Contacts of the helix formed by residues 255 - 281 (chain A) in PDB entry 4IKV
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 255 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A GLY 3.6 22.2 - - - +
253A TRP* 3.0 7.8 + - - -
254A PHE* 1.3 80.1 - - - +
256A VAL* 1.3 64.3 + - - +
257A GLU* 3.3 19.2 + - - +
258A THR* 3.0 26.4 + - - -
259A PHE* 3.2 19.4 + - - +
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Residues in contact with VAL 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 4.0 16.8 - - + -
69A ILE* 4.4 18.8 - - + -
255A THR* 1.3 71.9 - - - +
257A GLU* 1.3 80.4 - - - +
259A PHE* 3.3 12.0 + - + +
260A ILE* 2.9 45.6 + - + +
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Residues in contact with GLU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 4.2 18.4 - - + +
255A THR* 3.2 20.6 + - - +
256A VAL* 1.3 91.6 - - + +
258A THR* 1.3 64.7 + - - +
260A ILE* 3.4 10.2 + - + +
261A SER* 3.0 27.8 + - - -
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Residues in contact with THR 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.7 18.4 - - + -
253A TRP* 2.8 37.7 + - + +
255A THR* 3.0 14.9 + - - +
257A GLU* 1.3 76.4 - - - +
259A PHE* 1.3 58.6 + - - +
261A SER* 3.3 7.3 + - - -
262A LEU* 2.9 30.0 + - + +
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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
----------------------------------------------------------
72A ILE* 3.8 27.4 - - + -
76A LEU* 3.8 28.7 - - + -
255A THR 3.2 10.6 + - - +
256A VAL* 3.5 16.6 - - + +
258A THR* 1.3 77.7 - - - +
260A ILE* 1.3 66.0 + - + +
262A LEU* 3.2 23.0 + - + +
263A VAL* 2.9 33.6 + - + +
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Residues in contact with ILE 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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65A LEU* 4.1 15.5 - - + -
68A ALA* 3.9 25.8 - - + +
69A ILE* 4.4 6.1 - - + -
72A ILE* 4.1 20.9 - - + -
256A VAL* 2.9 37.8 + - + +
257A GLU* 3.7 8.7 - - + +
259A PHE* 1.3 74.8 - - + +
261A SER* 1.3 62.7 + - - +
263A VAL* 3.2 9.2 + - - +
264A GLY 3.1 7.8 + - - -
452A ALA* 4.0 19.3 - - + +
453A GLN* 2.9 37.4 + - - +
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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
----------------------------------------------------------
257A GLU 3.0 20.1 + - - -
258A THR* 3.6 8.1 - - - -
259A PHE 3.2 0.2 - - - -
260A ILE* 1.3 77.8 - - - +
262A LEU* 1.3 57.3 + - - +
264A GLY* 3.2 2.1 + - - -
265A ILE* 3.0 39.2 + - - +
453A GLN* 3.7 13.8 + - - +
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Residues in contact with LEU 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU* 5.8 8.1 - - + -
258A THR* 2.9 16.4 + - + +
259A PHE* 3.2 27.6 + - + +
261A SER* 1.3 75.6 - - - +
263A VAL* 1.3 66.9 + - + +
265A ILE* 3.3 16.3 + - + +
266A LEU* 3.0 55.3 + - + +
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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
----------------------------------------------------------
72A ILE* 3.8 28.5 - - + -
75A ALA* 4.4 9.9 - - + -
76A LEU* 4.4 10.3 - - + -
79A MET* 4.7 11.0 - - + +
259A PHE* 2.9 46.8 + - + +
260A ILE 3.5 7.9 - - - +
262A LEU* 1.3 77.8 - - + +
264A GLY* 1.3 56.9 + - - +
266A LEU* 3.3 11.5 + - + +
267A GLY 2.9 23.9 + - - -
449A ALA* 3.4 23.6 - - + +
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Residues in contact with GLY 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 ILE 3.1 11.1 + - - -
