Contacts of the helix formed by residues 235 - 257 (chain A) in PDB entry 1NVD
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 235 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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216A THR* 3.9 20.9 + - - +
217A ILE* 4.4 11.9 - - + +
220A ALA* 4.1 13.0 - - + -
232A PHE* 3.0 42.2 + - + +
233A GLU 2.8 2.6 + - - -
234A GLY* 1.3 76.1 - - - +
236A GLU* 1.3 68.1 + - - +
237A GLU 3.4 2.5 - - - -
238A ILE* 2.8 38.4 + - - +
239A LEU* 2.8 10.6 + - + +
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Residues in contact with GLU 236 (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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19A PHE* 5.7 7.3 - - + -
177A LEU* 5.3 2.7 - - + +
232A PHE* 2.8 22.6 + - + +
233A GLU* 2.7 38.9 + - - +
234A GLY 3.7 0.6 - - - -
235A THR* 1.3 74.2 - - - +
237A GLU* 1.3 66.0 + - + +
239A LEU* 2.8 12.1 + - - +
240A LYS* 2.8 29.2 + - - +
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Residues in contact with GLU 237 (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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235A THR 3.4 0.6 - - - -
236A GLU* 1.3 85.0 - - + +
238A ILE* 1.3 59.4 + - + +
240A LYS* 3.8 25.3 + - - +
241A ALA* 3.0 28.4 + - - +
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Residues in contact with ILE 238 (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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213A ASN* 3.4 36.6 - - + +
216A THR* 4.8 12.3 - - + -
217A ILE* 4.6 4.7 - - + -
234A GLY 4.1 7.6 - - - +
235A THR* 2.8 38.0 + - - +
237A GLU* 1.3 77.2 - - + +
239A LEU* 1.3 64.3 + - - +
241A ALA* 3.4 3.3 + - - -
242A ARG* 3.2 31.0 + - - +
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Residues in contact with LEU 239 (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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141A LEU* 5.6 1.3 - - + -
177A LEU* 5.4 8.7 - - + +
180A LEU* 3.8 18.8 - - + -
188A PHE* 3.9 26.9 - - + -
192A MET* 6.3 1.3 - - - -
217A ILE* 4.3 19.5 - - + -
232A PHE* 3.7 40.8 - - + -
235A THR* 2.8 13.5 + - + +
236A GLU* 3.2 10.5 - - - +
238A ILE* 1.3 75.6 - - - +
240A LYS* 1.3 64.4 + - - +
242A ARG* 3.3 5.4 + - + +
243A ILE* 3.0 41.8 + - + +
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Residues in contact with LYS 240 (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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4A PRO 4.2 10.1 - - - -
5A THR* 2.7 34.1 + - - +
17A ALA* 4.2 15.4 + - + -
18A ASP* 5.2 3.4 - - - +
177A LEU* 4.0 28.0 - - + +
236A GLU 2.8 15.0 + - - +
237A GLU* 3.8 25.4 + - - +
239A LEU* 1.3 77.0 - - - +
241A ALA* 1.3 56.8 + - - +
243A ILE* 3.8 5.0 - - - +
244A LEU* 2.9 50.6 + - + +
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Residues in contact with ALA 241 (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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237A GLU 3.0 20.2 + - - +
238A ILE* 3.7 5.4 - - - +
239A LEU 3.2 0.2 - - - -
240A LYS* 1.3 79.1 - - - +
242A ARG* 1.3 84.3 + - - +
244A LEU* 4.1 4.2 - - - +
245A ALA* 3.1 25.1 + - - +
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Residues in contact with ARG 242 (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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192A MET* 6.2 2.0 - - + -
195A VAL* 4.1 11.3 - - + +
205A GLU* 5.9 0.6 + - - -
206A GLU* 2.5 36.9 + - - +
209A ALA* 4.1 13.9 - - - +
210A LEU* 3.4 31.2 - - + -
213A ASN* 3.0 29.6 + - + +
217A ILE* 4.8 12.3 - - + -
238A ILE* 3.2 26.4 + - - +
239A LEU* 3.3 7.2 + - + +
241A ALA* 1.3 98.8 + - - +
