Contacts of the helix formed by residues 72 - 87 (chain B) 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 ASP 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LYS* 3.3 31.2 + - - +
70B GLY 3.4 0.4 - - - -
71B ARG* 1.3 80.8 - - + +
73B THR* 1.3 66.7 + - - +
74B ALA* 2.9 22.6 + - - +
75B ASP* 2.8 40.0 + - - +
76B MET* 3.4 10.3 + - - +
116B GLN* 4.0 18.0 + - - +
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Residues in contact with THR 73 (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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77A ILE* 5.4 6.7 - - + -
109A THR* 5.6 5.2 - - - +
70B GLY 5.5 0.2 - - - -
71B ARG 3.7 3.7 + - - -
72B ASP* 1.3 73.3 + - - +
74B ALA* 1.3 64.1 + - - +
76B MET* 3.1 18.1 - - - +
77B ILE* 3.0 26.5 - - + +
109B THR* 4.5 4.0 - - - +
112B SER* 2.6 39.2 + - - +
113B ALA* 3.3 26.3 + - + +
116B GLN* 3.9 20.3 + - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 4.7 2.0 - - - +
77A ILE* 3.9 23.8 - - + +
78A GLN* 3.7 21.8 - - - +
81A LYS* 3.9 14.4 - - + +
72B ASP* 2.9 19.7 + - - +
73B THR* 1.3 80.8 - - - +
75B ASP* 1.3 62.0 + - - +
76B MET 3.0 1.4 + - - -
77B ILE* 3.1 22.9 + - - +
78B GLN* 3.4 9.2 + - - +
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Residues in contact with ASP 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLN* 4.7 6.7 + - - +
45B ARG* 2.9 37.5 + - - +
70B GLY* 4.7 6.8 - - - -
72B ASP* 2.8 38.9 + - - +
74B ALA* 1.3 77.0 - - - +
76B MET* 1.3 65.3 + - - +
77B ILE 3.4 0.2 - - - -
78B GLN* 3.4 15.9 - - + +
79B LEU* 3.0 27.8 + - - +
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Residues in contact with MET 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.8 24.9 - - - -
69B LEU* 3.8 30.5 - - + -
70B GLY* 3.4 38.8 - - - +
72B ASP 3.5 5.4 - - - +
73B THR* 3.1 17.0 - - - +
74B ALA 3.0 0.4 - - - -
75B ASP* 1.3 84.1 + - - +
77B ILE* 1.3 63.9 + - + +
79B LEU* 3.4 6.8 + - + +
80B ILE* 3.2 40.3 + - + +
92B PHE* 4.4 2.9 - - + -
108B VAL* 4.4 6.7 - - - -
112B SER* 4.8 13.0 - - - +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 5.2 6.3 - - + +
74A ALA* 4.2 26.2 - - + +
77A ILE* 3.9 22.9 - - + -
73B THR* 3.0 31.9 - - + +
74B ALA* 3.1 17.2 + - - +
76B MET* 1.3 72.9 - - + +
78B GLN* 1.3 57.1 + - - +
80B ILE* 3.0 12.5 + - + -
81B LYS* 2.6 39.8 + - + +
109B THR* 3.3 35.7 - - + -
112B SER* 5.9 0.4 - - - +
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Residues in contact with GLN 78 (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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74A ALA* 3.9 25.2 - - - +
75A ASP* 5.1 7.8 + - - +
78A GLN* 4.7 20.7 - - - +
74B ALA 3.4 10.6 + - - +
75B ASP* 3.3 20.4 + - + +
76B MET 3.3 0.4 - - - -
77B ILE* 1.3 78.1 - - - +
79B LEU* 1.3 62.8 + - + +
81B LYS* 3.4 14.2 + - - +
82B GLU* 3.0 37.9 + - - +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ARG* 4.7 19.3 - - - +
48B LEU* 4.2 18.6 - - + -
52B ARG* 3.4 42.0 - - - +
69B LEU* 4.3 34.1 - - + +
70B GLY* 5.5 1.6 - - - +
75B ASP* 3.0 18.7 + - - +
76B MET* 3.6 10.8 - - + +
77B ILE 3.2 0.2 - - - -
78B GLN* 1.3 75.9 - - + +
80B ILE* 1.3 55.6 + - + +
82B GLU* 2.9 11.2 + - - +
83B PHE* 2.7 49.2 + - + +
90B ILE* 6.2 0.2 - - + -
