Contacts of the strand formed by residues 76 - 80 (chain A) in PDB entry 2VSH
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 ILE 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.7 28.9 - - + -
41A VAL* 4.6 0.7 - - + -
49A ILE* 3.3 16.8 - - + +
51A VAL* 4.0 10.3 - - + -
65A VAL* 4.0 27.4 - - + -
69A LEU* 4.1 9.4 - - + -
72A TYR* 3.4 30.7 - - + +
73A LYS 3.1 17.1 + - - +
74A GLU 3.3 2.0 - - - +
75A ARG* 1.3 84.7 - - + +
77A ILE* 1.3 66.4 + - - +
78A ILE* 3.9 26.9 + - + -
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LYS* 4.1 34.8 - - + -
49A ILE 2.9 10.9 + - - +
50A VAL* 3.3 23.4 - - + +
51A VAL* 2.7 31.7 + - - +
74A GLU 5.6 0.9 - - - +
75A ARG 4.2 0.2 + - - -
76A ILE* 1.3 76.2 - - - +
78A ILE* 1.3 69.8 + - - +
79A THR* 4.7 1.3 - - - -
95A ALA* 4.6 16.6 - - + +
99A TYR* 4.1 24.7 - - + -
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 5.7 1.1 - - + -
37A ILE* 5.2 2.2 - - + -
51A VAL* 3.6 33.0 - - + +
53A VAL* 4.3 5.4 - - + -
58A VAL* 3.8 38.9 - - + +
61A ALA* 3.9 20.9 - - + -
62A GLU* 3.7 38.5 + - + +
65A VAL* 4.2 11.7 - - + -
76A ILE* 3.9 14.9 + - + +
77A ILE* 1.3 77.2 - - - +
79A THR* 1.3 63.4 + - - +
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Residues in contact with THR 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A VAL* 4.1 12.6 - - + -
51A VAL 2.8 15.2 + - - +
52A GLY* 3.4 7.1 - - - -
53A VAL* 2.9 26.7 + - - +
58A VAL* 4.1 7.9 - - - +
77A ILE* 4.7 3.6 - - - -
78A ILE* 1.3 75.8 - - - +
80A LYS* 1.3 73.5 + - - +
91A ASN 4.2 11.3 + - - +
92A ILE* 4.4 4.9 - - + -
95A ALA* 3.9 30.1 - - + +
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A VAL 3.4 4.3 - - - -
55A GLY* 3.7 17.0 - - - +
58A VAL* 4.1 7.8 - - + +
79A THR* 1.3 78.5 + - - +
81A GLY* 1.3 70.2 + - - +
91A ASN* 2.8 29.6 + - - +
1235A PEG 3.1 62.1 + - - +
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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