - - +
256A PHE* 3.0 26.9 + - - +
754A TYR* 3.6 15.8 + - - -
822A ARG* 3.4 26.7 - - - +
824A PRO 3.3 18.8 + - - +
825A LYS* 4.9 2.9 - - - +
826A GLU 3.2 28.8 + - - +
827A PRO* 4.4 7.9 - - + -
828A LEU* 4.2 23.2 - - + +
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Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 6.0 0.5 - - - +
249A LEU* 2.7 46.4 + - + +
250A GLN* 3.9 5.8 - - + +
252A LYS* 1.3 73.4 - - - +
254A ASP* 1.3 58.3 + - - +
256A PHE* 3.3 18.1 + - + +
257A GLY* 3.0 23.2 + - - -
311A LEU* 5.1 11.4 - - + -
315A ILE* 3.9 24.5 - - + -
761A ILE* 4.8 12.6 - - + -
765A ILE* 5.8 1.8 - - + -
828A LEU* 3.8 25.4 - - + -
1002A PTY 6.0 3.4 - - - +
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Residues in contact with ASP 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 4.7 11.3 - - - +
246A LYS* 3.2 37.2 + - - +
250A GLN* 2.8 27.6 + - - +
251A GLN* 3.0 9.6 + - - +
253A LEU* 1.3 75.1 - - - +
255A GLU* 1.3 63.9 + - - +
257A GLY* 3.4 3.0 + - - +
258A GLU* 3.3 25.7 + - - +
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Residues in contact with GLU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN 3.0 11.2 + - - +
252A LYS* 3.2 27.9 + - - +
254A ASP* 1.3 74.8 - - - +
256A PHE* 1.3 59.7 + - - +
258A GLU* 3.3 8.6 + - - +
259A GLN* 3.0 51.7 + - + +
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Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 5.3 4.7 - - + -
252A LYS 3.0 13.2 + - - +
253A LEU* 3.5 21.3 - - + +
255A GLU* 1.3 77.5 - - - +
257A GLY* 1.3 56.0 + - - +
259A GLN* 4.3 7.4 - - + -
260A LEU* 2.7 77.0 + - + +
306A ALA 5.3 1.1 - - - -
308A PRO* 4.4 13.2 - - + -
311A LEU* 5.9 1.8 - - + -
765A ILE* 3.6 50.0 - - + -
768A ASN* 6.1 0.2 - - - -
828A LEU* 5.9 3.1 - - + -
829A ILE* 6.5 0.2 - - + -
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Residues in contact with GLY 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 6.1 1.1 - - - -
60A LEU* 4.7 7.5 - - - +
61A LEU* 3.8 30.7 - - - +
253A LEU 3.0 13.9 + - - -
254A ASP* 3.4 5.4 + - - -
255A GLU 3.2 0.4 - - - -
256A PHE* 1.3 75.6 - - - +
258A GLU* 1.3 55.8 + - - +
261A SER* 3.0 30.3 + - - -
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Residues in contact with GLU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.2 27.9 - - - +
254A ASP 3.3 16.1 + - - +
255A GLU* 3.3 8.9 + - - +
257A GLY* 1.3 73.1 - - - +
259A GLN* 1.3 66.2 - - - +
261A SER* 3.2 8.6 + - - -
262A LYS* 2.9 28.3 + - - +
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Residues in contact with GLN 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A GLU* 3.0 40.7 + - + +
256A PHE* 3.8 8.7 - - + +
258A GLU* 1.3 82.4 - - - +
260A LEU* 1.3 51.1 + - - +
262A LYS* 3.1 14.6 + - - +
263A VAL* 2.8 41.7 + - + +
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Residues in contact with LEU 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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61A LEU* 4.1 9.4 - - + -
256A PHE* 2.7 56.7 + - + +
257A GLY 4.0 1.8 - - - +
259A GLN* 1.3 68.5 - - - +
261A SER* 1.3 57.0 + - - +
263A VAL* 3.3 17.6 - - + +
264A ILE* 2.7 47.2 + - + +
306A ALA* 3.5 42.6 - - + +
307A ILE* 3.8 16.8 - - + -
308A PRO* 4.2 4.7 - - + -
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Residues in contact with SER 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 3.1 38.3 - - - +
61A LEU* 4.8 4.4 - - - +
64A ILE* 4.6 9.8 - - - +
257A GLY 3.0 15.8 + - - -
258A GLU 3.2 9.6 - - - -
260A LEU* 1.3 77.8 - - - +
262A LYS* 1.3 62.5 + - - +
264A ILE* 3.3 9.6 + - - +
265A SER* 3.1 23.7 + - - -
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Residues in contact with LYS 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 GLU 2.9 13.8 + - - +
259A GLN* 3.3 18.4 - - - +
261A SER* 1.3 76.2 + - - +
263A VAL* 1.3 59.8 + - + +
265A SER* 2.9 20.4 + - - +
266A LEU* 3.2 44.6 + - + +
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLN* 2.8 24.4 + - + +
260A LEU* 3.0 20.4 + - + +
262A LYS* 1.3 75.4 - - + +
264A ILE* 1.3 68.7 + - + +
