Contacts of the helix formed by residues 34 - 52 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2S THR* 5.6 8.1 + - - +
30S ILE* 3.2 29.9 + - + +
31S GLY* 2.9 8.1 + - - +
32S ILE 3.6 0.4 - - - -
33S ASP* 1.3 72.7 - - - +
35S ALA* 1.3 64.2 + - - +
36S GLU* 3.7 10.2 + - - +
37S ALA* 3.2 31.2 + - + +
38S ALA 3.3 12.1 + - - -
152S VAL* 3.3 15.9 - - - +
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Residues in contact with ALA 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S ASP 3.4 7.3 + - - +
34S ASN* 1.3 73.5 - - - +
36S GLU* 1.3 63.8 + - - +
38S ALA* 3.2 3.8 + - - +
39S TYR* 3.0 35.9 + - + -
151S PHE* 3.9 25.5 - - + -
152S VAL* 4.1 7.1 - - - +
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Residues in contact with GLU 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34S ASN* 3.3 8.2 + - - +
35S ALA* 1.3 78.4 - - - +
37S ALA* 1.3 57.5 + - - +
39S TYR* 3.6 6.8 + - - +
40S ALA* 3.1 26.7 + - + +
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Residues in contact with ALA 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S THR* 5.7 2.2 - - - +
6S LEU* 4.1 24.1 - - + +
30S ILE* 4.4 11.0 - - + -
34S ASN* 3.2 32.6 + - + +
35S ALA 3.2 0.6 - - - -
36S GLU* 1.3 77.3 - - - +
38S ALA* 1.3 60.0 + - - +
40S ALA* 3.1 8.7 + - - +
41S ILE* 2.9 34.5 + - - +
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Residues in contact with ALA 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S ILE* 4.5 6.8 - - + +
34S ASN 3.3 2.4 + - - -
35S ALA* 3.2 9.1 + - - +
37S ALA* 1.3 78.5 - - - +
39S TYR* 1.3 62.8 + - - +
41S ILE* 3.3 2.5 + - - +
42S GLN* 3.1 18.2 + - - +
152S VAL* 3.4 42.6 - - + +
155S VAL* 3.7 18.0 - - + +
156S ALA* 3.4 19.2 + - - +
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Residues in contact with TYR 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35S ALA* 3.0 30.9 + - + +
36S GLU* 3.9 5.8 - - - +
38S ALA* 1.3 76.0 - - - +
40S ALA* 1.3 57.5 + - - +
42S GLN* 3.4 10.0 + - - +
43S HIS* 2.9 29.7 + - - +
77S PRO 4.3 4.7 + - - -
78S ASP* 3.8 10.2 + - - -
79S PHE* 3.3 72.0 + + - -
151S PHE* 4.5 15.8 - + - -
155S VAL* 3.4 25.4 - - + +
210S TRP* 4.4 4.0 - - - -
214S LYS* 4.3 18.0 + - - -
218S LEU* 6.1 2.7 - - + -
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Residues in contact with ALA 40 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6S LEU* 4.0 20.0 - - + -
36S GLU* 3.1 16.8 + - + +
37S ALA* 3.1 9.1 + - - +
39S TYR* 1.3 74.0 - - - +
41S ILE* 1.3 59.9 + - - +
43S HIS* 3.3 7.6 + - - +
44S ILE* 2.9 39.1 + - + +
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Residues in contact with ILE 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6S LEU* 3.9 23.8 - - + +
9S LEU* 4.0 31.0 - - + -
10S ALA* 3.8 16.8 - - - -
13S LEU* 3.8 27.4 - - + -
26S LEU* 5.1 1.8 - - + -
30S ILE* 4.2 18.2 - - + -
37S ALA 2.9 18.0 + - - +
38S ALA 3.3 6.3 + - - +
40S ALA* 1.3 72.2 - - - +
42S GLN* 1.3 66.7 + - - +
44S ILE* 3.3 9.6 + - - +
45S ASN* 3.2 22.2 + - - +
156S ALA* 3.9 18.8 - - + +
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Residues in contact with GLN 42 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S ALA 3.1 8.6 + - - +
39S TYR* 3.4 18.0 + - - +
41S ILE* 1.3 74.7 - - - +
43S HIS* 1.3 58.7 + - - +
45S ASN* 3.2 6.5 + - - +
46S VAL* 2.9 31.3 + - + +
79S PHE* 3.0 41.1 + - - -
81S THR* 3.1 24.1 + - - -
155S VAL 3.1 25.8 + - - +
156S ALA 3.8 8.7 + - - -
158S ASN* 3.3 34.4 + - + +
159S ALA 4.0 0.2 - - - +
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Residues in contact with HIS 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S TYR 2.9 18.2 + - - +
40S ALA* 3.5 9.6 - - - +
41S ILE 3.2 0.2 - - - -
42S GLN* 1.3 73.8 - - - +
