Contacts of the helix formed by residues 84 - 104 (chain A) in PDB entry 1G2X
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 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LYS* 2.7 24.4 + - - -
81A ARG* 3.3 25.5 + - - +
82A THR 3.5 1.6 - - - +
83A ALA* 1.3 75.2 - - - +
85A ALA* 1.3 56.6 + - - +
86A CYS* 3.2 9.0 + - - +
87A ALA* 2.8 37.0 + - + -
88A LYS* 2.8 30.5 + - - +
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Residues in contact with ALA 85 (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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58A ILE* 4.4 11.7 - - + +
82A THR 5.0 2.9 - - - -
83A ALA 3.1 9.2 + - - +
84A ASP* 1.3 71.2 + - - +
86A CYS* 1.3 56.6 - - - +
88A LYS* 3.6 10.4 - - - +
89A PHE* 2.9 30.3 + - - +
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Residues in contact with CYS 86 (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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58A ILE* 3.9 14.2 - - + +
59A PRO 4.6 4.9 - - - +
60A GLY 4.0 2.0 - - - +
61A CYS* 2.0 56.4 - - + -
66A LYS* 3.3 33.2 - - - -
84A ASP* 3.2 7.9 + - - +
85A ALA* 1.3 75.9 - - - +
87A ALA* 1.3 67.5 + - - +
89A PHE* 3.2 1.9 + - - +
90A LEU* 3.0 27.4 + - - +
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Residues in contact with ALA 87 (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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66A LYS* 3.8 14.3 - - - +
68A TYR* 3.5 17.2 - - + +
81A ARG* 3.5 26.9 - - + +
84A ASP* 2.8 33.9 + - + +
86A CYS* 1.3 73.1 - - - +
88A LYS* 1.3 58.5 + - - +
90A LEU* 3.9 1.7 - - - +
91A CYS* 2.9 32.7 + - - +
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Residues in contact with LYS 88 (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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79A CYS* 5.1 4.6 - - + +
81A ARG* 3.5 30.9 - - - +
82A THR* 4.0 25.0 + - - +
84A ASP 2.8 17.4 + - - +
85A ALA* 3.6 8.5 - - - +
87A ALA* 1.3 76.6 - - - +
89A PHE* 1.3 64.6 + - - +
91A CYS* 3.5 3.9 + - - +
92A ASP* 3.1 24.8 + - + +
89B PHE* 4.8 18.0 - - - -
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Residues in contact with PHE 89 (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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51A CYS* 3.3 37.7 - - - -
54A GLN* 3.9 24.7 - - + -
55A ALA* 3.7 18.8 - - + -
58A ILE* 3.6 27.8 - - + -
85A ALA 2.9 19.0 + - - +
86A CYS 3.2 2.2 + - - +
88A LYS* 1.3 76.5 - - - +
90A LEU* 1.3 59.4 + - - +
92A ASP* 3.4 7.7 + - + +
93A CYS* 3.0 40.3 + - - -
82C THR* 5.1 6.3 - - + -
88C LYS* 4.7 20.2 - - - -
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Residues in contact with LEU 90 (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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52A TYR* 4.1 16.6 - - + -
55A ALA* 3.6 28.0 - - + -
61A CYS* 4.2 9.6 - - - -
62A ASN 3.8 1.6 - - - +
63A PRO* 3.5 35.7 - - + +
66A LYS* 3.3 39.5 - - + +
68A TYR* 4.0 13.5 - - + -
86A CYS* 3.0 12.5 + - - +
87A ALA* 3.9 2.7 - - - +
89A PHE* 1.3 74.2 - - + +
91A CYS* 1.3 67.8 + - - +
92A ASP 3.1 1.8 - - - -
93A CYS* 3.1 9.3 + - - +
94A ASP* 3.1 26.5 + - - +
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Residues in contact with CYS 91 (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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8A MET* 3.4 20.0 - - - +
68A TYR* 3.5 32.4 - - + -
69A SER 4.0 2.0 - - - +
70A TYR* 3.7 4.5 - - - -
79A CYS* 2.0 60.0 - - + -
81A ARG* 5.7 0.9 - - + -
87A ALA 2.9 19.6 + - - +
88A LYS* 3.9 2.7 - - - +
90A LEU* 1.3 76.4 - - - +
92A ASP* 1.3 56.3 + - - +
94A ASP* 3.4 2.6 + - - +
95A ARG* 2.8 25.1 + - - +
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Residues in contact with ASP 92 (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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79A CYS* 3.7 7.9 - - + -
88A LYS* 3.1 19.4 + - + +
89A PHE* 3.4 7.7 - - - +
91A CYS* 1.3 75.9 - - - +
93A CYS* 1.3 67.1 + - - +
95A ARG* 3.8 12.3 + - - +
96A THR* 2.8 40.8 + - - -
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Residues in contact with CYS 93 (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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48A HIS* 3.6 11.6 - - + +
51A CYS* 2.0 58.6 - - + -
52A TYR* 4.2 13.5 - - + -
89A PHE* 3.0 41.9 + - - -
90A LEU* 3.4 13.0 - - - +
92A ASP* 1.3 75.8 + - - +
94A ASP* 1.3 59.5 + - - +
96A THR* 3.3 7.3 + - - -
97A ALA 3.0 22.7 + - - -
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Residues in contact with ASP 94 (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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1A ASN 4.0 3.6 + - - +
5A PHE* 3.3 31.2 - - + +
8A MET* 3.7 7.0 - - - -
