Contacts of the helix formed by residues 45 - 55 (chain A) in PDB entry 2GM4
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 ARG 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TYR* 5.3 1.6 - - - +
8A ARG* 6.2 6.3 - - - +
36A ASP* 3.1 23.8 - - + +
44A ASP* 1.3 77.2 - - - +
46A LYS* 1.3 61.2 + - - +
48A LEU* 3.4 38.9 - - + +
49A ASP* 3.1 24.1 + - - +
52A ARG* 4.7 12.6 - - - +
69A LEU 5.8 0.8 + - - -
70A GLY* 5.8 3.0 - - - -
75A ASP* 3.8 30.9 + - - +
79A LEU* 4.1 17.8 - - - +
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Residues in contact with LYS 46 (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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36A ASP* 3.0 4.0 + - - -
44A ASP* 2.8 32.7 + - - +
45A ARG* 1.3 66.9 - - - +
47A GLY* 1.3 54.2 + - - +
48A LEU 2.6 16.2 + - - -
49A ASP* 2.7 25.7 + - - +
50A LEU* 3.1 10.9 + - - +
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Residues in contact with GLY 47 (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 TYR* 4.8 0.9 - - - -
34A PHE* 3.3 37.4 - - - +
35A THR 4.2 13.8 + - - -
36A ASP* 2.7 18.1 + - - -
46A LYS* 1.3 72.6 - - - +
48A LEU* 1.3 57.4 + - - -
50A LEU* 4.1 10.1 - - - -
51A LEU* 3.5 2.8 + - - +
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Residues in contact with LEU 48 (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 TYR* 3.9 33.9 - - + +
36A ASP* 3.2 16.0 + - - +
45A ARG* 3.4 45.5 - - + +
46A LYS 2.6 5.7 + - - -
47A GLY* 1.3 72.0 - - - +
49A ASP* 1.3 55.1 + - - +
50A LEU 3.0 1.6 - - - -
51A LEU* 2.8 14.8 + - + +
52A ARG* 2.7 41.0 + - - +
69A LEU* 4.4 15.9 - - + +
79A LEU* 4.1 19.7 - - + -
83A PHE* 5.3 10.1 - - + -
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Residues in contact with ASP 49 (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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45A ARG* 3.1 28.7 + - - +
46A LYS* 2.7 16.3 + - - +
48A LEU* 1.3 75.7 - - - +
50A LEU* 1.3 57.1 + - - +
52A ARG* 3.0 48.9 + - - +
53A MET* 3.2 24.2 + - + +
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Residues in contact with LEU 50 (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 PHE* 4.3 17.2 - - + -
46A LYS 3.1 11.4 + - - +
47A GLY* 4.2 9.9 - - - +
48A LEU 3.0 0.6 - - - -
49A ASP* 1.3 76.1 - - - +
51A LEU* 1.3 64.7 + - - +
53A MET* 3.2 21.7 + - + +
54A LYS* 3.0 21.9 + - + +
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Residues in contact with LEU 51 (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 PHE* 4.0 25.6 - - + -
5A GLY 4.5 1.3 - - - +
6A TYR* 3.7 33.4 - - + -
34A PHE* 3.4 39.6 - - + -
47A GLY 3.5 14.4 + - - +
48A LEU* 2.8 16.0 + - + +
50A LEU* 1.3 76.2 - - - +
52A ARG* 1.3 64.5 + - - +
53A MET 2.9 1.6 + - - -
54A LYS* 3.0 11.7 + - + +
55A VAL* 3.2 22.0 + - + +
61A ILE* 3.8 24.2 - - + -
83A PHE* 5.5 4.5 - - + -
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Residues in contact with ARG 52 (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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45A ARG* 4.7 13.1 - - - +
48A LEU* 2.7 17.6 + - - +
49A ASP* 3.0 41.9 + - - +
51A LEU* 1.3 73.2 - - - +
53A MET* 1.3 57.9 + - + +
55A VAL* 3.5 17.8 - - - +
78A GLN* 5.9 0.6 - - - +
79A LEU* 4.3 23.2 - - - +
82A GLU* 3.0 37.9 + - + +
83A PHE* 3.7 32.9 - - + -
86A GLN* 4.0 10.7 + - - +
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Residues in contact with MET 53 (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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49A ASP* 3.4 29.2 - - + +
50A LEU* 3.2 23.5 + - + +
51A LEU 3.0 1.0 - - - -
52A ARG* 1.3 80.6 - - + +
54A LYS* 1.3 62.6 + - - +
55A VAL 3.4 7.2 - - - +
56A LYS* 5.5 4.3 - - - +
86A GLN* 6.2 0.4 - - - +
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Residues in contact with LYS 54 (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 PHE* 4.2 23.4 - - + -
31A ASN* 4.0 19.2 + - - -
32A ARG* 4.7 16.7 - - - +
34A PHE* 3.7 26.4 - - + -
50A LEU* 3.0 13.7 + - + +
51A LEU* 3.0 9.6 + - + +
53A MET* 1.3 76.4 - - - +
55A VAL* 1.3 64.8 + - - +
56A LYS* 3.9 11.4 + - - +
59A ASP* 4.4 0.7 - - - +
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Residues in contact with VAL 55 (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 PHE* 3.5 28.5 - - + -
51A LEU* 3.4 16.2 - - + +
52A ARG* 3.5 16.9 - - - +
53A MET* 4.0 6.8 - - - +
54A LYS* 1.3 80.7 - - - +
56A LYS* 1.3 65.1 + - - +
59A ASP* 3.2 8.7 - - - +
61A ILE* 3.6 19.7 - - + -
83A PHE* 4.9 5.2 - - + -
86A GLN* 3.4 26.3 + - - +
88A VAL* 3.8 23.6 - - + -
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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
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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