Contacts of the helix formed by residues 75 - 91 (chain B) in PDB entry 2GS4
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 CYS 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ASP* 3.1 51.1 + - - +
19B SER* 2.9 15.3 + - - +
20B ALA* 3.9 11.7 - - - +
23B GLN* 2.8 25.7 + - - +
74B LYS* 1.3 69.3 - - - +
76B VAL* 1.3 61.8 + - - +
77B ALA* 4.0 2.9 - - - -
78B MSE 3.6 25.5 + - - -
79B GLU* 3.7 4.7 + - - +
112B TYR* 3.2 18.6 - - - -
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU* 3.5 21.6 - - + +
108A LYS* 3.3 61.5 - - + +
111A HIS* 3.6 36.9 - - + +
112A TYR* 4.9 3.6 - - + +
16B ASP* 5.0 0.2 + - - -
74B LYS* 3.2 8.8 + - + +
75B CYS* 1.3 70.3 - - - +
77B ALA* 1.3 65.3 + - - +
79B GLU* 3.1 24.6 + - - +
80B GLY 3.3 4.7 + - - -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ALA* 3.7 31.7 - - + +
81A LEU* 4.4 12.6 - - - +
112A TYR* 4.2 14.3 - - + -
16B ASP* 5.6 0.2 - - - +
75B CYS* 3.4 1.6 - - - -
76B VAL* 1.3 77.5 - - - +
78B MSE 1.3 61.9 + - - +
80B GLY* 3.2 4.3 + - - -
81B LEU* 3.1 26.2 + - - +
112B TYR* 3.6 25.8 - - + +
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Residues in contact with MSE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA* 3.7 28.0 - - + +
23B GLN* 3.8 7.2 - - - +
24B LEU* 4.0 19.3 - - + -
75B CYS* 3.6 23.2 - - - +
76B VAL 3.3 0.6 - - - -
77B ALA* 1.3 75.2 - - - +
79B GLU* 1.3 66.8 + - - +
81B LEU* 3.3 9.1 + - - +
82B ILE* 2.9 46.8 + - + +
109B VAL* 3.9 23.3 - - + -
112B TYR* 4.5 7.6 + - + -
113B GLU* 3.5 40.6 - - + +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 4.6 12.3 - - - +
108A LYS* 2.7 38.7 + - - +
23B GLN* 3.3 19.5 + - - +
74B LYS* 2.7 42.3 - - - +
75B CYS 3.7 4.9 + - - +
76B VAL* 3.1 16.9 + - - +
78B MSE 1.3 77.3 - - - +
80B GLY* 1.3 57.9 + - - +
82B ILE* 3.3 6.0 + - - +
83B GLU* 3.0 28.6 + - - +
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY* 4.1 23.7 - - - +
81A LEU* 4.6 1.8 - - - -
84A GLU* 3.9 16.7 + - - -
76B VAL 3.3 4.5 + - - -
77B ALA 3.2 7.3 + - - -
79B GLU* 1.3 80.4 - - - +
81B LEU* 1.3 60.1 + - - +
83B GLU* 3.2 16.0 + - - +
84B GLU* 3.3 17.0 + - - +
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL* 3.6 33.9 - - + +
77A ALA* 4.9 2.2 - - - -
80A GLY* 4.4 3.1 - - - -
77B ALA 3.1 14.7 + - - +
78B MSE 3.3 10.7 + - - +
80B GLY* 1.3 72.3 - - - +
82B ILE* 1.3 65.9 + - - +
84B GLU* 3.3 37.8 + - - +
85B ALA* 3.7 5.0 + - - +
105B ALA* 5.2 3.3 - - - +
108B LYS* 4.0 15.4 - - + +
109B VAL* 3.9 26.2 - - + +
112B TYR* 3.5 43.7 - - + -
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 3.7 32.3 - - + +
24B LEU* 4.1 5.6 - - + +
27B ALA* 3.6 34.5 - - + -
78B MSE 2.9 41.0 + - + +
79B GLU* 3.7 6.1 - - - +
81B LEU* 1.3 76.5 - - - +
83B GLU* 1.3 62.6 + - - +
85B ALA* 3.2 17.1 + - + +
86B ASN* 3.3 23.9 + - - +
109B VAL* 5.3 2.9 - - + -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 3.1 46.0 - - + +
87A GLU* 3.0 40.2 - - - +
