Contacts of the helix formed by residues 30 - 45 (chain E) in PDB entry 2QAR
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 SER 30 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E TYR 3.4 3.4 + - - -
29E TRP* 1.3 78.9 - - - +
31E ARG* 1.3 62.6 + - - +
32E ASP* 3.2 10.8 + - - +
33E ASP* 2.9 34.8 + - - -
34E VAL* 3.2 21.0 + - - +
58E ASN* 3.9 6.3 - - - -
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Residues in contact with ARG 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E SER* 1.3 74.9 - - - +
32E ASP* 1.3 67.1 + - - +
34E VAL* 3.3 5.7 + - - +
35E ALA* 3.1 20.7 + - + +
53E ASN* 4.6 5.7 + - - -
55E PHE 4.8 2.5 - - - +
56E GLU* 3.6 43.8 + - - +
57E MET* 3.5 35.4 - - - +
58E ASN* 3.9 6.4 - - + +
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Residues in contact with ASP 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E SER* 3.2 8.8 + - - +
31E ARG* 1.3 79.4 - - - +
33E ASP* 1.3 61.2 + - - +
35E ALA* 3.0 10.0 + - - +
36E GLN* 2.9 44.6 + - + +
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Residues in contact with ASP 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E HIS* 4.3 19.8 - - - +
22E LEU* 3.3 29.0 - - + +
24E LEU* 5.9 2.4 - - - +
28E TYR 4.3 2.6 - - - +
29E TRP* 3.6 18.5 - - + -
30E SER* 2.9 40.6 + - - +
32E ASP* 1.3 75.6 - - - +
34E VAL* 1.3 57.5 + - - +
36E GLN* 3.3 5.2 + - - +
37E TRP* 2.9 25.2 + - - +
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Residues in contact with VAL 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E TRP* 4.2 13.5 - - + -
30E SER 3.2 15.0 + - - +
31E ARG 3.4 8.1 - - - +
32E ASP 3.2 0.4 - - - -
33E ASP* 1.3 75.7 - - - +
35E ALA* 1.3 61.9 + - - +
37E TRP* 3.2 12.8 + - + +
38E LEU* 3.2 25.7 + - + +
55E PHE* 4.0 28.7 - - + +
57E MET 3.5 20.0 - - - +
58E ASN 3.7 2.0 - - - +
59E GLY* 3.6 23.1 - - - +
62E LEU* 4.3 18.2 - - + -
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Residues in contact with ALA 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ARG* 3.1 12.2 + - + +
32E ASP* 3.0 14.8 + - - +
34E VAL* 1.3 77.5 - - - +
36E GLN* 1.3 69.7 + - - +
38E LEU* 3.4 13.0 + - - +
39E LYS* 3.2 22.0 + - - +
52E SER* 5.0 15.0 - - - +
55E PHE 6.0 1.3 - - - +
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Residues in contact with GLN 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E PRO* 5.5 0.2 - - - +
21E HIS* 3.8 29.2 - - + +
22E LEU* 4.2 3.9 - - + +
32E ASP* 2.9 34.0 + - + +
33E ASP* 3.3 7.8 + - - +
35E ALA* 1.3 80.2 - - - +
37E TRP* 1.3 60.1 + - - +
39E LYS* 3.5 23.4 + - - +
40E TRP* 3.0 30.8 + - - +
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Residues in contact with TRP 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E LEU* 4.0 13.7 - - + -
22E LEU* 3.7 12.1 - - + +
29E TRP* 3.5 26.9 - + + -
33E ASP 2.9 13.7 + - - +
34E VAL* 3.2 14.6 - - + +
36E GLN* 1.3 77.9 - - - +
38E LEU* 1.3 84.5 + - + +
40E TRP* 3.7 6.0 - + - -
41E ALA* 2.9 30.5 + - + +
62E LEU* 3.9 28.3 - - + -
70E PHE* 4.1 13.5 - + - -
81E LEU* 3.4 38.8 - - + -
84E LEU* 3.5 24.0 - - + +
85E LEU* 4.1 16.4 - - + -
88E ILE* 3.3 20.7 - - + +
