Contacts of the strand formed by residues 72 - 76 (chain A) in PDB entry 3VNG
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 72 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A TYR* 3.8 20.4 - - + -
55A ALA 3.5 3.4 - - - +
56A VAL* 3.8 28.5 - - + -
70A SER 3.8 0.8 + - - +
71A ALA* 1.3 74.5 - - - +
73A ASP* 1.3 67.9 + - - +
84A PRO* 4.0 0.2 - - - +
85A CYS* 2.7 40.7 + - + +
86A ALA 3.5 14.9 + - - +
87A PRO* 4.6 1.0 - - + +
104A ILE* 4.5 3.8 - - + -
122A TYR* 3.5 52.5 - - + -
129A TRP* 3.5 21.5 - - + +
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Residues in contact with ASP 73 (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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37A LEU* 5.1 2.4 - - + +
38A GLN* 5.6 9.6 - - - +
39A VAL* 6.1 0.3 - - - +
41A ARG* 2.4 31.5 + - - +
53A LEU 3.8 0.2 - - - +
54A TYR* 3.3 7.7 - - - +
55A ALA 2.9 31.6 + - - +
71A ALA* 3.9 9.7 - - - +
72A LEU* 1.3 76.9 - - - +
74A CYS* 1.3 61.6 + - - +
82A TRP* 3.8 23.2 - - + +
83A SER 3.4 3.7 - - - +
84A PRO* 3.3 27.4 - - - +
85A CYS* 4.3 2.5 - - - +
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Residues in contact with CYS 74 (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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52A LEU* 3.6 44.9 - - - -
53A LEU 3.2 5.4 - - - -
54A TYR* 3.8 13.7 - - + -
73A ASP* 1.3 75.3 - - - +
75A TYR* 1.3 64.4 + - - +
76A ASN* 4.3 0.8 + - - -
81A GLN 3.6 1.2 - - - +
82A TRP* 3.2 6.1 - - - -
83A SER* 2.6 49.9 + - - +
85A CYS* 3.8 19.9 - - - -
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Residues in contact with TYR 75 (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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8A TYR* 3.9 15.7 - + - -
21A LEU* 3.5 30.7 - - + -
34A LEU* 3.4 14.2 - - - +
35A ALA* 4.4 1.6 - - + -
52A LEU* 3.7 3.8 - - - +
53A LEU* 2.7 51.5 + - + +
74A CYS* 1.3 76.4 - - - +
76A ASN* 1.3 58.8 + - - +
77A PRO* 3.5 31.6 + - + +
80A ASN* 2.5 57.3 + - - +
81A GLN 3.3 12.8 - - - -
82A TRP* 3.6 33.8 - + + -
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Residues in contact with ASN 76 (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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51A GLY 5.0 0.2 - - - +
52A LEU* 3.6 20.5 - - + +
74A CYS* 4.3 0.9 + - - -
75A TYR* 1.3 75.4 - - - +
77A PRO* 1.3 57.4 - - - +
78A MET* 2.9 31.8 + - - +
79A THR* 3.1 23.2 + - - +
80A ASN* 2.6 35.7 + - - -
81A GLN* 3.0 13.7 + - + +
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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