44S ILE* 1.3 70.4 + - + +
46S VAL* 3.2 10.1 + - + +
47S GLN* 2.9 60.0 + - + +
220S GLU* 4.2 27.2 + - - -
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Residues in contact with ILE 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3S LYS* 4.8 9.9 - - + -
6S LEU* 4.9 10.8 - - + +
7S GLU* 3.6 43.1 - - + +
10S ALA* 3.8 19.7 - - + -
14S ARG* 4.5 8.3 - - - +
40S ALA* 2.9 37.6 + - + +
41S ILE* 3.3 9.8 + - - +
43S HIS* 1.3 75.2 - - + +
45S ASN* 1.3 58.8 + - - +
47S GLN* 3.3 6.4 + - - +
48S HIS* 2.9 28.1 + - + +
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Residues in contact with ASN 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10S ALA* 3.3 27.2 + - - +
13S LEU* 3.9 19.6 - - - +
14S ARG* 2.8 41.9 + - + +
41S ILE* 3.2 10.0 + - - +
42S GLN* 3.7 8.3 - - - +
43S HIS 3.2 0.6 - - - -
44S ILE* 1.3 78.5 - - - +
46S VAL* 1.3 65.6 + - + +
48S HIS* 3.6 4.6 + - - +
49S ASP* 3.2 31.4 + - - +
156S ALA 4.8 4.2 + - - -
158S ASN* 6.6 0.4 - - + -
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Residues in contact with VAL 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S GLN* 2.9 29.4 + - + +
43S HIS* 3.7 9.6 - - + +
45S ASN* 1.3 76.2 - - + +
47S GLN* 1.3 65.0 + - - +
49S ASP* 3.2 3.6 + - - +
50S VAL* 2.9 38.5 + - + +
56S VAL* 4.4 4.7 - - + -
59S ARG* 5.3 3.6 - - - +
81S THR* 3.6 39.3 - - + +
83S PHE* 4.1 22.8 - - + -
158S ASN* 4.6 4.0 - - - +
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Residues in contact with GLN 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43S HIS* 2.9 49.8 + - + +
44S ILE* 3.4 7.0 - - - +
46S VAL* 1.3 82.5 - - - +
48S HIS* 1.3 62.5 + - - +
50S VAL* 3.5 19.1 + - - +
51S ALA* 3.1 22.3 + - - +
220S GLU* 5.4 1.0 - - - +
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Residues in contact with HIS 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14S ARG* 3.7 43.6 + - - +
44S ILE* 2.9 18.1 + - + +
45S ASN* 3.7 9.4 - - - +
46S VAL 3.2 0.2 - - - -
47S GLN* 1.3 75.7 - - - +
49S ASP* 1.3 75.7 + - - +
51S ALA* 3.3 16.4 + - - +
52S GLN* 3.3 37.1 + - + +
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Residues in contact with ASP 49 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H HIS* 3.6 15.2 - - - -
14S ARG* 4.8 2.8 - - - -
45S ASN 3.2 16.9 + - - +
46S VAL 3.7 3.6 - - - +
48S HIS* 1.3 88.6 - - - +
50S VAL* 1.3 64.5 + - - +
52S GLN* 3.1 24.3 + - - +
53S GLY 3.4 0.2 + - - -
54S ARG* 3.0 59.4 + - + +
83S PHE* 4.1 8.8 - - + -
1308S NA 3.4 17.6 - - - -
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Residues in contact with VAL 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S VAL* 2.9 25.9 + - + +
47S GLN* 3.8 20.6 - - - +
49S ASP* 1.3 75.3 - - - +
51S ALA* 1.3 58.3 + - - +
53S GLY* 2.8 21.5 + - - -
54S ARG 3.6 19.1 - - - +
56S VAL* 4.0 24.0 - - + -
83S PHE* 4.3 2.5 - - + -
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Residues in contact with ALA 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S GLN 3.1 13.4 + - - +
48S HIS* 3.4 12.3 - - - +
49S ASP 3.2 0.2 - - - -
50S VAL* 1.3 76.3 - - - +
52S GLN* 1.3 58.6 + - + +
53S GLY 3.3 1.2 + - - -
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Residues in contact with GLN 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3H LYS* 3.1 32.6 + - - +
4H HIS* 4.2 14.1 + - - +
7H GLU* 3.5 46.7 - - + +
48S HIS* 3.3 34.2 + - + +
49S ASP* 3.1 25.0 + - - +
51S ALA* 1.3 76.7 - - + +
53S GLY* 1.3 60.1 + - - +
54S ARG* 3.4 2.6 + - + -
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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) + - + + + + + -
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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