Contacts of the helix formed by residues 84 - 104 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B LYS* 2.6 26.0 + - - -
81B ARG* 3.4 23.6 + - - +
82B THR 3.5 1.8 - - - +
83B ALA* 1.3 75.5 - - - +
85B ALA* 1.3 58.3 + - - +
86B CYS* 3.2 10.9 + - - +
87B ALA* 2.9 29.0 + - + +
88B LYS* 2.8 29.9 + - - +
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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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58B ILE* 4.8 11.4 - - + -
82B THR 5.0 1.3 - - - -
83B ALA 3.1 10.2 + - - +
84B ASP* 1.3 69.8 + - - +
86B CYS* 1.3 58.0 + - - +
88B LYS* 3.3 11.0 + - - +
89B PHE* 2.8 32.9 + - - +
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Residues in contact with CYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.9 16.1 - - + +
59B PRO 4.5 5.2 - - - +
60B GLY 4.0 1.3 - - - +
61B CYS* 2.0 55.9 - - + -
66B LYS* 3.2 33.9 - - - -
84B ASP* 3.2 8.1 + - - +
85B ALA* 1.3 73.8 - - - +
87B ALA* 1.3 67.2 + - - +
89B PHE* 3.2 2.4 + - - +
90B LEU* 2.9 23.1 + - - +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS* 3.8 15.7 - - - +
68B TYR* 3.8 16.7 - - + +
81B ARG* 3.5 25.4 - - + +
84B ASP* 2.9 34.3 + - - +
86B CYS* 1.3 73.0 - - - +
88B LYS* 1.3 57.6 + - - +
90B LEU* 3.8 2.5 - - - +
91B CYS* 2.9 32.6 + - - +
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Residues in contact with LYS 88 (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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79B CYS* 5.1 2.9 - - + +
81B ARG* 3.6 32.4 - - + +
82B THR* 4.0 25.8 + - - +
84B ASP 2.8 18.4 + - - +
85B ALA* 3.4 9.0 - - - +
87B ALA* 1.3 76.9 - - - +
89B PHE* 1.3 64.1 + - - +
91B CYS* 3.4 4.7 + - - +
92B ASP* 3.1 37.6 + - - +
89C PHE* 5.1 15.9 - - - -
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Residues in contact with PHE 89 (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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82A THR* 5.3 6.7 - - + -
88A LYS* 4.8 18.8 - - - -
51B CYS* 3.2 37.5 - - - -
54B GLN* 3.8 26.5 - - + -
55B ALA* 3.6 22.4 - - + -
58B ILE* 3.6 20.2 - - + -
85B ALA 2.8 20.7 + - - +
86B CYS 3.6 4.3 - - - +
88B LYS* 1.3 73.4 - - - +
90B LEU* 1.3 60.5 + - - +
92B ASP* 3.2 8.5 + - - +
93B CYS* 3.0 33.9 + - - -
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Residues in contact with LEU 90 (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 TYR* 4.1 16.2 - - + -
55B ALA* 3.3 31.6 - - + -
61B CYS* 4.4 6.7 - - - -
62B ASN 3.6 1.6 - - - +
63B PRO* 3.3 38.4 - - + +
66B LYS* 3.3 38.8 - - + +
68B TYR* 4.1 11.7 - - + -
86B CYS 2.9 13.3 + - - +
87B ALA* 3.8 2.9 - - - +
89B PHE* 1.3 74.9 - - + +
91B CYS* 1.3 67.1 + - - +
93B CYS* 3.2 8.0 + - - +
94B ASP* 3.1 27.7 + - - +
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Residues in contact with CYS 91 (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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8B MET* 3.4 18.7 - - - +
68B TYR* 3.5 32.9 - - + -
69B SER 4.0 2.0 - - - +
70B TYR* 3.8 4.0 - - - -
79B CYS* 2.0 53.5 - - + -
81B ARG* 5.7 1.3 - - + -
87B ALA 2.9 18.8 + - - +
88B LYS* 3.8 4.7 - - - +
90B LEU* 1.3 76.7 - - - +
92B ASP* 1.3 57.4 + - - +
94B ASP 3.4 0.5 + - - -
95B ARG* 2.8 31.9 + - - +
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Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B CYS* 4.4 13.7 - - - +
88B LYS* 3.1 30.4 + - - +
89B PHE* 3.3 12.2 - - + +
90B LEU 3.1 0.2 - - - -
91B CYS* 1.3 76.2 - - - +
93B CYS* 1.3 62.5 + - - +
95B ARG* 4.0 11.7 + - - +
96B THR* 2.7 39.0 + - - +
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Residues in contact with CYS 93 (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 HIS* 3.6 14.1 - - + +
51B CYS* 2.0 60.3 - - + -
52B TYR* 4.2 7.0 - - + -
89B PHE* 3.0 37.6 + - - -
90B LEU* 3.4 13.9 - - - +
92B ASP* 1.3 78.6 - - - +
94B ASP* 1.3 58.3 - - - +
96B THR* 3.2 5.8 + - - -
97B ALA* 2.9 25.8 + - - +
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Residues in contact with ASP 94 (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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1B ASN 3.9 2.8 - - - +
5B PHE* 3.3 30.4 - - + +
8B MET* 3.6 6.3 - - - -
48B HIS* 2.7 16.1 + - - -
52B TYR* 2.7 32.3 + - - -
68B TYR* 2.8 37.5 + - - +
90B LEU* 3.1 11.5 + - - +
91B CYS 3.8 1.1 - - - +
93B CYS* 1.3 77.2 - - - +
95B ARG* 1.3 60.3 + - - +
97B ALA 3.2 0.5 + - - -
