Contacts of the strand formed by residues 82 - 87 (chain B) in PDB entry 3C3P
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 ARG 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLN 2.9 8.0 + - - +
58B LEU* 3.5 15.8 - - + +
59B VAL* 2.9 26.9 + - - +
77B ILE* 3.7 6.5 - - - +
79B ILE* 2.9 24.2 + - - +
80B SER 4.6 1.6 + - - +
81B SER* 1.3 103.8 + - - +
83B VAL* 1.3 63.8 + - - +
84B VAL* 4.1 5.6 - - + -
107B ASP 3.5 22.8 + - - -
108B ARG* 3.3 20.5 - - - +
109B VAL* 4.4 2.5 - - - +
110B GLU* 5.2 8.5 - - - +
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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
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59B VAL* 3.3 12.1 - - + +
61B VAL* 3.9 26.9 - - + -
70B SER* 4.1 21.1 - - - +
73B PHE* 3.9 11.4 - - + -
74B ALA* 3.9 24.9 - - + +
77B ILE* 3.7 20.4 - - + -
82B ARG* 1.3 74.7 - - - +
84B VAL* 1.3 67.0 + - - +
85B MSE 4.6 0.2 - - - +
108B ARG 2.9 11.0 + - - +
109B VAL* 3.3 11.3 - - + +
110B GLU 2.8 26.9 + - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.8 22.2 - - + -
59B VAL 2.7 13.3 + - - +
60B VAL* 3.5 10.3 - - + +
61B VAL 2.8 27.9 + - - +
82B ARG* 4.8 5.4 - - + -
83B VAL* 1.3 77.6 - - - +
85B MSE 1.3 60.8 + - - +
86B ILE* 4.0 21.7 - - + +
110B GLU* 3.4 35.7 - - + +
112B GLN* 4.6 3.8 - - - +
119B ILE* 5.9 0.2 - - + -
123B GLN* 4.0 27.8 - - + +
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Residues in contact with MSE 85 (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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61B VAL* 3.5 10.8 - - + +
64B ASP* 3.8 19.3 - - + +
67B GLY* 3.8 17.0 - - - -
70B SER* 3.3 25.6 - - - +
83B VAL* 3.9 2.8 - - + -
84B VAL* 1.3 74.7 - - - +
86B ILE* 1.3 78.7 + - - +
87B ASP* 3.9 11.7 - - - -
92B ASN 4.3 5.8 - - - +
93B VAL* 4.2 11.4 - - + -
96B ALA* 3.5 31.4 - - + -
110B GLU 2.7 10.2 + - - +
111B LEU* 3.3 27.3 - - + -
112B GLN* 2.9 25.5 + - - +
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Residues in contact with ILE 86 (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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60B VAL* 4.5 2.2 - - + -
61B VAL 3.1 10.0 + - - +
62B PRO* 3.7 1.1 - - + -
63B GLY* 2.6 34.8 + - - -
84B VAL* 4.0 22.7 - - + +
85B MSE 1.3 81.8 - - - +
87B ASP* 1.3 61.1 + - - +
112B GLN* 3.3 19.3 - - + +
114B GLY 3.7 18.2 - - - +
115B ASP 3.8 16.2 - - - +
116B PRO* 3.9 8.4 - - + +
119B ILE* 3.6 32.1 - - + -
120B ALA* 4.0 32.5 - - + +
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Residues in contact with ASP 87 (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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63B GLY* 3.5 4.9 - - - -
64B ASP 2.8 25.5 + - - +
65B GLY 4.3 0.3 + - - -
85B MSE 3.9 8.0 - - - -
86B ILE* 1.3 75.0 - - - +
88B PRO* 1.3 74.5 - - - +
89B ASP* 3.0 22.7 + - - +
92B ASN* 3.0 35.6 + - + +
93B VAL* 3.8 18.4 - - + +
112B GLN 3.1 6.3 + - - +
113B VAL* 3.3 8.8 - - - +
114B GLY 3.0 18.8 + - - -
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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