Contacts of the helix formed by residues 235 - 257 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B THR* 3.9 21.9 - - + +
217B ILE* 4.2 9.4 - - + +
220B ALA* 4.3 11.2 - - + -
232B PHE* 3.0 46.2 - - + +
233B GLU 2.8 1.8 + - - -
234B GLY* 1.3 79.4 - - - +
236B GLU* 1.3 66.4 + - - +
237B GLU 3.3 3.1 - - - -
238B ILE* 2.8 36.8 + - - +
239B LEU* 2.9 10.7 + - + +
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 4.9 15.0 - - - +
177B LEU* 5.2 3.6 - - + +
232B PHE* 2.8 32.5 + - + +
233B GLU* 3.0 28.7 + - - +
234B GLY 3.8 0.2 - - - -
235B THR* 1.3 77.1 - - - +
237B GLU* 1.3 65.1 + - + +
238B ILE 3.2 0.3 + - - -
239B LEU* 3.2 8.0 + - - +
240B LYS* 2.9 31.6 + - - +
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B THR 3.3 0.8 - - - -
236B GLU* 1.3 83.7 - - + +
238B ILE* 1.3 59.4 + - + +
240B LYS* 4.1 21.7 + - - +
241B ALA* 3.2 27.0 + - - +
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ASN* 3.0 44.6 - - + +
216B THR* 4.8 11.2 - - + -
217B ILE* 4.2 6.7 - - + -
234B GLY 4.4 6.3 - - - +
235B THR* 2.8 33.7 + - - +
237B GLU* 1.3 78.1 - - + +
239B LEU* 1.3 66.8 + - - +
241B ALA* 3.3 1.9 + - - -
242B ARG* 3.1 35.2 + - + +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 5.6 0.2 - - + -
177B LEU* 5.8 7.4 - - + -
180B LEU* 3.9 20.4 - - + -
188B PHE* 3.7 25.6 - - + -
192B MET* 6.1 2.0 - - - -
217B ILE* 3.8 24.2 - - + -
232B PHE* 3.6 41.7 - - + -
235B THR* 2.9 11.9 + - - +
236B GLU* 3.5 9.4 - - - +
238B ILE* 1.3 77.2 - - - +
240B LYS* 1.3 56.8 + - - +
242B ARG* 2.9 11.3 + - + +
243B ILE* 2.9 44.5 + - + +
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Residues in contact with LYS 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO 4.2 12.3 - - - -
5B THR* 3.2 26.6 + - - -
17B ALA* 3.9 17.6 + - - -
18B ASP* 4.4 10.7 + - - +
19B PHE 5.4 0.4 - - - +
177B LEU* 3.9 26.1 - - + +
236B GLU 2.9 17.3 + - - +
237B GLU* 4.2 22.8 + - - +
239B LEU* 1.3 77.7 - - - +
241B ALA* 1.3 56.6 + - - +
243B ILE* 4.0 8.3 - - - -
244B LEU* 2.9 53.4 + - + +
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Residues in contact with ALA 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLU 3.2 19.2 + - - +
238B ILE* 3.7 5.6 - - - +
239B LEU 3.2 0.2 - - - -
240B LYS* 1.3 78.3 - - - +
242B ARG* 1.3 81.0 + - - +
244B LEU* 4.1 6.1 - - - +
245B ALA* 3.1 24.4 + - - +
248B ARG* 5.3 0.3 + - - -
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B MET* 6.3 1.3 - - + -
195B VAL* 4.2 11.2 - - + +
206B GLU* 2.6 35.7 + - - +
209B ALA* 4.0 15.4 - - - +
210B LEU* 3.3 36.1 - - + +
213B ASN* 2.9 33.4 + - + +
217B ILE* 5.2 4.9 - - + -
238B ILE* 3.1 25.7 + - + +
239B LEU* 2.9 12.0 + - + +
241B ALA* 1.3 94.0 + - - +
243B ILE* 1.3 67.4 + - + +
245B ALA* 3.5 3.3 + - - +
246B SER* 3.3 19.2 + - - -
323B TYR* 6.0 0.2 - - - +
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Residues in contact with ILE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LEU* 3.2 35.4 - - + -