98B ALA* 2.8 32.1 + - - +
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Residues in contact with ARG 95 (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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8B MET* 3.3 16.0 - - - -
77B ILE* 2.9 42.7 + - + +
78B THR* 4.7 0.4 - - - +
79B CYS* 4.0 20.4 - - - +
91B CYS 2.8 21.4 + - - +
92B ASP* 4.0 12.2 + - - +
94B ASP* 1.3 73.7 - - - +
96B THR* 1.3 65.8 + - - +
98B ALA* 3.8 2.7 - - - +
99B ILE* 3.0 56.3 + - + +
47C THR* 4.9 13.9 + - - +
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Residues in contact with THR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 4.9 17.7 - - + -
48B HIS* 6.5 0.4 - - - -
92B ASP* 2.7 29.1 + - - +
93B CYS* 3.2 6.7 - - - +
95B ARG* 1.3 83.2 + - - +
97B ALA* 1.3 59.2 + - - +
99B ILE* 3.7 6.0 - - - +
100B CYS* 2.8 37.1 + - + +
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Residues in contact with ALA 97 (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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5B PHE* 3.4 27.6 - - + -
44B CYS 5.2 2.0 - - - -
48B HIS* 3.5 33.9 - - + -
93B CYS 2.9 5.2 + - - +
94B ASP 3.6 0.2 - - - +
96B THR* 1.3 74.9 - - - +
98B ALA* 1.3 56.6 + - - +
100B CYS* 3.2 5.8 + - - -
101B PHE* 2.7 49.4 + - + -
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Residues in contact with ALA 98 (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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5B PHE* 4.0 1.0 - - - -
8B MET* 3.6 36.3 - - + +
9B ILE* 4.0 14.7 - - + +
12B ALA* 3.8 5.9 - - - +
13B GLY 4.9 1.0 + - - -
77B ILE* 3.8 12.3 - - + -
94B ASP 2.8 20.6 + - - +
95B ARG 3.8 3.8 - - - +
97B ALA* 1.3 72.1 - - - +
99B ILE* 1.3 61.6 + - - +
101B PHE* 3.4 7.4 - - - +
102B ALA* 3.1 21.7 + - - +
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Residues in contact with ILE 99 (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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12B ALA* 4.3 15.3 - - + -
77B ILE* 5.0 4.7 - - + +
95B ARG* 3.0 61.2 + - + +
96B THR* 3.7 5.2 - - - +
98B ALA* 1.3 73.9 - - - +
100B CYS* 1.3 67.6 + - - +
102B ALA* 2.9 14.7 + - + +
103B SER* 3.0 22.9 + - - +
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Residues in contact with CYS 100 (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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40B LYS* 4.8 6.3 - - - -
43B ARG* 6.0 0.4 - - - -
44B CYS* 2.0 55.0 - - + -
47B THR* 6.3 0.4 - - - -
96B THR* 2.8 26.7 + - + +
97B ALA* 3.6 5.8 - - - +
99B ILE* 1.3 73.2 - - - +
101B PHE* 1.3 57.8 + - - +
103B SER* 3.4 3.6 + - - -
104B ALA* 2.9 34.1 + - - +
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Residues in contact with PHE 101 (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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5B PHE* 4.1 19.7 - + - -
9B ILE* 4.2 17.0 - - + -
17B ARG* 3.1 25.1 + - - -
22B TYR* 3.5 46.5 + + + +
41B LEU* 3.5 15.9 - - + +
44B CYS* 3.2 31.0 - - + -
45B CYS* 3.3 34.1 - - - -
48B HIS* 5.4 1.3 - + + -
97B ALA* 2.7 38.4 + - + +
98B ALA* 3.4 6.5 - - - +
100B CYS* 1.3 75.2 - - - +
102B ALA* 1.3 58.3 + - - +
104B ALA* 3.5 6.1 + - - +
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Residues in contact with ALA 102 (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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12B ALA* 3.1 31.4 - - + +
13B GLY* 3.7 10.3 - - - -
17B ARG* 4.5 5.2 + - - +
22B TYR* 5.1 1.1 - - - -
98B ALA 3.1 9.7 + - - +
99B ILE* 2.9 11.7 + - + +
101B PHE* 1.3 82.4 - - - +
103B SER* 1.3 61.3 + - - +
104B ALA 3.7 3.6 + - - +
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Residues in contact with SER 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 3.3 20.2 + - - -
99B ILE* 3.0 21.4 + - - +
100B CYS* 4.2 4.0 - - - -
102B ALA* 1.3 76.2 - - - +
104B ALA* 1.3 64.7 + - - +
105B PRO* 3.8 2.6 - - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ARG* 3.1 25.6 + - - -
40B LYS* 3.7 14.1 - - + -
41B LEU* 3.7 35.2 - - + +
44B CYS* 4.1 2.2 - - - -
100B CYS 2.9 18.9 + - - +
101B PHE 3.5 3.3 - - - +
102B ALA 3.4 2.1 - - - +
103B SER* 1.3 79.1 - - - +
105B PRO* 1.3 69.1 - - + +
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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
------------------------------------------------------------
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