Contacts of the helix formed by residues 34 - 52 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F THR* 5.6 8.7 + - - +
30F ILE* 3.2 30.1 + - + +
31F GLY* 2.9 9.4 + - - +
32F ILE 3.6 0.4 - - - -
33F ASP* 1.3 73.5 - - - +
35F ALA* 1.3 63.8 + - - +
36F GLU* 3.7 9.4 + - - +
37F ALA* 3.2 29.6 + - + +
38F ALA 3.3 12.1 + - - -
152F VAL* 3.3 14.2 - - - +
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Residues in contact with ALA 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ASP 3.4 7.7 + - - +
34F ASN* 1.3 72.9 + - - +
36F GLU* 1.3 64.3 + - - +
38F ALA* 3.2 4.0 + - - +
39F TYR* 3.0 35.9 + - + -
151F PHE* 4.0 28.5 - - + -
152F VAL* 4.2 3.8 - - - +
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Residues in contact with GLU 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F ASN* 3.3 8.8 + - - +
35F ALA* 1.3 78.6 - - - +
37F ALA* 1.3 56.2 + - - +
39F TYR* 3.5 6.1 + - - +
40F ALA* 3.0 27.8 + - + +
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Residues in contact with ALA 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F THR* 5.7 2.2 - - - +
6F LEU* 4.2 23.9 - - + +
30F ILE* 4.4 10.8 - - + -
34F ASN* 3.2 33.3 + - + +
35F ALA 3.2 0.4 - - - -
36F GLU* 1.3 77.1 - - - +
38F ALA* 1.3 66.0 + - - +
40F ALA* 3.0 8.8 + - - +
41F ILE* 2.9 28.5 + - - +
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Residues in contact with ALA 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F ILE* 4.5 6.3 - - + +
34F ASN 3.3 3.2 + - - -
35F ALA* 3.2 9.5 + - - +
37F ALA* 1.3 77.9 - - - +
39F TYR* 1.3 62.0 + - - +
41F ILE* 3.3 2.7 + - - -
42F GLN* 3.1 17.8 + - - +
152F VAL* 3.4 42.6 - - + +
155F VAL* 3.7 18.2 - - + -
156F ALA* 3.4 20.0 + - + +
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Residues in contact with TYR 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ALA* 3.0 30.9 + - + +
36F GLU* 3.9 6.3 - - - +
38F ALA* 1.3 76.7 - - - +
40F ALA* 1.3 57.4 + - - +
42F GLN* 3.4 10.1 + - - +
43F HIS* 2.9 28.8 + - - +
77F PRO 4.3 4.5 + - - -
78F ASP* 3.8 11.3 + - - -
79F PHE* 3.2 71.0 + + - -
151F PHE* 4.4 15.7 - + - -
155F VAL* 3.5 24.6 - - + +
210F TRP* 4.4 4.2 - - - -
214F LYS* 4.3 18.6 + - - -
218F LEU* 6.0 2.2 - - + -
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Residues in contact with ALA 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 4.1 20.2 - - + -
36F GLU* 3.0 16.3 + - + +
37F ALA* 3.0 10.6 + - - +
39F TYR* 1.3 76.8 - - - +
41F ILE* 1.3 57.1 + - - +
43F HIS* 3.3 8.5 + - - +
44F ILE* 2.8 37.8 + - + +
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Residues in contact with ILE 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F LEU* 3.9 23.3 - - + +
9F LEU* 3.9 31.0 - - + -
10F ALA* 3.8 17.0 - - - +
13F LEU* 3.8 27.6 - - + -
26F LEU* 5.0 1.6 - - + -
30F ILE* 4.2 17.7 - - + -
37F ALA 2.9 16.8 + - - +
38F ALA 3.3 6.5 + - - +
40F ALA* 1.3 72.6 - - - +
42F GLN* 1.3 65.4 + - - +
44F ILE* 3.3 9.3 + - - +
45F ASN* 3.2 23.4 + - - +
156F ALA* 3.9 18.2 - - + +
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Residues in contact with GLN 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F ALA 3.1 8.8 + - - +
39F TYR* 3.6 17.8 - - - +
41F ILE* 1.3 75.3 - - - +
43F HIS* 1.3 58.5 + - - +
45F ASN* 3.2 6.6 + - - +
46F VAL* 2.9 31.1 + - + +
79F PHE* 3.0 40.3 + - - -
81F THR* 3.1 24.3 + - - -
155F VAL 3.1 26.0 + - - +
156F ALA 3.8 8.2 + - - +
158F ASN* 3.2 35.1 + - + +
159F ALA 4.0 0.4 - - - +
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Residues in contact with HIS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39F TYR 2.9 18.1 + - - +
40F ALA* 3.4 9.6 - - - +
