Contacts of the strand formed by residues 80 - 85 (chain B) in PDB entry 3OQU
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 LEU 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B PHE* 4.0 2.2 - - - -
70B THR 4.1 0.7 - - - +
71B VAL* 3.7 23.0 - - - +
72B ILE 4.7 1.4 + - - -
78B GLY 4.2 4.3 - - - +
79B SER* 1.3 74.1 - - - +
81B ARG* 1.3 58.4 + - - +
95B THR* 4.3 18.6 - - + -
96B GLU 3.3 4.7 - - - +
97B ARG* 3.5 32.3 - - + +
113B ILE* 3.6 25.4 - - + -
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG 4.6 1.0 + - - -
56B PHE* 2.8 66.9 + - + +
59B PRO* 3.7 22.1 - - - +
63B LYS* 3.4 22.0 - - - +
69B CYS* 4.0 13.9 - - - -
70B THR 3.5 3.6 - - - -
71B VAL* 3.4 21.1 - - + -
80B LEU* 1.3 74.3 - - - +
82B GLU* 1.3 60.9 + - - +
83B VAL* 4.0 9.5 - - + +
94B SER 3.7 0.7 - - - +
95B THR* 3.4 5.8 - - - +
96B GLU* 2.8 65.5 + - + +
108B LEU* 6.0 0.6 - - - +
110B ILE* 3.8 24.4 - - - +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ARG 3.9 0.7 - - - +
69B CYS* 3.4 2.5 - - - -
70B THR* 3.0 47.9 + - + +
81B ARG* 1.3 71.5 - - - +
83B VAL* 1.3 62.0 + - - +
84B ASN* 4.1 7.8 + - - +
93B THR* 3.8 28.9 + - - +
94B SER 3.5 2.9 - - - +
95B THR* 3.1 28.4 + - + +
115B GLY* 5.8 0.7 - - - -
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PRO* 5.2 2.9 - - + -
66B VAL* 3.9 29.8 - - + -
68B ARG 3.3 8.1 - - - +
69B CYS* 4.7 4.7 - - + -
81B ARG* 4.0 18.4 - - + +
82B GLU* 1.3 75.4 - - - +
84B ASN* 1.3 62.5 + - - +
85B VAL* 4.0 15.8 + - + +
93B THR* 3.2 5.1 - - - -
94B SER* 2.9 46.8 + - - +
96B GLU* 3.7 32.5 - - - +
191B A8S 5.0 2.5 - - - +
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Residues in contact with ASN 84 (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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66B VAL* 3.5 4.9 - - - +
67B SER* 2.8 36.2 + - - +
68B ARG* 2.9 43.6 + - + +
70B THR* 5.1 5.1 - - - +
82B GLU* 4.7 9.9 + - - +
83B VAL* 1.3 74.2 - - - +
85B VAL* 1.3 63.8 + - - +
92B THR 3.3 5.3 - - - +
93B THR* 3.1 24.9 - - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE 3.1 15.3 - - - +
66B VAL* 4.6 1.3 - - + -
67B SER* 4.1 6.5 + - - -
83B VAL* 4.1 13.2 - - + +
84B ASN* 1.3 79.5 - - - +
86B LYS* 1.3 69.5 + - - +
89B LEU* 4.2 11.4 - - + -
91B ALA* 3.3 42.8 - - + +
92B THR* 3.0 17.9 + - - +
191B A8S 3.7 37.9 - - + +
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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