Contacts of the strand formed by residues 57 - 63 (chain B) in PDB entry 1GCZ
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 ALA 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B VAL* 4.2 6.3 - - + -
6B ASN 3.2 10.1 - - - +
7B THR* 4.5 0.4 - - - -
47B MET* 4.0 0.7 - - - -
56B CYS* 1.3 78.3 - - - +
58B LEU* 1.3 69.5 + - - +
59B CYS* 4.0 17.7 - - - -
83B LEU* 4.2 16.6 - - + -
89B ILE* 4.2 10.1 - - + -
93B ARG 3.0 5.6 + - - +
94B VAL* 3.4 9.9 - - + -
95B TYR 3.0 24.1 + - - -
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Residues in contact with LEU 58 (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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6B ASN* 2.9 35.5 + - - +
47B MET* 3.5 22.7 - - + -
48B ALA 5.4 0.4 - - - +
49B PHE* 4.5 4.9 - - + -
57B ALA* 1.3 82.7 - - - +
59B CYS* 1.3 60.4 + - - +
95B TYR* 3.6 22.2 - - + +
551B CIT 3.6 19.5 - - + +
2C MET* 3.9 25.4 - - + -
4C ILE* 4.0 15.0 - - + -
38C ALA* 3.7 29.2 - - + -
39C VAL 4.6 5.6 - - - +
40C HIS* 4.0 11.0 - - + -
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Residues in contact with CYS 59 (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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3B PHE* 3.8 17.7 - - + -
4B ILE 3.0 13.2 - - - +
5B VAL* 3.8 25.4 - - - -
57B ALA* 4.0 12.6 - - - -
58B LEU* 1.3 78.4 - - - +
60B SER* 1.3 63.9 + - - +
83B LEU* 4.1 14.4 - - - -
94B VAL* 4.4 0.9 - - - -
95B TYR 2.8 18.7 + - - +
96B ILE* 3.4 12.3 - - + -
97B ASN* 2.8 25.3 + - - +
551B CIT 3.7 10.2 - - - +
2C MET* 4.8 1.3 - - - +
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Residues in contact with SER 60 (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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550A CIT 4.6 0.2 + - - -
2B MET 3.7 0.8 - - - +
3B PHE* 3.1 9.9 - - - -
4B ILE* 2.9 42.8 + - - +
59B CYS* 1.3 77.2 - - - +
61B LEU* 1.3 60.8 + - - +
62B HIS* 4.0 9.7 - - - -
96B ILE* 4.4 0.9 - - - -
97B ASN 3.1 13.5 - - - +
99B TYR* 3.7 9.9 - - - -
551B CIT 2.9 38.8 + - - -
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Residues in contact with LEU 61 (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 PRO* 4.3 10.3 - - + -
2B MET 3.3 17.0 - - - +
3B PHE* 4.1 17.7 - - + -
26B LEU* 4.7 17.0 - - + -
30B THR* 4.8 6.1 - - + -
60B SER* 1.3 75.6 - - - +
62B HIS* 1.3 77.4 + - - +
63B SER* 4.9 1.8 - - - -
67B ILE* 4.6 6.6 - - + +
75B TYR* 3.6 40.2 - - + -
79B LEU* 4.9 1.3 - - + -
96B ILE* 4.4 2.0 - - + +
97B ASN 2.9 6.9 + - - +
98B TYR* 3.5 25.6 - - + -
99B TYR* 2.9 24.9 + - - +
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Residues in contact with HIS 62 (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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97A ASN* 3.4 17.2 + - - -
99A TYR* 2.9 22.2 + - - -
550A CIT 3.3 22.8 + - + -
1B PRO* 3.3 4.5 - - - +
2B MET* 2.8 44.0 + - + +
4B ILE* 5.4 0.6 - - + +
60B SER* 4.0 14.4 + - - -
61B LEU* 1.3 77.4 - - - +
63B SER* 1.3 62.6 + - - +
99B TYR* 3.5 47.1 - + + -
101B MET* 3.5 17.0 - - + -
551B CIT 5.1 0.9 - - - -
902B YZ9 3.2 20.7 - - + +
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Residues in contact with SER 63 (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 PRO* 4.3 11.8 - - - +
30B THR* 5.1 4.2 - - - +
32B LYS* 3.9 5.9 - - - +
61B LEU* 4.2 5.4 - - - -
62B HIS* 1.3 75.5 - - - +
64B ILE* 1.3 63.0 + - - +
65B GLY 2.8 27.2 + - - +
66B LYS* 3.9 9.3 - - - +
67B ILE* 4.0 14.8 - - - +
75B TYR* 6.0 0.2 - - - -
99B TYR 3.1 9.5 + - - +
100B ASP* 3.5 2.4 - - - -
101B MET* 2.8 24.3 + - - +
902B YZ9 3.3 14.9 + - - -
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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