266A LEU* 3.0 15.2 + - - +
267A ILE* 3.0 38.7 + - + +
306A ALA* 6.4 0.2 - - + -
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Residues in contact with ILE 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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64A ILE* 4.4 18.4 - - + -
260A LEU* 2.7 27.3 + - + +
261A SER* 3.6 8.3 - - - +
263A VAL* 1.3 75.8 - - + +
265A SER* 1.3 65.4 + - - +
267A ILE* 3.2 3.8 + - + -
268A CYS* 3.2 23.1 + - - -
299A ALA 5.8 0.2 - - - +
302A LEU* 3.7 25.2 - - + +
303A ALA* 4.1 18.8 - - + -
306A ALA* 3.7 32.5 - - + -
307A ILE* 3.8 24.0 - - + -
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A SER 3.1 13.7 + - - -
262A LYS* 2.9 23.6 + - - +
264A ILE* 1.3 78.2 - - - +
266A LEU* 1.3 66.2 + - - +
268A CYS* 3.2 11.9 + - - +
269A VAL* 3.1 25.7 + - - +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A LYS* 3.2 46.2 + - + +
263A VAL* 3.0 11.6 + - - +
265A SER* 1.3 83.8 + - - +
267A ILE* 1.3 54.4 + - + +
269A VAL* 3.1 16.1 + - + +
270A ALA* 2.7 35.1 + - - +
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Residues in contact with ILE 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 VAL* 3.0 32.9 + - + +
264A ILE* 3.2 9.6 + - + +
266A LEU* 1.3 77.2 - - + +
268A CYS* 1.3 57.6 + - - +
270A ALA* 3.3 7.9 + - - +
271A VAL* 2.9 29.6 + - - +
302A LEU* 3.5 25.8 - - + -
306A ALA* 6.3 1.1 - - + -
772A VAL* 3.6 30.3 - - + -
776A PHE* 3.8 24.0 - - + -
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Residues in contact with CYS 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 ILE* 3.2 23.4 + - - -
265A SER* 3.3 11.9 - - - +
266A LEU 3.2 0.2 - - - -
267A ILE* 1.3 73.0 - - - +
269A VAL* 1.3 60.8 + - + +
271A VAL* 3.2 10.0 + - - +
272A TRP* 3.0 24.1 + - - +
298A ILE* 6.1 1.1 - - - -
299A ALA* 4.3 24.2 - - - -
302A LEU* 3.8 18.6 - - - -
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Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A SER* 3.1 16.7 + - - +
266A LEU* 3.1 17.8 + - + +
268A CYS* 1.3 71.9 - - + +
270A ALA* 1.3 56.5 + - - +
272A TRP* 2.8 19.7 + - + +
273A LEU* 2.7 54.1 + - + +
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Residues in contact with ALA 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 LEU 2.7 16.5 + - - +
267A ILE* 3.4 14.8 - - + +
269A VAL* 1.3 74.4 - - - +
271A VAL* 1.3 61.5 + - - +
273A LEU* 3.6 9.1 + - - +
274A ILE* 3.2 30.6 + - + +
776A PHE* 4.0 19.1 - - + -
1004A PTY 5.5 0.2 - - - +
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Residues in contact with VAL 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ILE 2.9 20.0 + - - +
268A CYS* 3.6 9.0 - - - +
269A VAL 3.2 0.2 - - - -
270A ALA* 1.3 72.8 - - - +
272A TRP* 1.3 65.4 + - - +
274A ILE* 3.8 7.6 + - + +
275A ASN* 3.6 25.0 + - - +
294A TYR* 5.7 3.1 - - + -
295A TYR* 4.8 15.5 + - + -
298A ILE* 3.3 36.1 - - + -
302A LEU* 4.6 5.2 - - + -
776A PHE* 3.9 24.7 - - + -
779A ALA* 4.7 13.9 - - + -
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Residues in contact with TRP 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 CYS 3.0 11.5 + - - +
269A VAL* 2.8 23.0 + - + +
271A VAL* 1.3 72.1 - - - +
273A LEU* 1.3 87.9 + - + +
274A ILE 3.0 3.6 - - - -
275A ASN* 2.7 28.2 + - - +
276A ILE* 3.3 25.2 + - + +
279A PHE* 4.2 33.2 - + - -
295A TYR* 4.3 25.1 - + + -
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Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A VAL* 2.7 36.3 + - + +
270A ALA* 4.2 7.4 - - - +
272A TRP* 1.3 89.4 - - + +
274A ILE* 1.3 58.9 + - - +
275A ASN 3.3 0.2 - - - -
276A ILE* 3.5 40.2 + - + +
1004A PTY 3.1 31.7 - - + +
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ALA* 3.2 20.4 + - + +
271A VAL* 4.1 7.9 - - + +
272A TRP 2.9 1.4 + - - -
273A LEU* 1.3 78.0 - - - +
275A ASN* 1.3 73.9 + - - +
276A ILE 3.5 0.6 + - - -
277A GLY* 4.7 2.6 + - - -
776A PHE* 3.7 27.8 - - + -
779A ALA 5.5 0.7 - - - +
780A ALA* 3.9 26.7 - - + -
1004A PTY 3.7 62.2 + - + +
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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