243A ILE* 1.3 69.1 + - + +
245A ALA* 3.5 3.6 + - - +
246A SER* 3.3 18.4 + - - -
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Residues in contact with ILE 243 (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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141A LEU* 4.0 20.0 - - + -
144A MET* 4.5 14.8 - - + +
145A VAL* 3.9 20.2 - - + +
175A ILE* 4.7 14.1 - - + -
177A LEU* 3.5 28.7 - - + -
180A LEU* 4.0 20.0 - - + -
195A VAL* 5.7 0.9 - - + -
239A LEU* 3.0 27.0 + - + +
240A LYS* 3.8 4.5 - - - +
242A ARG* 1.3 77.0 - - + +
244A LEU* 1.3 68.7 + - + +
246A SER* 3.0 8.1 + - - -
247A ALA* 2.9 25.2 + - + +
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Residues in contact with LEU 244 (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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5A THR* 4.0 12.8 - - + -
7A ILE* 4.3 13.2 - - + -
17A ALA* 4.1 22.2 - - + -
175A ILE* 5.4 3.6 - - + -
177A LEU* 6.4 0.7 - - + -
240A LYS* 2.9 54.5 + - + +
241A ALA* 4.1 4.7 - - - +
243A ILE* 1.3 86.8 - - + +
245A ALA* 1.3 51.7 + - - +
247A ALA* 3.8 6.7 - - + +
248A ARG* 2.7 68.7 + - - +
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Residues in contact with ALA 245 (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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198A THR* 4.7 0.4 - - - +
206A GLU* 3.4 39.7 - - + +
241A ALA 3.1 18.9 + - - +
242A ARG 3.8 2.7 - - - +
243A ILE 3.3 0.2 - - - -
244A LEU* 1.3 75.2 - - - +
246A SER* 1.3 62.6 + - - +
248A ARG* 3.9 7.2 - - - +
249A HIS* 3.1 24.3 + - - +
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Residues in contact with SER 246 (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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145A VAL* 3.1 32.1 + - - +
194A GLU 4.8 0.2 - - - -
195A VAL* 4.1 15.7 - - - -
198A THR* 3.5 35.6 + - - +
242A ARG 3.3 9.0 + - - -
243A ILE* 3.0 10.3 + - - -
245A ALA* 1.3 80.3 - - - +
247A ALA* 1.3 62.0 + - - +
249A HIS 3.2 2.4 + - - -
250A LYS* 3.2 21.5 + - - +
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Residues in contact with ALA 247 (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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7A ILE* 4.7 10.3 - - + +
15A ILE* 5.2 2.0 - - + +
144A MET 4.5 7.9 - - - +
145A VAL* 4.2 3.9 + - - +
149A ILE* 3.5 30.6 - - + +
175A ILE* 4.7 9.4 - - + -
243A ILE 2.9 15.2 + - - +
244A LEU* 3.8 12.1 - - + +
246A SER* 1.3 76.8 - - - +
248A ARG* 1.3 60.9 + - - +
250A LYS* 3.5 3.4 + - - +
251A ALA* 3.1 24.8 + - - +
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Residues in contact with ARG 248 (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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5A THR* 3.4 29.3 - - - +
6A LYS 4.7 4.0 + - - -
7A ILE* 4.1 31.9 - - + +
244A LEU* 2.7 65.7 + - - +
245A ALA* 3.9 7.3 - - - +
247A ALA* 1.3 73.3 - - - +
249A HIS* 1.3 62.4 + - - +
251A ALA* 3.5 2.8 + - - +
252A TYR* 3.1 21.5 + - - +
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Residues in contact with HIS 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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198A THR* 3.8 26.7 - - + -
201A ILE* 4.0 21.6 + - + +
202A SER* 3.3 39.4 - - - +
245A ALA 3.1 17.7 + - - +
246A SER 3.2 0.2 + - - -
248A ARG* 1.3 74.5 - - - +
250A LYS* 1.3 66.4 + - - +
252A TYR* 3.2 21.0 - + - +
253A VAL* 3.0 45.3 + - + +
266A LEU* 6.2 1.6 - - - +
267A LEU* 4.9 2.0 - - + -
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Residues in contact with LYS 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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145A VAL 5.0 2.2 - - - +