144B MET* 4.4 18.6 - - + +
145B VAL* 3.7 19.9 - - + +
175B ILE* 4.7 12.8 - - + -
177B LEU* 4.4 11.2 - - + -
180B LEU* 4.7 6.7 - - + -
195B VAL* 5.7 2.0 - - + -
239B LEU* 2.9 38.5 + - + +
240B LYS* 3.6 8.1 - - - +
241B ALA 3.4 0.2 - - - -
242B ARG* 1.3 77.0 - - + +
244B LEU* 1.3 67.3 + - + +
246B SER* 3.0 8.3 + - - -
247B ALA* 2.9 24.5 + - + +
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B THR* 3.5 40.4 - - + +
7B ILE* 4.6 8.1 - - + -
17B ALA* 4.2 17.9 - - + -
175B ILE* 5.9 2.0 - - + -
177B LEU* 5.7 2.5 - - + -
240B LYS* 2.9 45.8 + - + +
241B ALA* 4.1 5.2 - - - +
243B ILE* 1.3 85.2 - - + +
245B ALA* 1.3 56.4 + - - +
247B ALA* 4.3 6.5 - - + -
248B ARG* 2.7 63.6 + - - +
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B THR* 4.8 0.4 - - - +
206B GLU* 3.4 36.1 - - + +
241B ALA 3.1 19.6 + - - +
242B ARG 3.8 3.6 - - - +
243B ILE 3.3 0.2 - - - -
244B LEU* 1.3 75.8 - - - +
246B SER* 1.3 62.7 + - - +
248B ARG* 3.8 9.8 - - - +
249B HIS* 3.1 24.3 + - - +
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL* 3.1 32.1 + - - +
195B VAL* 4.1 14.7 - - - -
198B THR* 3.5 35.5 + - - +
242B ARG 3.3 9.5 + - - -
243B ILE* 3.0 10.0 + - - -
245B ALA* 1.3 79.2 - - - +
247B ALA* 1.3 63.5 + - - +
249B HIS 3.2 2.4 + - - -
250B LYS* 3.2 20.6 + - - +
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Residues in contact with ALA 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.7 9.0 - - + +
15B ILE* 5.3 4.7 - - + -
144B MET 4.5 7.2 - - - +
145B VAL 4.3 4.0 + - - -
149B ILE* 3.5 31.5 - - + +
175B ILE* 4.7 10.1 - - + -
243B ILE 2.9 16.0 + - - +
244B LEU* 3.8 8.5 - - + +
246B SER* 1.3 75.3 + - - +
248B ARG* 1.3 63.6 + - + +
250B LYS* 3.5 3.0 + - - +
251B ALA* 3.1 24.4 + - - +
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Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B THR* 3.3 30.9 - - - +
6B LYS 5.3 1.0 + - - -
7B ILE* 3.9 29.2 - - + +
241B ALA 5.3 0.6 + - - -
244B LEU* 2.7 66.7 + - - +
245B ALA* 3.8 8.7 - - - +
247B ALA* 1.3 75.0 - - - +
249B HIS* 1.3 60.8 + - - +
251B ALA* 3.5 2.8 + - - +
252B TYR* 3.1 21.8 + - - +
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Residues in contact with HIS 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B THR* 3.8 27.1 - - + -
201B ILE* 4.0 21.4 + - + +
202B SER* 3.3 37.4 - - - +
245B ALA 3.1 17.5 + - - +
246B SER 3.2 0.2 + - - -
248B ARG* 1.3 74.2 - - - +
250B LYS* 1.3 66.6 + - - +
252B TYR* 3.3 22.4 - + - +
253B VAL* 3.1 45.4 + - + +
266B LEU* 6.2 2.0 - - - +
267B LEU* 4.9 2.0 - - + -
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Residues in contact with LYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B VAL 4.8 1.8 - - - +
146B ASP* 2.5 60.5 + - - +
147B SER* 4.1 4.0 + - - +
149B ILE* 2.8 31.4 + - + +
152B LYS* 6.2 0.2 - - - +
198B THR* 4.8 2.9 - - + +
246B SER 3.2 15.4 + - - +
