Contacts of the strand formed by residues 68 - 73 (chain B) in PDB entry 4OD2
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 VAL 68 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL* 4.5 2.9 - - + -
60B TYR* 3.7 23.0 - - + -
64B VAL* 3.5 39.3 - - + +
66B GLY* 4.2 7.3 + - - +
67B ARG* 1.3 87.8 + - + +
69B THR* 1.3 67.2 + - - +
81B LEU* 3.8 16.8 - - + -
82B GLN 3.2 10.3 - - - +
83B MET* 3.5 41.5 - - + +
84B ASN* 4.9 0.4 - - - +
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR* 3.3 12.6 - - - +
66B GLY 5.5 0.5 + - - -
67B ARG 5.1 0.2 + - - -
68B VAL* 1.3 78.8 + - - +
70B ILE* 1.3 74.1 + - - +
71B SER* 5.5 2.7 - - - -
80B TYR 4.5 0.2 - - - -
81B LEU* 3.2 9.7 - - - +
82B GLN* 2.8 43.7 + - + -
84B ASN* 4.9 7.0 + - - -
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B SER* 4.8 2.0 - - - -
36B TRP* 3.2 30.3 - - + +
49B SER* 3.5 44.9 - - - +
50B GLY 3.9 11.4 - - - +
51B ILE* 4.0 6.9 - - + +
58B THR* 3.5 29.1 - - + +
60B TYR* 2.5 26.7 + - + +
69B THR* 1.3 80.1 - - - +
71B SER* 1.3 65.4 + - - +
79B LEU* 3.9 13.2 - - + -
80B TYR 3.2 17.7 - - - +
81B LEU* 4.3 2.0 - - + -
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Residues in contact with SER 71 (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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51B ILE* 3.8 8.1 - - - -
69B THR* 5.5 2.9 - - - -
70B ILE* 1.3 80.0 - - - +
72B ARG* 1.3 59.5 + - - +
79B LEU* 3.5 3.9 - - - +
80B TYR* 2.6 60.4 + - - +
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 2.6 57.3 + - + -
30B ASP* 3.9 1.6 - - - +
32B TYR 2.8 21.5 + - - -
34B MET* 3.2 24.4 - - - +
51B ILE* 3.8 16.4 - - + +
52B ASN 3.2 20.6 + - - -
53B TRP 2.9 20.5 + - - -
54B GLN 4.6 1.7 - - - +
55B GLY* 4.3 6.7 - - - +
71B SER* 1.3 75.1 - - - +
73B ASP* 1.3 59.9 + - - +
74B ASN* 2.6 25.2 + - - +
78B SER 3.3 13.7 - - - +
79B LEU* 4.2 10.8 - - + -
80B TYR* 4.7 2.5 - - - -
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Residues in contact with ASP 73 (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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72B ARG* 1.3 71.8 - - - +
74B ASN* 1.3 52.9 + - - +
75B ALA* 2.9 31.0 - - - +
76B LYS* 2.7 56.0 + - + +
77B ASN 3.3 7.1 + - - -
78B SER* 2.9 15.3 + - - +
80B TYR* 3.7 25.9 + - + +
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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