Contacts of the helix formed by residues 34 - 52 (chain P) in PDB entry 2WQT
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 34 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2P THR* 5.6 7.9 + - - +
30P ILE* 3.2 30.1 + - - +
31P GLY* 2.9 8.1 + - - +
32P ILE 3.6 0.2 - - - -
33P ASP* 1.3 72.9 - - - +
35P ALA* 1.3 65.0 + - - +
36P GLU* 3.7 10.2 + - - +
37P ALA* 3.3 30.2 + - + +
38P ALA 3.3 11.6 + - - -
152P VAL* 3.2 16.0 - - - +
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Residues in contact with ALA 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P ASP 3.4 7.4 + - - +
34P ASN* 1.3 72.2 - - - +
36P GLU* 1.3 66.6 + - - +
38P ALA* 3.2 3.0 + - - +
39P TYR* 3.0 36.3 + - + -
151P PHE* 3.9 25.3 - - + -
152P VAL* 4.2 7.2 - - - +
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Residues in contact with GLU 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P ASN* 3.3 8.6 + - - +
35P ALA* 1.3 79.0 - - - +
37P ALA* 1.3 56.4 + - - +
39P TYR* 3.6 6.9 + - - +
40P ALA* 3.0 27.5 + - + +
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Residues in contact with ALA 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P THR* 5.7 2.2 - - - +
6P LEU* 4.2 24.3 - - + +
30P ILE* 4.4 10.8 - - + -
34P ASN* 3.3 32.6 + - + +
35P ALA 3.2 0.8 - - - -
36P GLU* 1.3 76.2 - - - +
38P ALA* 1.3 61.7 + - - +
40P ALA* 3.1 9.0 + - - +
41P ILE* 2.9 34.5 + - - +
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Residues in contact with ALA 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P ILE* 4.5 5.3 - - + +
34P ASN 3.3 2.6 + - - -
35P ALA* 3.2 10.4 + - - +
37P ALA* 1.3 78.0 - - - +
39P TYR* 1.3 61.4 + - - +
41P ILE* 3.3 2.0 + - - -
42P GLN 3.1 17.8 + - - -
152P VAL* 3.4 43.5 - - + +
155P VAL* 3.7 16.9 - - + +
156P ALA* 3.3 19.3 + - - -
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Residues in contact with TYR 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P ALA* 3.0 31.1 + - + +
36P GLU* 3.9 6.5 - - - +
38P ALA* 1.3 73.6 - - - +
40P ALA* 1.3 60.0 + - - +
42P GLN* 3.4 10.2 + - - +
43P HIS* 2.9 29.7 + - - +
77P PRO 4.3 4.3 + - - -
78P ASP* 3.8 11.1 + - - -
79P PHE* 3.2 73.1 + + - -
151P PHE* 4.5 11.9 - + - -
155P VAL* 3.4 28.2 - - + +
210P TRP* 4.4 3.5 - - - -
214P LYS* 4.3 19.5 + - - -
218P LEU* 6.1 2.2 - - + -
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Residues in contact with ALA 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P LEU* 4.0 20.6 - - + -
36P GLU* 3.0 16.7 + - + +
37P ALA* 3.1 9.8 + - - +
39P TYR* 1.3 73.5 - - - +
41P ILE* 1.3 59.4 + - - +
43P HIS* 3.3 7.9 + - - +
44P ILE* 2.8 37.0 + - + +
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Residues in contact with ILE 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P LEU* 4.0 23.8 - - + +
9P LEU* 4.0 31.0 - - + -
10P ALA* 3.8 17.3 - - - +
13P LEU* 3.8 27.1 - - + -
26P LEU* 5.0 1.8 - - + -
30P ILE* 4.2 17.5 - - + -
37P ALA 2.9 18.0 + - - +
38P ALA 3.3 6.0 + - - +
40P ALA* 1.3 72.8 - - - +
42P GLN* 1.3 66.6 + - - +
44P ILE* 3.2 9.8 + - - +
45P ASN* 3.2 23.0 + - - +
156P ALA* 3.8 18.8 - - + +
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Residues in contact with GLN 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38P ALA 3.1 8.6 + - - +
39P TYR* 3.6 13.1 - - - +
40P ALA 3.4 0.2 - - - -
41P ILE* 1.3 74.3 - - - +
43P HIS* 1.3 58.6 + - - +
45P ASN* 3.2 7.0 + - - +
46P VAL* 2.9 31.3 + - + +
79P PHE* 3.0 41.8 + - - -
81P THR* 3.1 24.1 + - - -
155P VAL* 3.1 30.6 + - - +
156P ALA 3.8 8.2 + - - -
158P ASN* 3.3 33.3 + - + +
159P ALA 4.0 0.4 - - - +
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Residues in contact with HIS 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P TYR 2.9 17.3 + - - +