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Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 5.1 0.2 - - + -
76B MET* 3.2 34.1 + - + +
77B ILE* 3.0 17.1 + - + +
79B LEU* 1.3 78.2 - - - +
81B LYS* 1.3 53.6 + - - +
83B PHE* 3.0 8.0 + - - +
84B ASP* 2.7 34.5 + - - +
90B ILE* 3.7 22.4 - - + -
92B PHE* 4.7 2.5 - - + -
99B THR* 4.0 14.9 + - + +
105B ARG* 3.5 33.4 - - + +
108B VAL* 3.6 32.5 - - + -
109B THR* 6.2 2.2 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 2.8 31.0 + - - +
74A ALA* 3.9 17.9 - - + +
75A ASP* 4.4 9.7 + - - -
77B ILE* 2.6 23.4 + - + +
78B GLN* 3.6 14.4 + - - +
80B ILE* 1.3 69.9 - - - +
82B GLU* 1.3 67.4 + - + +
83B PHE 2.9 5.1 + - - -
84B ASP* 3.1 6.0 + - - +
85B ALA* 3.1 24.1 + - + +
105B ARG* 5.9 1.6 - - - +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ARG* 3.5 39.1 + - + -
78B GLN* 3.0 25.1 + - - +
79B LEU* 2.9 16.2 + - - +
81B LYS* 1.3 74.7 - - + +
83B PHE* 1.3 65.6 + - + +
85B ALA* 3.8 7.0 + - - +
86B GLN* 3.3 31.6 + - - +
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Residues in contact with PHE 83 (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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48B LEU* 5.2 11.7 - - + -
51B LEU* 5.6 0.4 - - + -
52B ARG* 3.2 47.3 - - + -
55B VAL* 5.4 1.8 - - + -
61B ILE* 3.4 31.0 - - + -
69B LEU* 5.6 4.5 - - + -
79B LEU* 2.7 26.2 + - + +
80B ILE* 3.1 12.3 - - + +
81B LYS 2.9 1.6 + - - -
82B GLU* 1.3 77.3 - - + +
84B ASP* 1.3 63.4 + - - +
85B ALA 3.2 1.1 - - - -
86B GLN* 3.3 12.4 + - - +
87B GLY 3.1 5.2 + - - -
88B VAL* 3.0 50.2 + - + +
90B ILE* 3.3 30.3 - - + -
99B THR* 5.4 0.4 - - - +
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Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE 2.7 17.6 + - - +
81B LYS* 4.0 3.8 - - - +
83B PHE* 1.3 72.2 - - - +
85B ALA* 1.3 61.3 - - - +
87B GLY* 3.3 13.4 + - - -
88B VAL 3.6 8.7 + - - +
89B SER* 5.1 0.5 - - - -
99B THR* 3.5 21.6 + - - +
100B SER* 4.5 5.9 - - - -
105B ARG* 2.7 44.1 + - - +
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Residues in contact with ALA 85 (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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81B LYS* 3.1 18.0 + - + +
82B GLU* 3.8 8.5 - - - +
84B ASP* 1.3 79.5 - - - +
86B GLN* 1.3 61.0 + - + +
87B GLY 3.5 0.3 + - - -
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Residues in contact with GLN 86 (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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52B ARG* 3.7 25.3 + - - +
53B MET* 4.8 10.3 - - - +
55B VAL* 4.3 17.3 + - - +
56B LYS* 5.1 1.5 - - - -
57B GLU* 3.7 25.1 + - - +
82B GLU* 3.3 18.6 + - - +
83B PHE* 3.3 26.2 + - - +
85B ALA* 1.3 80.8 - - + +
87B GLY* 1.3 57.4 + - - +
88B VAL* 3.7 11.9 - - + +
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Residues in contact with GLY 87 (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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57B GLU* 4.0 17.1 - - - +
58B GLY* 3.5 19.3 + - - -
59B ASP 3.9 3.6 - - - +
83B PHE 3.1 1.8 + - - -
84B ASP* 3.3 10.5 + - - -
85B ALA 3.3 3.4 - - - -
86B GLN* 1.3 79.2 - - - +
88B VAL* 1.3 64.8 + - - +
89B SER* 5.5 0.5 + - - -
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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