261A SER 3.2 2.4 + - - -
262A LEU 3.2 0.2 - - - -
263A VAL* 1.3 73.8 - - - +
265A ILE* 1.3 64.5 + - - +
267A GLY* 3.0 11.8 + - - -
268A ILE* 3.3 19.5 + - - +
449A ALA* 3.8 10.0 - - - +
450A ILE* 5.0 2.5 - - - +
453A GLN* 3.2 30.2 - - - +
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Residues in contact with ILE 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 SER* 3.0 27.0 + - - +
262A LEU* 3.3 16.8 + - + +
264A GLY* 1.3 73.7 - - - +
266A LEU* 1.3 62.7 + - + +
268A ILE* 3.1 9.5 + - - +
269A ILE* 2.9 48.8 + - + +
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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
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79A MET* 4.6 19.1 - - + -
262A LEU* 3.0 49.0 + - + +
263A VAL* 3.7 8.7 - - + +
265A ILE* 1.3 76.9 - - + +
267A GLY* 1.3 64.5 + - - +
269A ILE* 4.3 7.4 - - + +
270A ILE* 3.0 57.1 + - + +
271A PRO* 3.6 0.2 - - - +
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Residues in contact with GLY 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 2.9 14.3 + - - -
264A GLY 3.0 8.1 + - - -
266A LEU* 1.3 76.4 - - - +
268A ILE* 1.3 58.7 + - - +
271A PRO* 3.1 22.6 - - - +
442A LEU* 6.5 0.2 - - - -
446A ALA* 3.4 21.1 - - - +
449A ALA* 3.9 16.8 - - - -
450A ILE* 4.8 5.8 - - - +
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Residues in contact with ILE 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 GLY 3.3 13.4 + - - +
265A ILE* 3.1 9.7 + - - +
266A LEU 3.1 0.4 - - - -
267A GLY* 1.3 80.4 - - - +
269A ILE* 1.3 72.6 + - + +
271A PRO* 3.4 8.9 - - - +
272A ILE* 3.3 34.8 + - + +
450A ILE* 4.5 18.6 - - + -
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Residues in contact with ILE 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ILE* 2.9 38.3 + - + +
266A LEU* 4.5 8.1 - - + +
268A ILE* 1.3 85.6 - - + +
270A ILE* 1.3 62.3 + - + +
272A ILE* 3.3 10.7 + - + +
273A ILE* 2.9 48.4 + - + +
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Residues in contact with ILE 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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78A TYR* 6.2 0.2 - - + -
79A MET* 5.1 11.2 - - + -
266A LEU* 3.0 51.4 + - + +
269A ILE* 1.3 78.5 - - + +
271A PRO* 1.3 69.0 - - + +
273A ILE* 3.4 5.8 + - + +
274A TYR* 3.0 23.4 + - + +
442A LEU* 4.3 21.1 - - + -
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Residues in contact with PRO 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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266A LEU 3.6 1.1 - - - +
267A GLY* 3.1 29.2 - - - +
268A ILE* 3.4 7.6 - - - +
270A ILE* 1.3 93.8 - - + +
272A ILE* 1.3 62.3 + - + +
274A TYR* 3.3 1.6 + - - +
275A PHE* 3.0 32.2 + - + -
299A PHE* 3.7 37.5 - - + -
442A LEU* 4.0 18.2 - - + -
446A ALA* 4.1 7.4 - - + -
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Residues in contact with ILE 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 ILE* 3.3 34.0 + - + +
269A ILE* 3.3 16.3 + - + +
270A ILE 3.3 0.8 - - - -
271A PRO* 1.3 78.3 - - + +
273A ILE* 1.3 74.3 + - + +
275A PHE* 3.2 6.5 + - - +
276A VAL* 3.1 35.8 + - + +
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Residues in contact with ILE 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 ILE* 2.9 43.2 + - + +
270A ILE* 3.9 6.1 - - + +
272A ILE* 1.3 87.2 - - + +
274A TYR* 1.3 60.3 + - + +
276A VAL* 3.1 9.4 + - + +