146A ASP* 2.7 46.3 + - - +
147A SER* 4.2 4.0 + - - +
149A ILE* 2.7 37.3 + - + +
152A LYS* 6.0 0.8 - - - +
198A THR* 4.8 2.9 - - + +
246A SER 3.2 14.8 + - - +
247A ALA* 3.9 5.8 - - - +
249A HIS* 1.3 74.5 - - - +
251A ALA* 1.3 57.3 + - - +
253A VAL* 3.0 2.4 + - - +
254A VAL* 2.8 43.1 + - + +
264A ARG* 4.2 4.0 - - - +
267A LEU* 3.6 32.1 - - + -
500A CRB 2.8 30.8 + - - +
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Residues in contact with ALA 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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7A ILE* 4.0 12.8 - - + -
8A SER 3.6 22.0 - - - +
9A ILE* 3.8 24.4 - - + +
15A ILE* 4.6 3.6 - - + -
149A ILE* 4.6 1.5 - - + +
247A ALA 3.1 16.1 + - - +
248A ARG 3.7 4.9 - - - +
250A LYS* 1.3 77.9 - - - +
252A TYR* 1.3 55.7 + - - +
254A VAL* 4.0 0.7 - - - +
255A SER* 2.8 38.6 + - - -
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Residues in contact with TYR 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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248A ARG 3.1 14.1 + - - +
249A HIS* 3.2 24.7 - + - +
250A LYS 3.0 0.4 - - - -
251A ALA* 1.3 76.9 - - - +
253A VAL* 1.3 74.0 + - + +
255A SER* 3.2 7.8 + - - -
256A ALA* 3.1 29.2 + - + +
263A LEU* 4.7 15.1 - - + +
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Residues in contact with VAL 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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201A ILE* 5.7 0.9 - - + -
249A HIS* 3.2 40.4 - - + +
250A LYS 3.0 6.1 + - - +
252A TYR* 1.3 79.1 - - + +
254A VAL* 1.3 66.2 + - - +
256A ALA* 3.2 2.8 + - - +
257A ASP* 3.0 22.5 + - - +
263A LEU* 3.7 27.1 - - + +
264A ARG* 3.7 28.7 - - - -
266A LEU* 5.5 4.0 - - + -
267A LEU* 4.1 23.6 - - + +
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Residues in contact with VAL 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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9A ILE* 4.0 13.2 - - + -
10A LEU* 3.7 12.9 - - + +
150A GLY* 3.8 32.1 - - - +
169A GLN* 4.5 0.2 - - - +
250A LYS* 2.8 39.6 + - + +
251A ALA 4.0 2.7 - - - +
253A VAL* 1.3 74.3 - - - +
255A SER* 1.3 58.3 + - - +
257A ASP 4.6 1.6 - - - -
258A GLU* 2.9 37.0 + - - +
264A ARG* 3.9 30.5 - - - +
267A LEU* 4.1 3.4 - - + -
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Residues in contact with SER 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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8A SER 4.6 1.0 + - - -
9A ILE* 3.6 4.5 - - - +
10A LEU* 2.8 45.0 + - - +
11A GLY 4.8 0.4 + - - -
251A ALA 2.8 23.4 + - - -
252A TYR* 3.5 7.4 - - - -
254A VAL* 1.3 77.8 - - - +
256A ALA* 1.3 59.4 + - - +
258A GLU 4.9 0.9 + - - -
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Residues in contact with ALA 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 TYR* 3.1 22.6 + - + +
253A VAL 3.8 0.2 - - - +
254A VAL 3.2 0.2 - - - -
255A SER* 1.3 79.6 - - - +
257A ASP* 1.3 61.4 + - - +
258A GLU 4.0 0.4 - - - -
263A LEU* 3.8 25.8 - - + -
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Residues in contact with ASP 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 VAL 3.0 9.6 + - - +
254A VAL 3.6 2.2 - - - -
256A ALA* 1.3 80.8 - - - +
258A GLU* 1.3 66.3 + - - +
259A ARG 3.3 1.7 + - - -
260A GLU* 3.0 9.5 + - - -
261A GLY* 2.5 28.1 + - - -
262A GLY 2.7 23.8 + - - -
263A LEU* 3.1 10.9 + - + -
264A ARG* 2.9 37.6 + - - +
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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
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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