247B ALA* 3.8 5.6 - - - +
248B ARG 3.3 0.2 - - - -
249B HIS* 1.3 75.6 - - - +
251B ALA* 1.3 66.0 + - - +
253B VAL* 3.0 2.8 + - - +
254B VAL* 2.8 31.7 + - + +
264B ARG* 4.3 3.6 - - - +
267B LEU* 3.7 29.8 - - + -
501B CRB 2.9 28.8 + - - +
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.0 11.2 - - + -
8B SER 3.5 23.8 - - - +
9B ILE* 3.6 26.1 - - + +
15B ILE* 4.5 4.0 - - + -
149B ILE* 4.5 1.2 - - + +
247B ALA 3.1 16.0 + - - +
248B ARG 3.7 4.7 - - - +
249B HIS 3.4 0.2 - - - -
250B LYS* 1.3 78.1 - - - +
252B TYR* 1.3 54.2 + - - +
255B SER* 2.6 39.0 + - - -
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Residues in contact with TYR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ARG 3.1 14.5 + - - +
249B HIS* 3.3 32.8 - + - +
250B LYS 3.0 0.2 - - - -
251B ALA* 1.3 77.0 - - - +
253B VAL* 1.3 68.9 + - + +
255B SER* 3.2 9.3 + - - -
256B ALA* 3.1 28.4 + - + +
263B LEU* 5.0 10.4 - - + +
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Residues in contact with VAL 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ILE* 5.8 0.7 - - + -
249B HIS* 3.1 41.3 + - + +
250B LYS 3.0 5.7 + - - +
252B TYR* 1.3 77.6 - - + +
254B VAL* 1.3 61.0 + - - +
256B ALA* 3.2 2.1 + - - +
257B ASP* 2.9 27.9 + - - +
263B LEU* 3.7 26.9 - - + +
264B ARG* 3.7 30.5 - - + +
266B LEU* 5.6 4.5 - - + -
267B LEU* 4.1 22.2 - - + +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 3.5 25.4 - - + -
10B LEU* 3.7 15.3 - - + +
150B GLY* 3.8 20.2 - - - +
169B GLN* 4.5 0.4 - - - +
250B LYS* 2.8 35.0 + - + +
253B VAL* 1.3 73.1 - - - +
255B SER* 1.3 57.9 + - - +
257B ASP 4.5 2.7 - - - +
258B GLU* 3.0 30.2 + - - +
264B ARG* 3.5 42.8 - - - +
267B LEU* 4.2 3.6 - - + -
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B SER 4.7 0.5 + - - -
9B ILE* 3.6 3.5 - - - -
10B LEU* 2.8 45.6 + - - +
11B GLY 5.5 0.2 - - - -
251B ALA 2.6 23.0 + - - -
252B TYR* 3.4 8.5 - - - -
254B VAL* 1.3 80.6 - - - +
256B ALA* 1.3 60.7 + - - +
258B GLU 4.6 1.2 + - - -
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Residues in contact with ALA 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B TYR* 3.1 25.4 + - + +
253B VAL 3.2 3.8 + - - +
255B SER* 1.3 79.0 - - - +
257B ASP* 1.3 60.3 + - - +
258B GLU 4.0 0.2 - - - -
263B LEU* 3.9 21.1 - - + -
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Residues in contact with ASP 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253B VAL 2.9 11.0 + - - +
254B VAL 3.5 2.2 - - - -
256B ALA* 1.3 80.6 - - - +
258B GLU* 1.3 64.5 + - - +
259B ARG 3.6 1.3 + - - -
260B GLU* 3.0 9.7 + - - -
261B GLY* 2.6 36.9 + - - -
262B GLY 3.0 9.6 + - - -
263B LEU* 3.8 12.6 - - + -
264B ARG* 2.8 43.2 + - - +
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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
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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