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Residues in contact with LEU 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E VAL* 3.2 16.0 + - + +
35E ALA* 3.7 12.8 - - - +
36E GLN 3.3 0.2 - - - -
37E TRP* 1.3 100.7 - - + +
39E LYS* 1.3 60.2 + - - +
41E ALA* 3.2 4.7 + - - +
42E GLU* 2.9 31.1 + - - +
50E ILE* 3.8 19.1 - - + +
51E ASP 4.8 4.0 - - - +
52E SER* 5.0 6.3 - - - +
54E THR* 4.2 8.3 - - - +
55E PHE* 3.7 39.3 - - + +
81E LEU* 3.8 27.4 - - + -
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Residues in contact with LYS 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E ALA 3.2 14.3 + - - +
36E GLN* 3.9 22.4 + - - +
37E TRP 3.5 0.2 - - - -
38E LEU* 1.3 78.3 - - - +
40E TRP* 1.3 63.5 + - - +
42E GLU* 3.4 11.3 + - - +
43E ASN* 3.1 38.7 + - - +
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Residues in contact with TRP 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E ILE* 4.0 22.9 - - + -
17E ARG 3.4 26.8 + - - -
18E LEU* 3.9 22.4 - - + -
19E PRO* 3.5 34.0 - - + +
36E GLN 3.0 18.8 + - - +
37E TRP* 3.7 12.1 - + - +
39E LYS* 1.3 78.0 - - - +
41E ALA* 1.3 68.6 + - - +
43E ASN* 3.5 4.6 + - - +
44E GLU* 2.9 60.6 + - + +
45E PHE* 4.0 13.7 - + - -
84E LEU* 3.8 24.9 - - + -
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Residues in contact with ALA 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E TRP* 2.9 19.7 + - + +
38E LEU 3.2 4.7 + - - +
40E TRP* 1.3 80.3 - - + +
42E GLU* 1.3 60.0 + - - +
45E PHE* 2.9 43.4 + - + +
47E LEU* 3.8 2.4 - - + +
81E LEU* 3.8 20.2 - - + -
84E LEU* 3.8 26.7 - - + -
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Residues in contact with GLU 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E LEU 2.9 17.6 + - - +
39E LYS* 3.5 12.4 - - - +
40E TRP 3.3 0.2 - - - -
41E ALA* 1.3 75.4 - - - +
43E ASN* 1.3 65.9 + - - +
46E SER* 2.9 9.7 + - - -
47E LEU* 2.9 52.9 + - - +
48E SER 4.0 7.2 - - - +
49E PRO* 3.4 26.7 - - - +
50E ILE* 3.0 28.5 + - + +
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Residues in contact with ASN 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ASN* 5.0 0.2 + - - -
39E LYS* 3.1 35.0 + - - +
40E TRP* 4.0 3.7 - - - +
41E ALA 3.3 0.2 - - - -
42E GLU* 1.3 82.6 - - - +
44E GLU* 1.3 65.5 + - - +
45E PHE 3.3 0.5 + - - -
46E SER* 3.5 14.1 + - - +
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Residues in contact with GLU 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ASN* 2.9 15.4 + - - -
60D LYS* 3.1 41.6 + - - +
15E SER 4.7 7.3 - - - +
16E ILE* 5.2 2.3 - - - +
17E ARG 5.0 6.4 + - - +
40E TRP* 2.9 48.9 + - + +
41E ALA 4.0 2.7 - - - +
43E ASN* 1.3 78.2 - - - +
45E PHE* 1.3 85.8 + - + +
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Residues in contact with PHE 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D MET* 3.5 4.9 - - - +
58D ASN* 3.1 24.7 + - - +
60D LYS* 3.9 23.1 - - + -
61D ALA* 3.5 31.4 - - + -
64D LEU* 3.8 24.0 - - + -
16E ILE* 4.5 13.0 - - + -
40E TRP* 4.0 9.4 - + - -
41E ALA* 2.9 32.8 + - + +
44E GLU* 1.3 95.9 - - + +
46E SER* 1.3 68.2 + - - +
47E LEU* 3.2 13.7 + - + +
80E VAL* 4.6 7.0 - - + -
84E LEU* 3.7 34.1 - - + -
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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