42F GLN* 1.3 75.3 - - - +
44F ILE* 1.3 70.6 + - + +
46F VAL* 3.8 8.7 - - + +
47F GLN* 2.8 58.0 + - + +
220F GLU* 4.2 25.9 + - - -
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Residues in contact with ILE 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LYS* 4.8 10.3 - - + -
6F LEU* 5.0 10.5 - - + +
7F GLU* 3.6 42.2 - - + +
10F ALA* 3.8 20.4 - - + -
14F ARG* 4.5 6.7 - - - +
40F ALA* 2.8 36.8 + - + +
41F ILE* 3.3 10.1 + - - +
43F HIS* 1.3 77.6 - - + +
45F ASN* 1.3 58.9 + - - +
47F GLN* 3.3 5.7 + - - +
48F HIS* 2.9 27.9 + - + +
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Residues in contact with ASN 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10F ALA* 3.2 28.2 + - - +
13F LEU* 3.8 19.6 - - - +
14F ARG* 2.8 44.5 + - + +
41F ILE* 3.2 10.3 + - - +
42F GLN* 3.7 8.5 - - - +
43F HIS 3.2 0.6 - - - -
44F ILE* 1.3 76.7 - - - +
46F VAL* 1.3 65.5 + - + +
48F HIS* 3.6 4.4 + - - +
49F ASP* 3.2 31.3 + - - +
156F ALA 4.8 3.6 + - - -
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Residues in contact with VAL 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F GLN* 2.9 29.9 + - + +
43F HIS* 3.8 9.0 - - - +
45F ASN* 1.3 76.0 - - + +
47F GLN* 1.3 66.2 + - - +
49F ASP* 3.2 3.5 + - - +
50F VAL* 2.9 38.5 + - + +
56F VAL* 4.4 4.3 - - + -
59F ARG* 5.3 2.9 - - - +
81F THR* 3.6 38.8 - - + +
83F PHE* 4.0 23.7 - - + -
158F ASN* 4.6 4.0 - - - +
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Residues in contact with GLN 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43F HIS* 2.8 50.4 + - + +
44F ILE* 3.5 7.4 - - - +
46F VAL* 1.3 82.5 - - - +
48F HIS* 1.3 61.0 + - - +
50F VAL* 3.4 21.0 + - - +
51F ALA* 3.1 22.7 + - - +
220F GLU* 5.4 1.0 - - - +
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Residues in contact with HIS 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F ARG* 3.7 44.0 + - - +
44F ILE* 2.9 17.8 + - + +
45F ASN* 3.7 9.0 - - - +
46F VAL 3.3 0.2 - - - -
47F GLN* 1.3 77.2 - - - +
49F ASP* 1.3 74.7 + - - +
51F ALA* 3.3 16.1 + - - +
52F GLN* 3.3 38.0 + - + +
1265F K 4.2 5.6 - - - -
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Residues in contact with ASP 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ARG* 4.7 1.9 - - - -
45F ASN 3.2 16.2 + - - +
46F VAL 3.7 4.0 - - - +
48F HIS* 1.3 87.0 - - - +
50F VAL* 1.3 65.4 + - - +
52F GLN* 3.0 24.6 + - - +
53F GLY 3.4 0.3 + - - -
54F ARG* 3.0 58.9 + - + +
83F PHE* 4.2 7.9 - - + -
1265F K 4.1 6.4 - - - -
1312F NA 3.5 17.1 - - - -
4N HIS* 3.5 11.4 - - - -
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Residues in contact with VAL 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F VAL* 2.9 25.5 + - + +
47F GLN* 3.8 20.2 - - - +
48F HIS 3.4 0.2 - - - -
49F ASP* 1.3 75.5 - - - +
51F ALA* 1.3 59.4 + - - +
53F GLY* 2.8 21.3 + - - -
54F ARG 3.6 18.6 - - - +
56F VAL* 4.0 24.9 - - + +
83F PHE* 4.3 2.7 - - + -
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Residues in contact with ALA 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F GLN 3.1 13.2 + - - +
48F HIS* 3.4 12.8 - - - +
49F ASP 3.2 0.2 - - - -
50F VAL* 1.3 77.0 - - - +
52F GLN* 1.3 58.9 + - + +
53F GLY 3.3 1.2 + - - -
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Residues in contact with GLN 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F HIS* 3.3 32.0 + - + +
49F ASP* 3.0 23.0 + - - +
51F ALA* 1.3 78.5 - - + +
53F GLY* 1.3 57.3 + - - +
54F ARG* 3.4 3.2 + - + +
1265F K 3.6 19.9 - - - -
3N LYS* 2.8 35.7 + - - +
4N HIS* 4.6 6.5 + - - +
7N GLU* 3.3 44.9 - - + +
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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