79B GLU 3.0 12.7 + - - +
80B GLY 3.2 9.8 + - - +
82B ILE* 1.3 76.3 - - - +
84B GLU* 1.3 59.9 + - - +
86B ASN* 3.1 15.2 + - + +
87B GLU* 2.9 27.4 + - - +
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A VAL 4.8 0.3 - - - +
79A GLU* 4.8 3.2 - - - +
80A GLY* 3.1 30.4 + - - -
83A GLU* 3.3 35.9 - - + +
87A GLU* 5.3 0.2 - - - -
80B GLY 3.3 13.3 + - - +
81B LEU* 3.6 22.8 - - - +
82B ILE 3.3 0.8 - - - -
83B GLU* 1.3 75.6 - - - +
85B ALA* 1.3 62.4 + - - +
87B GLU* 3.3 8.2 + - - +
88B VAL* 3.0 27.6 + - + +
105B ALA* 4.5 10.8 - - + -
108B LYS* 3.9 24.4 - - - +
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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
----------------------------------------------------------
31B LEU* 3.9 31.0 - - + -
81B LEU 3.7 4.0 + - - +
82B ILE* 3.2 12.7 + - + +
83B GLU 3.2 0.2 - - - -
84B GLU* 1.3 78.4 - - - +
86B ASN* 1.3 67.7 + - - +
88B VAL* 3.1 4.9 + - - +
89B ILE* 3.0 26.8 + - - +
102B LEU* 3.7 7.9 - - + +
105B ALA* 4.2 17.1 - - + +
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Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 2.7 42.1 + - - +
31B LEU* 6.3 0.4 - - - +
82B ILE* 3.3 23.4 + - - +
83B GLU* 3.1 20.1 + - + +
85B ALA* 1.3 80.9 - - - +
87B GLU* 1.3 61.1 + - - +
89B ILE* 3.2 12.3 + - - +
90B GLU* 3.0 33.9 + - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 3.5 41.8 - - + +
83B GLU 2.9 11.1 + - - +
84B GLU* 3.6 7.9 - - - +
86B ASN* 1.3 72.2 - - - +
88B VAL* 1.3 65.5 + - + +
90B GLU* 3.3 16.3 + - - +
91B SER* 2.8 37.6 + - - +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 3.0 20.2 + - - +
85B ALA* 3.1 10.3 + - - +
87B GLU* 1.3 75.4 - - + +
89B ILE* 1.3 65.5 + - - +
91B SER* 3.0 15.9 + - - -
92B THR* 2.9 29.5 + - + +
98B ARG* 3.9 7.6 - - + +
101B ALA* 3.4 44.9 - - + +
102B LEU* 3.8 18.6 - - + -
105B ALA* 4.8 3.1 - - + -
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LYS* 4.1 28.9 - - + -
31B LEU* 4.5 12.8 - - + -
34B ALA* 3.7 27.6 - - + -
85B ALA 3.0 21.9 + - - +
86B ASN* 3.4 9.0 - - - +
88B VAL* 1.3 78.2 - - - +
90B GLU* 1.3 64.6 + - + +
92B THR* 3.3 11.6 - - - +
98B ARG* 3.3 39.1 + - - +
102B LEU* 4.1 10.1 - - + -
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Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 4.4 6.6 - - - +
86B ASN* 3.0 23.2 + - - +
87B GLU* 3.6 24.6 - - - +
88B VAL 3.2 0.4 - - - -
89B ILE* 1.3 80.3 - - + +
91B SER* 1.3 58.3 + - - +
92B THR 3.6 1.3 + - - -
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Residues in contact with SER 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 2.8 32.3 + - - +
88B VAL* 3.0 9.4 + - - -
90B GLU* 1.3 77.3 - - - +
92B THR* 1.3 67.3 + - - +
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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
------------------------------------------------------------
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