Contacts of the helix formed by residues 274 - 285 (chain B) in PDB entry 5V6Y
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 274 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ILE* 4.7 0.2 - - - +
5B GLU 3.2 18.2 + - - -
6B GLU* 3.4 9.8 - - - +
7B GLY 3.3 19.0 + - - -
8B LYS 2.7 29.1 + - - +
9B LEU* 4.3 4.4 - - + +
60B ASP* 3.4 14.6 + - - +
272B SER* 3.1 11.3 + - - +
273B PRO* 1.3 85.8 - - - +
275B LYS* 1.3 58.4 + - - +
276B GLU 3.3 2.7 - - - +
277B LEU* 3.3 23.9 + - + +
278B ALA* 3.0 28.1 + - - +
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Residues in contact with LYS 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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79B ALA* 3.7 26.2 - - + -
268B ILE* 4.3 25.7 - - + +
269B ASN 3.9 1.3 - - - +
270B ALA* 2.9 28.4 + - - +
271B ALA 4.5 0.4 - - - -
272B SER* 2.7 30.1 + - - +
273B PRO* 3.5 4.4 + - - +
274B ASN* 1.3 77.8 - - - +
276B GLU* 1.3 62.0 + - + +
278B ALA* 3.4 2.6 + - - +
279B LYS* 3.1 27.4 + - - +
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Residues in contact with GLU 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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82B THR* 5.2 2.9 + - - -
274B ASN* 3.3 0.6 - - - +
275B LYS* 1.3 79.8 - - + +
277B LEU* 1.3 68.2 + - + +
279B LYS* 3.5 26.0 + - - +
280B GLU* 3.1 22.9 + - - +
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Residues in contact with LEU 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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7B GLY* 4.5 9.2 - - - +
8B LYS 5.0 0.9 - - - +
9B LEU* 3.8 14.6 - - + +
29B PHE* 3.9 13.1 - - + -
33B THR* 6.2 2.0 - - + -
35B ILE* 4.2 36.3 - - + -
274B ASN* 3.3 34.6 + - + +
276B GLU* 1.3 78.0 - - + +
278B ALA* 1.3 65.3 + - - +
280B GLU* 3.4 8.4 + - + +
281B PHE* 3.1 23.0 + - - +
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Residues in contact with ALA 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.2 10.9 - - + +
60B ASP* 4.8 2.5 - - + +
61B ILE* 3.8 28.9 - - + -
268B ILE* 3.9 22.9 - - + -
274B ASN 3.0 17.2 + - - +
275B LYS 3.7 4.9 - - - +
277B LEU* 1.3 74.8 - - - +
279B LYS* 1.3 64.2 + - - +
281B PHE* 3.3 1.8 + - - +
282B LEU* 3.1 29.5 + - - +
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Residues in contact with LYS 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 2.8 43.2 + - - +
83B PRO* 4.8 0.9 - - - -
84B ASP 5.6 0.6 - - - +
108B TYR* 3.6 10.1 - - - +
268B ILE* 4.2 10.0 - - + +
275B LYS 3.1 16.5 + - - +
276B GLU* 3.8 24.9 + - - +
277B LEU 3.3 0.2 - - - -
278B ALA* 1.3 76.5 - - - +
280B GLU* 1.3 62.4 + - - +
282B LEU* 4.9 2.7 - - - -
283B GLU* 3.1 55.1 + - - +
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Residues in contact with GLU 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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29B PHE* 3.8 18.6 - - + -
33B THR* 5.6 5.3 - - + +
276B GLU 3.1 17.7 + - - +
277B LEU* 3.7 10.5 - - + +
278B ALA 3.3 0.2 - - - -
279B LYS* 1.3 77.7 - - - +
281B PHE* 1.3 62.0 + - - +
284B ASN* 3.1 48.7 + - - +
285B TYR* 3.7 17.0 - - + -
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Residues in contact with PHE 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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9B LEU* 4.1 11.0 - - + -
11B ILE* 3.5 32.3 - - + -
22B LEU* 4.1 19.5 - - + -
25B VAL* 3.7 44.6 - - + -
26B GLY* 3.9 11.2 - - - -
29B PHE* 3.6 34.3 - + + -
37B VAL* 4.8 4.0 - - + -
61B ILE* 4.2 4.5 - - + -
63B PHE* 5.4 0.7 - + - -
277B LEU 3.1 15.9 + - - +
278B ALA* 3.8 3.4 - - - +
279B LYS 3.3 0.2 - - - -
280B GLU* 1.3 78.9 - - - +
282B LEU* 1.3 77.7 + - + +
285B TYR* 3.3 9.1 + - + +
286B LEU* 3.0 27.9 + - + -
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Residues in contact with LEU 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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61B ILE* 3.8 27.8 - - + -
63B PHE* 4.0 4.9 - - + -
108B TYR* 3.6 41.1 - - + -
110B ILE* 5.6 0.4 - - + -
266B ALA* 4.0 24.7 - - + +
268B ILE* 4.3 11.9 - - + -
278B ALA 3.1 17.9 + - - +
279B LYS 4.3 1.6 - - - +
281B PHE* 1.3 83.9 - - + +
283B GLU* 1.3 57.9 + - - +
286B LEU* 3.7 26.1 - - + +
287B LEU* 3.0 37.7 + - + +
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Residues in contact with GLU 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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83B PRO* 3.5 11.2 - - - +
84B ASP* 5.4 2.8 + - - +
87B PHE* 3.6 40.8 - - + +
90B LYS* 5.0 2.8 + - - -
108B TYR* 2.5 46.2 + - + +
279B LYS* 3.1 39.1 + - - +
282B LEU* 1.3 77.1 - - - +
284B ASN* 1.3 73.8 + - - +
285B TYR 3.6 0.2 - - - -
287B LEU 3.6 19.2 - - - +
288B THR* 4.0 2.9 - - - +
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Residues in contact with ASN 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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87B PHE* 5.9 1.6 - - - -
90B LYS* 6.1 1.0 - - - +
280B GLU* 3.1 46.0 + - - +
283B GLU* 1.3 91.0 + - - +
285B TYR* 1.3 71.7 + - + +
288B THR* 3.6 16.6 + - - +
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Residues in contact with TYR 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 VAL* 3.8 16.5 - - + +
28B LYS* 4.0 26.9 - - + -
29B PHE* 3.5 38.4 - + + -
32B ASP* 3.0 39.1 + - + +
33B THR* 4.5 5.2 - - + +
280B GLU* 3.7 26.6 + - + -
281B PHE* 3.3 14.3 + - + +
283B GLU 3.6 0.2 - - - -
284B ASN* 1.3 89.5 - - + +
286B LEU* 1.3 62.4 + - - +
288B THR* 2.9 18.1 + - - -
291B GLY* 3.2 14.2 + - - -
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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
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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