Contacts of the helix formed by residues 263 - 285 (chain A) in PDB entry 3NIA
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 SER 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A LYS 3.9 0.6 + - - -
262A LEU* 1.3 75.8 - - - +
264A ALA* 1.3 66.3 + - - +
265A VAL* 3.6 7.1 + - - +
266A GLU* 2.9 42.0 + - - +
267A ARG* 2.9 22.6 + - - +
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Residues in contact with ALA 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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238A ARG* 5.2 0.5 + - - -
263A SER* 1.3 72.8 - - - +
265A VAL* 1.3 66.3 + - + +
267A ARG* 3.2 23.3 + - - +
268A ASP* 3.1 26.7 + - - +
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A SER* 3.3 7.2 + - - +
264A ALA* 1.3 77.6 - - + +
266A GLU* 1.3 59.1 + - + +
268A ASP* 3.2 14.2 + - + +
269A GLU* 3.0 46.5 + - + +
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Residues in contact with GLU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 6.5 0.2 - - + -
261A LYS 4.6 1.2 - - - +
262A LEU* 3.5 28.0 - - + +
263A SER* 2.9 45.6 + - - +
265A VAL* 1.3 77.3 - - + +
267A ARG* 1.3 57.0 + - - +
269A GLU* 3.3 19.6 + - - +
270A LEU* 2.8 27.2 + - - +
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Residues in contact with ARG 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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232A THR* 6.3 2.6 - - - +
236A GLY* 3.4 35.1 - - - +
237A GLY 4.8 2.0 - - - -
238A ARG* 4.0 24.0 - - + +
257A THR* 5.6 0.9 - - - +
259A ALA* 2.9 20.1 + - + +
260A PRO* 3.1 22.6 + - - +
262A LEU* 3.0 37.4 + - + -
263A SER 2.9 15.8 + - - +
264A ALA* 3.2 24.5 + - - +
266A GLU* 1.3 73.9 - - - +
268A ASP* 1.3 65.9 + - - +
270A LEU* 3.2 9.6 + - + +
271A VAL* 3.1 26.9 + - - +
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Residues in contact with ASP 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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214A ALA* 3.2 39.9 - - + +
215A THR* 3.7 7.1 - - - +
238A ARG* 2.8 41.6 + - - +
264A ALA 3.1 17.2 + - - +
265A VAL* 3.3 16.4 - - + +
267A ARG* 1.3 74.8 - - - +
269A GLU* 1.3 65.2 + - + +
271A VAL* 3.1 4.2 + - - +
272A ALA 3.0 18.7 + - - -
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Residues in contact with GLU 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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214A ALA 4.9 0.2 - - - -
265A VAL* 3.0 36.9 + - + +
266A GLU* 3.5 21.0 - - - +
267A ARG 3.2 0.2 - - - -
268A ASP* 1.3 77.5 - - + +
270A LEU* 1.3 57.7 + - - +
272A ALA* 3.3 8.1 + - - +
273A SER* 2.8 34.6 + - - +
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Residues in contact with LEU 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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31A LEU* 4.0 25.6 - - + +
35A LYS* 4.0 25.4 - - + +
37A ALA* 3.8 24.0 - - + -
39A ILE* 4.1 12.1 - - + -
257A THR* 3.9 27.6 - - + +
259A ALA* 4.3 4.7 - - + -
262A LEU* 4.2 14.6 - - + -
266A GLU 2.8 14.2 + - - +
267A ARG* 3.4 11.2 - - + +
268A ASP 3.2 0.2 - - - -
269A GLU* 1.3 76.5 - - - +
271A VAL* 1.3 63.1 + - - +
273A SER* 3.1 7.5 + - - -
274A VAL* 2.9 22.2 + - - +
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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
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215A THR* 4.0 10.5 - - + -
216A LEU* 3.6 34.5 - - + +