48A HIS* 2.7 20.9 + - - -
52A TYR* 2.7 32.0 + - - -
68A TYR* 2.7 36.2 + - - +
90A LEU* 3.1 8.3 + - - +
91A CYS 3.7 4.9 - - - +
93A CYS* 1.3 78.2 - - - +
95A ARG* 1.3 54.5 + - - +
97A ALA 3.2 1.0 + - - -
98A ALA* 2.7 36.2 + - - +
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Residues in contact with ARG 95 (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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8A MET* 3.4 13.9 - - - -
77A ILE* 2.8 41.3 + - + +
78A THR* 4.8 0.4 - - - +
79A CYS* 4.1 18.4 - - - +
91A CYS 2.8 20.2 + - - +
92A ASP* 3.8 13.9 + - - +
94A ASP* 1.3 72.8 - - - +
96A THR* 1.3 66.6 + - - +
98A ALA* 4.4 2.0 - - - -
99A ILE* 2.9 57.5 + - + +
47B THR* 4.8 14.1 + - - +
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Residues in contact with THR 96 (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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47A THR* 4.8 18.2 - - + -
92A ASP* 2.8 37.0 + - - -
93A CYS* 3.3 6.9 - - - -
95A ARG* 1.3 81.1 + - - +
97A ALA* 1.3 58.8 + - - +
99A ILE* 3.9 5.0 - - - +
100A CYS* 2.9 34.6 + - + +
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Residues in contact with ALA 97 (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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5A PHE* 3.5 17.5 - - + -
44A CYS 4.9 2.7 - - - +
48A HIS* 3.5 42.6 - - + -
93A CYS 3.0 5.8 + - - +
94A ASP 3.6 0.7 - - - +
96A THR* 1.3 75.1 - - - +
98A ALA* 1.3 55.9 + - - +
100A CYS* 3.1 6.8 + - - +
101A PHE* 2.7 50.2 + - + -
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Residues in contact with ALA 98 (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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5A PHE* 3.9 5.7 - - + -
8A MET* 3.7 40.8 - - + +
9A ILE* 3.9 10.8 - - - +
12A ALA* 3.8 6.6 - - - +
13A GLY 4.8 1.4 + - - -
77A ILE* 3.9 8.1 - - + -
94A ASP 2.7 20.1 + - - +
95A ARG 3.8 2.9 - - - +
97A ALA* 1.3 71.9 - - - +
99A ILE* 1.3 63.4 + - - +
101A PHE* 3.6 6.5 + - - +
102A ALA* 3.2 20.8 + - - +
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Residues in contact with ILE 99 (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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12A ALA* 4.3 16.8 - - + -
77A ILE* 4.9 5.4 - - + +
95A ARG* 2.9 68.1 + - + +
96A THR* 3.9 4.0 - - - +
98A ALA* 1.3 72.6 - - - +
100A CYS* 1.3 67.1 + - - +
102A ALA* 3.1 6.0 + - + +
103A SER* 3.1 29.4 + - - +
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Residues in contact with CYS 100 (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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40A LYS* 4.5 6.2 - - - -
44A CYS* 2.0 55.4 - - + -
47A THR* 6.4 0.4 - - - -
96A THR* 2.9 24.2 + - + +
97A ALA* 3.4 5.8 - - - +
99A ILE* 1.3 76.6 - - - +
101A PHE* 1.3 57.0 + - - +
103A SER* 3.3 5.5 + - - -
104A ALA* 2.9 32.2 + - - +
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Residues in contact with PHE 101 (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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5A PHE* 3.9 21.5 - + - -
9A ILE* 4.2 22.2 - - + -
17A ARG* 2.8 23.0 + - - -
22A TYR* 3.7 40.1 + + + +
41A LEU* 3.4 21.0 - - + +
44A CYS* 3.3 26.0 - - + -
45A CYS* 3.3 35.2 - - - -
48A HIS* 5.3 2.0 - - + -
97A ALA* 2.7 32.9 + - + +
98A ALA* 3.7 5.6 - - - +
100A CYS* 1.3 72.0 - - - +
102A ALA* 1.3 59.9 + - - +
104A ALA* 3.4 9.2 + - - +
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Residues in contact with ALA 102 (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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12A ALA* 3.2 30.5 - - + +
13A GLY* 3.8 10.3 - - - -
15A THR 5.6 0.2 - - - +
17A ARG* 3.6 13.7 + - - +
98A ALA 3.2 9.9 + - - +
99A ILE* 3.1 12.9 + - + +
101A PHE* 1.3 80.8 - - - +
103A SER* 1.3 61.6 + - - +
104A ALA 3.5 0.7 + - - +
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Residues in contact with SER 103 (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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40A LYS* 3.1 17.8 + - - -
99A ILE* 3.1 22.6 + - - +
100A CYS* 4.1 4.7 - - - -
102A ALA* 1.3 76.5 - - - +
104A ALA* 1.3 62.4 + - - +
105A PRO* 3.8 2.4 - - - +
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Residues in contact with ALA 104 (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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17A ARG* 3.2 23.7 + - - -
40A LYS* 3.2 16.8 - - - +
41A LEU* 3.8 31.8 - - + +
44A CYS* 4.1 3.1 - - - -
100A CYS 2.9 18.6 + - - +
101A PHE 3.4 5.2 - - - +
102A ALA 3.3 0.7 - - - +
103A SER* 1.3 79.6 - - - +
105A PRO* 1.3 68.8 - - + +
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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