277A VAL* 2.9 38.5 + - + +
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Residues in contact with TYR 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 ILE* 3.0 19.5 + - + +
271A PRO* 3.7 6.7 - - + +
272A ILE 3.3 0.2 - - - -
273A ILE* 1.3 80.2 - - + +
275A PHE* 1.3 58.5 + + + +
277A VAL* 3.6 9.8 - - + +
278A MET* 3.0 53.0 + - + +
432A PHE* 3.6 28.3 - + - +
435A GLN* 3.2 35.7 + - + +
439A LEU* 3.7 36.2 - - + +
442A LEU* 4.8 7.6 - - + -
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Residues in contact with PHE 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 PRO* 3.0 28.8 + - + -
272A ILE* 3.2 8.5 + - - +
274A TYR* 1.3 80.3 - - + +
276A VAL* 1.3 57.1 + - + +
278A MET* 3.4 14.5 + - + +
279A TYR* 3.0 30.9 + - - +
292A VAL* 3.8 23.2 - - + +
295A TYR* 3.4 35.4 - + - -
296A ILE* 3.7 36.6 - - + -
299A PHE* 3.6 42.2 - + + -
439A LEU* 4.7 6.1 - - + -
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Residues in contact with VAL 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 ILE* 3.1 28.7 + - + +
273A ILE* 3.1 9.4 + - + +
275A PHE* 1.3 74.1 - - + +
277A VAL* 1.3 62.1 + - + +
279A TYR* 4.5 4.3 - - + -
280A ARG* 2.9 55.3 + - + +
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Residues in contact with VAL 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ILE* 2.9 30.0 + - + +
274A TYR* 3.6 17.0 - - + +
276A VAL* 1.3 77.4 - - + +
278A MET* 1.3 61.7 + - - +
280A ARG* 4.0 2.1 - - - -
281A SER* 3.2 24.0 + - - -
432A PHE* 4.0 21.5 - - + -
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Residues in contact with MET 278 (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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274A TYR* 3.0 50.3 + - + +
275A PHE* 3.8 29.6 - - + +
277A VAL* 1.3 76.5 - - - +
279A TYR* 1.3 64.3 + - - +
281A SER* 3.5 6.9 + - - -
284A THR* 3.6 20.8 + - - +
289A ARG* 5.2 0.5 - - - +
292A VAL* 4.2 17.5 - - + +
295A TYR* 5.3 1.6 - - + -
428A ALA* 4.7 2.2 - - - -
429A PRO* 4.0 21.9 - - + +
432A PHE* 3.8 35.2 - - + -
439A LEU* 3.9 20.4 - - + -
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Residues in contact with TYR 279 (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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275A PHE 3.0 19.3 + - - +
276A VAL* 3.9 5.6 - - + +
278A MET* 1.3 77.2 - - - +
280A ARG* 1.3 72.9 + - + +
281A SER 3.6 0.2 + - - -
289A ARG* 3.6 61.2 + - + +
292A VAL* 4.3 10.5 - - + +
293A ILE* 3.6 36.1 - - + +
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Residues in contact with ARG 280 (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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276A VAL* 2.9 37.1 + - + +
277A VAL* 4.0 2.2 - - - +
279A TYR* 1.3 88.3 - - + +
281A SER* 1.3 65.5 + - - +
282A PRO* 3.4 6.1 - - - +
289A ARG* 4.7 4.3 + - - +
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Residues in contact with SER 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A VAL* 3.2 18.3 + - - -
278A MET 3.7 9.9 - - - -
279A TYR 3.3 1.8 - - - -
280A ARG* 1.3 76.8 - - - +
282A PRO* 1.3 66.2 - - - +
283A LYS* 3.0 26.4 + - - +
284A THR* 2.6 35.3 + - - +
289A ARG* 3.1 9.2 + - - -
432A PHE* 3.8 15.6 - - - -
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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) + - + + + + + -
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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