Contacts of the helix formed by residues 277 - 292 (chain B) in PDB entry 2AY6
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 ALA 277 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 3.5 36.9 - - + +
99B THR* 4.0 3.6 - - - +
276B ASP* 1.3 72.4 - - - +
278B ALA* 1.3 59.9 + - - +
280B ARG* 3.1 3.0 + - - +
281B GLU* 2.8 40.3 + - + +
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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
----------------------------------------------------------
276B ASP* 3.1 17.7 + - - +
277B ALA* 1.3 76.6 - - - +
279B THR* 1.3 62.5 + - - +
281B GLU* 3.2 16.8 + - - +
282B LEU* 3.3 15.8 + - - +
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.5 41.7 - - + +
7A GLY* 3.8 8.6 - - - +
249B GLU* 4.3 5.6 - - - +
274B CYS* 4.0 14.1 - - + -
275B ALA* 5.0 3.1 + - - +
276B ASP* 2.8 25.6 + - - -
277B ALA 3.4 0.2 - - - -
278B ALA* 1.3 77.3 - - - +
280B ARG* 1.3 58.5 + - - +
282B LEU* 3.0 12.8 + - - +
283B ALA* 2.9 27.2 + - - +
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B SER* 3.0 19.4 + - - -
98B GLU* 3.6 13.2 + - - +
99B THR 3.5 27.4 - - - +
100B THR 3.0 25.1 + - - +
101B ALA* 4.0 5.7 - - - +
102B THR 5.0 0.6 - - - +
274B CYS* 3.7 10.1 - - - +
276B ASP 3.1 13.9 + - - +
277B ALA* 3.1 13.6 + - - +
279B THR* 1.3 76.9 - - - +
281B GLU* 1.3 75.8 + - - +
283B ALA* 3.3 1.9 + - - +
284B GLN* 2.9 55.7 + - - +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ALA* 2.8 23.6 + - + +
278B ALA* 3.2 9.2 + - - +
280B ARG* 1.3 102.0 + - - +
282B LEU* 1.3 61.8 + - - +
284B GLN* 4.0 7.6 - - - +
285B GLY* 3.1 19.2 + - - -
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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
----------------------------------------------------------
6A LEU 4.1 9.6 - - - +
7A GLY* 3.7 22.2 - - - +
9A LEU* 3.3 37.7 - - + +
10A LYS 5.7 0.9 - - - +
11A PRO* 3.7 33.7 - - + -
12A GLN 5.5 2.4 + - - -
278B ALA 3.3 12.4 + - - +
279B THR* 3.0 16.3 + - - +
281B GLU* 1.3 76.2 - - - +
283B ALA* 1.3 59.8 + - - +
285B GLY* 3.2 2.6 + - - -
286B ALA* 3.0 29.3 + - - +
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.5 7.6 - - + -
9A LEU* 3.8 19.0 - - + +
101B ALA* 4.2 8.5 - - + -
118B LEU* 4.4 3.8 - - + +
272B ALA* 4.4 9.9 - - + -
274B CYS* 4.1 18.2 - - - -
279B THR 2.9 15.2 + - - +
280B ARG 3.8 3.8 - - - +
282B LEU* 1.3 76.0 - - - +
284B GLN* 1.3 53.5 + - - +
286B ALA* 3.2 1.9 + - - +
287B MET* 2.8 42.6 + - - +
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Residues in contact with GLN 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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74B SER* 3.8 16.7 + - - +
80B GLN* 4.7 4.0 + - - -
101B ALA* 3.2 12.5 - - + +
102B THR 2.9 47.1 + - - +
280B ARG* 2.9 37.4 + - - +
281B GLU* 4.0 10.5 - - - +
283B ALA* 1.3 76.4 - - - +
285B GLY* 1.3 61.4 + - - +
287B MET* 4.2 8.9 - - - +
288B ALA* 3.2 23.2 + - - +
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 3.7 18.3 - - - +
13A ALA 5.7 0.3 - - - +
281B GLU 3.1 15.9 + - - -
282B LEU 3.7 3.1 - - - -
284B GLN* 1.3 78.4 - - - +
286B ALA* 1.3 55.6 + - - +
288B ALA* 3.8 4.1 + - - +
289B PHE* 3.3 26.3 + - - +
