Contacts of the helix formed by residues 273 - 286 (chain B) in PDB entry 1NVT
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 ASN 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B ALA* 5.0 3.3 + - - +
36B ASP* 3.4 27.1 + - - +
37B LYS* 4.3 9.1 - - - +
272B PRO* 1.3 73.6 - - - +
274B ILE* 1.3 63.0 + - - +
275B GLU* 2.8 26.9 + - - +
276B VAL* 3.0 25.1 + - + +
277B MET* 3.2 24.0 + - - +
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Residues in contact with ILE 274 (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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257B ILE* 3.8 15.9 - - + -
258B TYR* 4.1 35.4 - - + +
261B ALA* 4.0 12.3 - - + -
272B PRO* 4.1 9.2 - - + +
273B ASN* 1.3 71.6 + - - +
275B GLU* 1.3 64.3 + - + +
277B MET* 3.3 27.4 + - + +
278B LYS* 2.8 39.1 + - + +
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Residues in contact with GLU 275 (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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273B ASN* 2.8 15.0 + - - +
274B ILE* 1.3 77.0 - - + +
276B VAL* 1.3 59.3 + - + +
278B LYS* 3.8 22.8 + - - +
279B ASN* 2.9 35.3 + - - +
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Residues in contact with VAL 276 (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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32B ALA* 3.6 38.8 - - + +
33B ALA* 4.0 5.2 - - - +
36B ASP* 3.9 18.4 - - + +
273B ASN* 3.0 36.5 + - + +
275B GLU* 1.3 77.3 - - + +
277B MET* 1.3 65.2 + - - +
279B ASN* 4.1 2.0 - - - +
280B ALA* 3.0 26.9 + - - +
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Residues in contact with MET 277 (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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29B MET* 3.7 35.4 - - + +
30B HIS* 5.2 5.2 - - - -
33B ALA* 4.0 19.5 - - + -
257B ILE* 3.3 38.6 - - + +
260B GLY 4.7 1.6 - - - -
261B ALA* 3.3 32.1 - - + -
264B PHE* 5.3 0.4 - - - -
272B PRO* 3.7 17.7 - - + -
273B ASN 3.2 10.0 + - - +
274B ILE* 3.3 19.5 + - + +
276B VAL* 1.3 79.5 - - - +
278B LYS* 1.3 63.6 + - - +
280B ALA* 3.7 1.6 - - - +
281B ILE* 3.2 28.4 + - - +
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Residues in contact with LYS 278 (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 LEU* 3.9 16.8 - - + +
257B ILE* 3.2 25.4 - - + +
274B ILE* 2.8 26.7 + - + +
275B GLU* 3.8 23.5 + - - +
277B MET* 1.3 75.6 - - - +
279B ASN* 1.3 59.0 + - - +
281B ILE* 3.4 3.5 + - - +
282B ILE* 3.1 46.6 + - + +
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Residues in contact with ASN 279 (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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275B GLU* 2.9 21.3 + - - +
276B VAL* 4.3 2.0 - - - +
278B LYS* 1.3 73.8 - - - +
280B ALA* 1.3 67.2 + - - +
282B ILE* 4.4 10.1 - - - +
283B ASP* 2.9 52.8 + - - +
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Residues in contact with ALA 280 (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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28B ILE* 3.5 28.5 - - + +
32B ALA* 3.6 25.4 - - + -
276B VAL 3.0 20.0 + - - +
277B MET* 3.7 5.2 - - - +
278B LYS 3.3 0.2 - - - -
279B ASN* 1.3 81.7 + - - +
281B ILE* 1.3 61.9 + - - +
283B ASP* 3.7 5.0 + - - +
284B LYS* 3.4 14.6 + - - +
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Residues in contact with ILE 281 (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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25B PHE* 4.3 19.7 - - + +
28B ILE* 4.7 4.5 - - - -
29B MET* 3.5 36.3 - - + -
253B LEU* 4.4 11.4 - - + -
256B LEU* 3.4 29.4 - - + -
257B ILE* 4.0 15.3 - - + -
277B MET 3.2 13.8 + - - +
278B LYS 3.7 5.6 - - - +
279B ASN 3.2 0.6 - - - -
280B ALA* 1.3 75.2 - - - +
282B ILE* 1.3 67.7 + - - +
284B LYS* 3.0 5.3 + - - +
285B ILE* 2.9 43.9 + - + +
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Residues in contact with ILE 282 (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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234B LEU* 4.4 11.4 - - + -
253B LEU* 3.7 34.8 - - + -
278B LYS* 3.1 33.7 + - + +
279B ASN* 3.4 12.1 + - - +
281B ILE* 1.3 76.0 - - - +
283B ASP* 1.3 61.5 + - - +
285B ILE* 3.1 6.0 + - - -
286B THR* 2.8 53.7 + - + +
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Residues in contact with ASP 283 (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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279B ASN* 2.9 47.8 + - - +
280B ALA* 4.0 5.5 - - - +
282B ILE* 1.3 80.4 - - - +
284B LYS* 1.3 62.7 + - + +
285B ILE 3.4 0.2 - - - -
286B THR* 3.5 8.4 + - - +
287B LYS* 3.1 24.2 - - - +
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Residues in contact with LYS 284 (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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6A MET* 6.2 1.8 - - - +
7A ILE 5.0 1.4 + - - -
8A ASN* 4.9 8.3 - - - +
25B PHE* 3.9 24.8 - - + -
28B ILE* 3.3 42.4 - - + +
280B ALA 3.4 9.7 + - - +
281B ILE 3.0 8.5 + - - +
283B ASP* 1.3 82.9 - - + +
285B ILE* 1.3 65.1 + - - +
286B THR 3.8 3.2 - - - +
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Residues in contact with ILE 285 (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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25B PHE* 3.6 26.7 - - + -
231B TYR* 3.5 33.7 - - + +
232B ASN* 4.1 19.2 + - + +
233B PRO* 5.4 0.4 - - + -
234B LEU* 4.1 30.7 - - + +
253B LEU* 4.6 0.7 - - + -
281B ILE* 2.9 36.9 + - + +
282B ILE* 3.7 4.9 - - - +
284B LYS* 1.3 77.8 - - - +
286B THR* 1.3 69.0 + - + +
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Residues in contact with THR 286 (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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234B LEU* 4.0 18.6 - - + -
282B ILE* 2.8 41.3 + - + +
283B ASP* 3.5 12.7 + - - +
284B LYS 3.8 3.5 - - - +
285B ILE* 1.3 80.8 - - + +
287B LYS* 1.3 78.6 + - - +
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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