40P ALA* 3.4 9.2 - - - +
41P ILE 3.2 0.2 - - - -
42P GLN* 1.3 74.4 - - - +
44P ILE* 1.3 71.0 + - + +
46P VAL* 3.2 8.7 + - - +
47P GLN* 2.9 59.2 + - + +
220P GLU* 4.2 27.4 + - - -
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Residues in contact with ILE 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P LYS* 4.8 10.3 - - + -
6P LEU* 5.0 12.1 - - + +
7P GLU* 3.6 40.4 - - + +
10P ALA* 3.9 19.7 - - + -
14P ARG* 4.5 8.5 - - - +
40P ALA* 2.8 36.8 + - + +
41P ILE* 3.5 9.9 - - - +
43P HIS* 1.3 76.9 - - + +
45P ASN* 1.3 57.6 + - - +
47P GLN* 3.3 6.1 + - - +
48P HIS* 2.9 28.1 + - + +
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Residues in contact with ASN 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P ALA* 3.3 27.7 + - - +
13P LEU* 3.8 20.2 - - - +
14P ARG* 2.8 45.3 + - + +
41P ILE* 3.2 9.8 + - - +
42P GLN* 3.7 7.9 - - - +
43P HIS 3.2 0.6 - - - -
44P ILE* 1.3 77.8 - - - +
46P VAL* 1.3 65.3 + - + +
48P HIS* 3.7 3.4 - - - +
49P ASP* 3.1 31.3 + - - +
156P ALA 4.8 3.6 + - - +
158P ASN* 6.6 0.4 - - + -
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Residues in contact with VAL 46 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P GLN* 2.9 29.0 + - + +
43P HIS* 3.2 9.6 + - - +
45P ASN* 1.3 75.2 - - + +
47P GLN* 1.3 65.2 + - - +
49P ASP* 3.2 3.8 + - - +
50P VAL* 2.9 38.4 + - + +
56P VAL* 4.4 4.7 - - + -
59P ARG* 5.3 3.1 - - - +
81P THR* 3.6 39.0 - - + +
83P PHE* 4.1 22.8 - - + -
158P ASN* 4.6 4.3 - - - +
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Residues in contact with GLN 47 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P HIS* 2.9 49.9 + - + +
44P ILE* 3.5 6.7 - - - +
46P VAL* 1.3 82.4 - - - +
48P HIS* 1.3 61.1 + - - +
50P VAL* 3.4 19.1 + - - +
51P ALA* 3.1 23.6 + - - +
220P GLU* 5.3 1.0 - - - +
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Residues in contact with HIS 48 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ARG* 3.7 45.7 + - - +
44P ILE* 2.9 17.9 + - + +
45P ASN* 3.7 8.7 - - - +
46P VAL 3.3 0.2 - - - -
47P GLN* 1.3 76.7 - - - +
49P ASP* 1.3 75.5 + - - +
51P ALA* 3.3 14.1 + - - +
52P GLN* 3.3 39.3 + - + +
1265P K 4.0 5.5 - - - -
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Residues in contact with ASP 49 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P ARG* 4.7 1.9 - - - -
45P ASN 3.1 17.5 + - - +
46P VAL 3.2 4.0 + - - +
48P HIS* 1.3 87.8 - - - +
50P VAL* 1.3 67.0 + - - +
52P GLN* 3.0 26.6 + - - +
53P GLY 3.4 0.3 + - - -
54P ARG* 3.0 62.4 + - + +
83P PHE* 4.1 8.9 - - + -
1265P K 3.9 6.9 - - - -
1317P NA 3.6 17.1 - - - -
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Residues in contact with VAL 50 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P VAL* 2.9 25.7 + - + +
47P GLN* 3.7 21.1 - - - +
49P ASP* 1.3 75.7 - - - +
51P ALA* 1.3 56.3 + - - +
53P GLY* 2.8 25.3 + - - -
54P ARG 3.6 18.6 - - - +
56P VAL* 4.0 24.2 - - + +
83P PHE* 4.3 2.5 - - + -
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Residues in contact with ALA 51 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47P GLN 3.1 13.7 + - - +
48P HIS* 3.4 12.8 - - - +
49P ASP 3.2 0.2 - - - -
50P VAL* 1.3 78.2 - - - +
52P GLN* 1.3 57.2 + - + +
53P GLY 3.3 1.4 + - - -
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Residues in contact with GLN 52 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P HIS* 3.3 33.1 + - + +
49P ASP* 3.0 22.0 + - - +
51P ALA* 1.3 78.3 - - + +
53P GLY* 1.3 60.3 + - - +
54P ARG* 3.4 3.7 + - + +
1265P K 3.6 19.6 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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