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Residues in contact with ALA 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 4.0 12.8 - - + -
10A LYS 5.4 0.9 - - - +
12A GLN* 3.9 21.9 - - + +
118B LEU* 3.9 18.2 - - + -
121B MET* 4.6 10.9 - - - +
282B LEU 3.0 16.6 + - - +
283B ALA 3.2 3.8 + - - +
285B GLY* 1.3 75.0 - - - +
287B MET* 1.3 64.5 + - - +
288B ALA 3.5 0.2 - - - -
289B PHE* 4.0 2.9 - - - +
290B LEU* 3.2 29.1 + - - +
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Residues in contact with MET 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 3.5 38.1 - - - +
103B LEU* 3.2 40.6 - - + +
118B LEU* 3.9 18.6 - - + -
270B LEU* 3.4 52.5 - - + +
272B ALA* 3.9 13.7 - - + -
283B ALA 2.8 20.7 + - - +
284B GLN* 3.8 9.0 - - - +
286B ALA* 1.3 76.9 - - - +
288B ALA* 1.3 63.4 + - - +
290B LEU* 3.1 22.1 + - + +
291B ASN 3.2 5.4 + - - -
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.8 22.6 - - + +
74B SER* 3.2 26.8 + - - +
103B LEU* 4.7 1.8 - - - -
284B GLN* 3.2 12.9 + - + +
285B GLY* 4.2 4.5 - - - +
287B MET* 1.3 75.9 - - - +
289B PHE* 1.3 66.1 + - - +
291B ASN* 3.0 9.1 + - - +
292B ARG* 3.0 22.0 + - - +
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 3.7 33.4 - - + -
13A ALA 5.2 0.7 - - - -
145A SER* 5.8 0.9 - - - -
149A PHE* 3.7 32.5 - + + -
121B MET* 3.8 25.6 - - + -
285B GLY 3.3 18.3 + - - +
286B ALA 4.0 4.0 - - - +
287B MET 3.3 0.2 - - - -
288B ALA* 1.3 77.3 - - - +
290B LEU* 1.3 68.3 + - + +
292B ARG* 3.2 34.5 + - - +
293B GLN* 3.0 58.2 + - + +
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Residues in contact with LEU 290 (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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149A PHE* 4.3 21.0 - - + -
114B GLN* 3.5 43.0 + - + +
117B GLU* 3.8 14.4 - - + -
118B LEU* 3.7 25.1 - - + +
121B MET* 4.0 19.1 - - + -
286B ALA 3.2 18.9 + - - +
287B MET* 3.1 16.8 + - + +
288B ALA 3.1 0.4 - - - -
289B PHE* 1.3 85.2 - - + +
291B ASN* 1.3 55.2 + - - +
293B GLN* 3.8 2.5 + - - +
294B THR* 2.7 32.8 + - - +
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Residues in contact with ASN 291 (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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73B LEU* 3.0 17.9 + - + +
103B LEU* 2.9 36.6 - - - +
104B ALA 3.1 13.0 + - - +
114B GLN* 2.8 14.2 + - - +
287B MET 3.2 5.2 + - - +
288B ALA 3.0 9.9 + - - +
290B LEU* 1.3 74.8 - - - +
292B ARG* 1.3 60.9 + - - +
294B THR* 3.1 1.4 + - - -
295B TYR* 2.7 57.9 + - - -
296B SER 2.9 16.9 + - - +
298B PRO* 3.8 8.3 - - - +
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Residues in contact with ARG 292 (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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13A ALA 3.1 26.5 + - - -
14A PRO 4.8 0.4 + - - -
15A ASP* 2.7 43.3 + - - +
109A THR* 4.1 9.9 - - - +
142A ASN* 5.1 19.1 + - + +
145A SER* 4.9 9.2 + - - -
146A ILE* 4.8 2.4 - - - +
73B LEU* 4.1 9.9 - - + +
288B ALA 3.0 10.8 + - - +
289B PHE* 3.2 32.3 + - - +
291B ASN* 1.3 78.4 - - - +
293B GLN* 1.3 92.4 + - - +
294B THR 3.3 0.9 + - - -
295B TYR 4.0 0.5 + - - -
296B SER* 3.5 23.1 + - - +
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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