Contacts of the strand formed by residues 76 - 83 (chain B) in PDB entry 1A4Y
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 PHE 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ILE* 3.6 28.5 - - + -
47B HIS 4.3 8.3 - - - -
49B ASN 5.3 0.4 - - - -
52B SER* 3.6 31.2 - - - -
53B ILE* 4.0 12.3 - - + -
56B ILE* 3.8 15.5 - - + -
61B ASN* 3.3 22.9 - - - -
72B SER* 3.6 18.4 - - - -
74B SER* 3.5 19.7 - - - -
75B SER* 1.3 78.8 - - - +
77B GLN* 1.3 61.9 + - - +
78B VAL* 3.4 9.8 + - + +
99B GLY 3.5 0.2 - - - +
100B PHE* 3.2 10.3 - - - -
101B ARG 2.6 34.7 + - - +
103B VAL* 4.1 13.7 - - + -
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Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 2.3 41.6 + - - +
46B ILE* 3.8 0.7 - - - +
47B HIS* 2.8 49.6 + - + +
76B PHE* 1.3 71.3 - - - +
78B VAL* 1.3 61.0 + - - +
99B GLY 3.5 5.4 - - - +
100B PHE* 3.4 31.9 - - + +
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ARG* 2.5 25.0 + - - +
44B THR* 4.0 10.5 - - + -
45B PHE 3.1 13.9 - - - +
46B ILE* 4.0 20.0 - - + -
47B HIS* 3.9 0.7 - - - -
76B PHE* 4.0 16.2 - - + +
77B GLN* 1.3 78.7 - - - +
79B THR* 1.3 58.8 + - - +
80B THR* 5.0 2.2 - - - +
97B THR 5.5 0.7 - - - +
98B ALA* 3.5 0.2 - - - -
99B GLY* 2.9 41.9 + - - +
101B ARG* 4.8 8.5 - - + +
103B VAL* 4.3 10.5 - - + -
120B PHE* 4.2 20.6 - - + -
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Residues in contact with THR 79 (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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21B ARG* 3.2 35.1 - - + +
25B TYR* 3.9 29.1 - - + -
26B CYS* 4.4 3.6 - - - -
43B ASN 3.8 1.6 - - - +
44B THR* 3.4 0.7 - - - -
45B PHE* 2.8 36.2 + - - +
47B HIS* 2.5 29.5 + - - -
78B VAL* 1.3 71.2 - - - +
80B THR* 1.3 64.1 + - - +
81B CYS* 3.9 0.8 + - - -
96B ALA* 4.2 13.5 - - + -
97B THR 3.5 10.3 - - - +
98B ALA* 4.6 0.7 - - - -
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.8 30.7 - - + -
43B ASN 3.5 4.0 - - - +
44B THR* 2.7 30.1 + - - +
78B VAL* 5.0 2.4 - - - +
79B THR* 1.3 74.1 + - - +
81B CYS* 1.3 64.1 + - - +
82B LYS* 3.9 4.1 + - + +
95B ARG 3.6 2.1 - - - +
96B ALA* 3.4 3.1 - - - -
97B THR* 2.8 47.5 + - - -
101B ARG* 5.6 0.2 + - - -
120B PHE* 3.7 24.0 + - - +
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Residues in contact with CYS 81 (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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25B TYR* 4.9 0.7 - - - -
26B CYS* 2.0 57.7 - - + -
29B ILE* 4.5 1.1 - - - -
30B MET* 4.3 10.1 - - - -
41B ASP 4.0 0.5 - - - +
42B ILE* 3.4 4.7 - - - +
43B ASN 2.7 36.0 + - - +
45B PHE* 4.2 26.0 - - - -
79B THR* 4.7 3.8 - - - -
80B THR* 1.3 72.8 - - - +
82B LYS* 1.3 60.8 + - - +
94B TYR* 3.9 15.5 - - + -
95B ARG 3.6 0.9 - - - -
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Residues in contact with LYS 82 (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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320A LYS* 4.6 9.2 - - - +
349A ASN* 3.9 11.5 + - - -
41B ASP* 2.8 45.4 + - - +
42B ILE* 4.3 16.5 - - + +
80B THR* 3.9 5.3 + - + +
81B CYS* 1.3 73.4 - - - +
83B LEU* 1.3 78.6 + - - +
84B HIS* 3.3 1.6 + - + +
94B TYR* 3.3 5.9 - - - -
95B ARG* 2.9 47.3 + - + +
97B THR* 6.1 0.9 - - - +
121B ARG* 4.8 10.9 - - - +
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Residues in contact with LEU 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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320A LYS* 5.0 10.3 + - + -
346A GLN* 6.3 0.4 - - - +
39B CYS* 3.5 35.0 - - + +
40B LYS 4.0 1.8 - - - +
41B ASP* 2.8 39.4 + - + +
82B LYS* 1.3 89.6 - - - +
84B HIS* 1.3 66.9 + - - +
85B GLY* 4.0 3.7 + - - +
87B SER 4.6 14.6 - - - +
88B PRO* 5.0 5.4 - - + -
92B CYS* 4.3 1.8 - - + -
93B GLN 3.1 34.5 - - - +
94B TYR* 3.5 15.3 - - + -
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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
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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