Contacts of the helix formed by residues 35 - 43 (chain B) in PDB entry 2GZG
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 PRO 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS 3.4 8.3 - - - +
18B VAL* 4.0 22.0 - - + -
22B TRP* 3.5 39.5 - - + +
33B PRO 3.5 1.5 - - - +
34B ILE* 1.3 92.2 - - + +
36B ASP* 1.3 67.5 + - - +
37B ARG* 4.3 5.2 - - + +
38B ILE* 3.0 32.2 + - + +
39B ALA* 3.1 10.2 + - - +
57B VAL* 6.2 1.1 - - + -
67B LEU* 4.1 18.4 - - + -
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Residues in contact with ASP 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LYS* 3.4 24.9 - - + +
15B GLY 4.3 1.3 - - - +
16B LYS* 2.9 24.5 + - - +
17B PRO* 3.5 26.4 - - + +
18B VAL 4.8 1.9 + - - -
34B ILE 3.5 1.0 + - - -
35B PRO* 1.3 71.5 - - - +
37B ARG* 1.3 84.5 + - - +
39B ALA* 3.2 3.1 + - - +
40B ASP* 3.0 37.5 + - - +
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 5.7 4.3 - - - -
35B PRO* 3.1 5.6 - - + -
36B ASP* 1.3 95.2 + - - +
38B ILE* 1.3 61.5 + - - +
40B ASP* 3.5 13.1 + - - +
41B LYS* 3.5 25.1 + - - +
64B ASP* 2.7 45.3 + - - +
65B PRO* 4.6 8.5 - - - +
66B GLU* 3.5 29.7 - - - +
67B LEU* 4.9 12.6 - - - -
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Residues in contact with ILE 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 4.1 15.9 - - + -
35B PRO* 3.0 19.0 + - + +
37B ARG* 1.3 74.6 - - - +
39B ALA* 1.3 66.1 + - - +
41B LYS* 3.0 18.0 + - + +
42B LEU* 3.0 33.7 + - + +
57B VAL* 4.1 14.1 - - + +
60B GLU* 3.4 31.2 - - + +
61B VAL* 3.7 21.8 - - + +
64B ASP* 4.9 3.1 - - + +
67B LEU* 3.6 28.9 - - + -
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLY 3.6 16.6 - - - +
14B LYS 3.4 29.6 - - - +
15B GLY* 4.1 2.7 - - - +
34B ILE* 4.4 2.0 - - + +
35B PRO 3.1 11.1 + - - +
36B ASP 3.2 2.7 + - - +
38B ILE* 1.3 75.3 - - - +
40B ASP* 1.3 58.0 + - - +
43B ARG* 2.9 38.8 + - - +
116B MET* 3.6 22.9 - - + -
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Residues in contact with ASP 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS 5.2 0.5 - - - +
36B ASP* 3.0 22.1 + - - +
37B ARG* 3.6 14.3 - - - +
38B ILE 3.2 0.2 - - - -
39B ALA* 1.3 77.5 - - - +
41B LYS* 1.3 61.9 + - + +
43B ARG* 3.0 37.2 + - - +
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ARG 3.5 15.5 - - - +
38B ILE* 3.0 8.7 + - + +
40B ASP* 1.3 82.2 - - + +
42B LEU* 1.3 60.8 + - - +
43B ARG 3.6 2.0 - - - +
45B LYS* 3.2 23.0 - - - +
60B GLU* 3.7 39.7 - - + +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 3.5 14.0 - - + +
38B ILE* 3.0 28.1 + - + +
41B LYS* 1.3 80.1 - - - +
43B ARG* 1.3 68.3 + - - +
44B ASP 3.3 0.5 + - - -
45B LYS* 3.1 33.4 + - + +
47B PHE* 4.2 8.7 - - + -
53B PHE* 3.8 15.9 - - + -
56B ALA* 4.0 17.5 - - + -
57B VAL* 3.8 37.5 - - + +
60B GLU* 3.9 22.9 - - + +
116B MET* 4.1 12.1 - - + -
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA 3.7 3.8 - - - +
12B THR* 4.1 6.1 - - - +
13B GLY 3.1 40.9 + - - +
14B LYS* 4.0 10.1 + - - +
39B ALA* 2.9 31.7 + - - +
40B ASP* 3.0 40.2 + - - +
41B LYS 3.6 2.9 - - - +
42B LEU* 1.3 78.3 - - - +
44B ASP* 1.3 73.2 + - - +
45B LYS* 3.2 6.4 + - - +
116B MET* 3.7 8.9 - - + +
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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
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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