238A ARG* 3.8 35.4 - - + +
239A ASN 5.4 0.2 - - - -
240A ASP* 4.1 13.9 - - + +
255A VAL* 4.4 8.5 - - + -
257A THR* 4.0 14.1 - - + +
267A ARG 3.1 15.1 + - - +
268A ASP 3.1 6.2 + - - +
270A LEU* 1.3 76.0 - - - +
272A ALA* 1.3 62.6 + - - +
274A VAL* 3.2 9.5 + - - +
275A GLY 3.0 17.2 + - - -
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Residues in contact with ALA 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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214A ALA 3.9 6.7 - - - +
215A THR 3.4 22.3 + - - +
216A LEU* 4.6 0.4 - - - +
218A ALA* 3.9 15.0 - - + +
219A GLY* 3.3 14.1 - - - +
268A ASP 3.0 12.7 + - - +
269A GLU* 3.6 10.1 - - - +
271A VAL* 1.3 76.9 - - - +
273A SER* 1.3 62.4 + - - +
275A GLY 3.0 2.3 + - - +
276A GLN* 3.0 20.1 + - - +
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Residues in contact with SER 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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31A LEU* 3.8 28.5 - - - +
269A GLU* 2.8 19.2 + - - +
270A LEU* 3.1 10.4 + - - -
272A ALA* 1.3 72.8 - - - +
274A VAL* 1.3 63.9 + - - +
276A GLN* 3.1 25.6 + - - +
277A VAL* 3.1 16.8 + - - +
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Residues in contact with VAL 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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28A LEU* 4.1 9.9 - - + -
31A LEU* 4.3 7.0 - - + -
39A ILE* 3.8 35.4 - - + -
41A VAL* 4.0 21.8 - - + -
216A LEU* 4.6 0.2 - - + -
255A VAL* 4.1 11.9 - - + -
257A THR* 4.7 6.1 - - + -
270A LEU 2.9 20.9 + - - +
271A VAL* 3.2 11.0 + - - +
273A SER* 1.3 75.0 - - - +
275A GLY* 1.3 64.2 + - - +
277A VAL* 3.1 5.4 + - - +
278A ILE* 2.9 39.6 + - + +
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Residues in contact with GLY 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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216A LEU* 3.7 26.2 - - - +
219A GLY 3.4 6.2 - - - +
220A PHE* 3.5 14.5 - - - -
271A VAL 3.0 10.7 + - - -
272A ALA 3.0 5.5 + - - -
274A VAL* 1.3 78.4 - - - +
276A GLN* 1.3 56.8 + - - +
278A ILE* 3.3 1.2 + - - -
279A THR* 2.9 31.4 + - - -
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Residues in contact with GLN 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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218A ALA 5.1 3.6 + - - -
219A GLY* 3.4 21.0 - - - +
272A ALA 3.0 18.0 + - - +
273A SER* 3.1 16.7 + - - +
275A GLY* 1.3 73.2 - - - +
277A VAL* 1.3 65.7 + - + +
279A THR* 3.3 4.8 + - - -
280A GLN* 3.1 22.9 + - - +
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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
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24A PHE* 3.6 38.1 - - + +
27A ASP* 3.9 24.5 - - + +
28A LEU* 3.8 18.2 - - + -
31A LEU* 4.1 18.6 - - + -
273A SER 3.1 13.8 + - - +
274A VAL 3.1 5.8 + - - +
276A GLN* 1.3 73.2 - - + +
278A ILE* 1.3 66.1 + - - +
280A GLN* 3.3 9.6 + - + +
281A LEU* 3.2 20.8 + - - +
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Residues in contact with ILE 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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24A PHE* 4.2 16.4 - - + -
41A VAL* 4.2 6.1 - - + -
43A ILE* 3.8 26.2 - - + -
216A LEU* 4.2 10.3 - - + -
220A PHE* 3.9 16.2 - - + -
224A TRP* 4.9 0.7 - - + -
244A PHE* 4.1 10.3 - - + -
253A VAL* 4.1 14.1 - - + -
255A VAL* 4.0 18.4 - - + -
