Contacts of the helix formed by residues 32 - 41 (chain A) in PDB entry 2HQR
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A ILE* 3.9 1.1 - - - -
8A LYS* 5.2 10.3 - - - +
30A THR* 3.9 2.6 + - - -
31A GLU* 1.3 92.2 - - - +
33A LEU* 1.3 67.9 + - - +
34A GLU* 3.0 28.9 + - - +
35A ASP* 3.1 20.8 + - - +
36A GLY 3.6 2.3 + - - -
52A ASP* 4.0 4.9 - - - -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.1 13.7 - - + -
32A SER* 1.3 75.6 - - - +
34A GLU* 1.3 56.3 + - + +
36A GLY* 2.8 2.3 + - - -
37A GLU* 2.6 36.6 + - - +
50A VAL* 3.9 11.4 - - + -
52A ASP* 3.3 28.0 + - + +
54A ASN* 4.8 9.4 - - + +
55A ALA* 3.7 24.9 - - + +
58A PHE* 3.5 50.9 - - + -
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A SER* 3.0 15.7 + - - +
33A LEU* 1.3 77.8 - - + +
35A ASP* 1.3 61.4 + - - +
37A GLU* 3.8 11.8 - - - +
38A TYR* 2.9 30.7 + - - +
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Residues in contact with ASP 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A THR* 4.1 15.4 - - + -
31A GLU* 2.4 42.6 - - - +
32A SER* 3.1 8.8 + - - +
33A LEU 3.1 0.6 - - - -
34A GLU* 1.3 82.1 - - - +
36A GLY* 1.3 58.6 - - - +
38A TYR* 3.6 5.3 - - - +
39A LEU* 2.7 33.6 + - - +
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 4.7 9.7 - - - +
6A ILE* 4.4 12.6 - - - -
30A THR* 4.1 16.6 + - - -
32A SER 3.6 2.2 + - - -
33A LEU 2.8 7.8 + - - -
35A ASP* 1.3 79.9 - - - +
37A GLU* 1.3 52.8 + - - +
39A LEU* 4.2 4.9 - - - -
40A MET* 2.7 40.3 + - - +
58A PHE* 5.2 2.7 - - - -
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU 2.6 19.5 + - - +
34A GLU* 3.8 10.9 - - - +
36A GLY* 1.3 72.1 - - - -
38A TYR* 1.3 61.6 + - - +
40A MET* 3.4 12.6 - - + +
41A ASP* 3.3 24.7 + - + +
58A PHE* 3.9 31.8 - - + -
61A ARG* 5.3 2.9 - - - -
65A LYS* 4.7 12.6 + - - -
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Residues in contact with TYR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU 2.9 17.8 + - - +
35A ASP* 3.9 4.9 - - - +
37A GLU* 1.3 74.8 - - - +
39A LEU* 1.3 57.3 + - + +
41A ASP* 2.3 38.4 - - - +
42A ILE* 3.8 14.7 - - + +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 5.8 2.7 - - + -
28A ASP* 3.4 30.1 - - + +
30A THR* 4.4 10.1 - - + -
35A ASP 2.7 18.3 + - - +
36A GLY* 3.8 4.3 - - - +
38A TYR* 1.3 81.5 - - + +
40A MET* 1.3 60.3 + - - +
41A ASP* 3.4 0.4 - - - -
42A ILE* 3.0 36.3 - - + +
43A ARG* 3.3 21.2 + - - +
45A TYR* 3.9 23.3 - - + +
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Residues in contact with MET 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU* 5.0 9.6 - - + -
36A GLY 2.7 24.6 + - - +
37A GLU* 3.4 17.5 - - + +
39A LEU* 1.3 70.3 - - - +
41A ASP* 1.3 76.6 + - - +
42A ILE 3.1 1.8 - - - -
43A ARG 2.4 31.5 + - - +
44A ASN* 4.4 1.3 - - - -
45A TYR* 4.2 15.3 - - + +
48A VAL* 5.8 7.0 - - + -
58A PHE* 5.2 4.0 - - + -
62A ILE* 4.2 18.8 - - + -
66A HIS* 3.6 35.7 - - + +
69A ILE* 6.3 1.8 - - + -
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Residues in contact with ASP 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A GLU* 3.3 12.1 + - + +
38A TYR* 2.3 43.8 - - - +
40A MET* 1.3 89.9 - - - +
42A ILE* 1.3 85.5 + - - +
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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