274A VAL* 2.9 34.8 + - + +
275A GLY* 3.5 7.2 - - - +
277A VAL* 1.3 75.7 - - - +
279A THR* 1.3 64.2 + - - +
281A LEU* 3.2 3.7 + - - +
282A ILE* 3.0 31.4 + - + +
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Residues in contact with THR 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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219A GLY 3.0 15.9 + - - +
220A PHE* 3.5 6.2 - - - -
221A PRO* 3.4 37.7 - - + +
224A TRP* 3.8 10.3 - - + -
275A GLY 2.9 17.9 + - - -
276A GLN* 3.4 10.3 - - - -
277A VAL 3.3 0.2 - - - -
278A ILE* 1.3 76.8 - - - +
280A GLN* 1.3 63.5 + - - +
282A ILE* 3.2 1.4 + - - +
283A LEU* 2.9 39.9 + - + +
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Residues in contact with GLN 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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23A THR* 3.5 29.9 - - + +
27A ASP* 4.1 10.6 + - - +
276A GLN 3.1 11.2 + - - +
277A VAL* 3.7 10.7 - - - +
278A ILE 3.3 0.4 - - - -
279A THR* 1.3 80.0 - - - +
281A LEU* 1.3 62.9 + - - +
283A LEU* 4.0 4.0 - - - +
284A SER* 3.2 27.4 + - - -
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Residues in contact with LEU 281 (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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20A GLU* 3.4 49.8 - - + +
21A LYS* 4.4 5.4 - - + +
24A PHE* 3.6 26.9 - - + -
43A ILE* 4.7 7.6 - - + -
51A VAL* 5.0 7.9 - - + +
52A ALA* 3.3 34.3 - - + -
277A VAL 3.2 13.7 + - - +
278A ILE 3.6 7.2 - - - +
280A GLN* 1.3 77.8 - - - +
282A ILE* 1.3 65.6 + - + +
284A SER* 2.8 20.2 + - - -
285A THR* 2.9 15.5 - - + +
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Residues in contact with ILE 282 (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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43A ILE* 4.6 8.7 - - + -
51A VAL* 4.4 14.6 - - + -
224A TRP* 3.8 22.4 - - + -
244A PHE* 4.0 22.4 - - + -
246A ALA* 4.0 15.7 - - + +
247A GLN* 3.7 11.7 - - - +
251A TYR* 3.8 38.8 - - + +
278A ILE* 3.0 25.5 + - + +
279A THR 3.8 2.9 - - - +
281A LEU* 1.3 77.9 - - + +
283A LEU* 1.3 63.6 + - + +
285A THR* 2.9 26.9 + - + +
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Residues in contact with LEU 283 (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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221A PRO* 4.4 9.2 - - + -
224A TRP* 4.0 22.4 - - + +
247A GLN* 3.7 36.5 + - + +
279A THR* 2.9 38.6 + - + +
280A GLN* 4.2 4.0 - - - +
282A ILE* 1.3 76.7 - - + +
284A SER* 1.3 60.4 + - - +
285A THR 3.2 6.6 + - - +
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Residues in contact with SER 284 (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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20A GLU* 2.7 43.4 + - - +
280A GLN* 3.2 18.1 + - - -
281A LEU 2.8 12.8 + - - -
282A ILE 3.2 0.2 - - - -
283A LEU* 1.3 77.7 - - - +
285A THR* 1.3 61.2 + - - +
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Residues in contact with THR 285 (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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20A GLU* 3.1 27.6 - - - +
51A VAL* 6.0 4.7 - - + -
247A GLN* 4.3 9.7 + - - +
249A ARG* 3.8 24.8 + - - -
251A TYR* 4.5 5.7 + - - -
281A LEU* 2.9 24.7 - - + +
282A ILE* 2.9 20.1 + - + +
283A LEU 3.2 7.6 - - - +
284A SER* 1.3 82.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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