Contacts of the strand formed by residues 84 - 88 (chain A) in PDB entry 1V72
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 GLY 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A THR* 3.4 17.7 - - - -
81A PRO* 2.9 14.3 + - - +
82A PRO 3.2 0.2 - - - -
83A TRP* 1.3 81.0 - - - +
85A ASN* 1.3 65.0 + - - -
109A ALA* 3.6 3.8 - - - +
110A LYS* 3.0 24.8 + - - +
140A THR* 4.6 0.5 - - - +
141A GLN* 3.2 10.3 - - - -
143A ALA* 4.0 5.2 - - - -
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Residues in contact with ASN 85 (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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84A GLY* 1.3 75.5 + - - -
86A ILE* 1.3 63.1 + - - +
87A TYR* 3.3 24.6 + - + +
110A LYS* 3.2 14.3 + - - +
112A MET* 3.5 30.5 - - + +
140A THR* 2.7 50.1 + - - +
141A GLN 2.6 18.3 + - - +
142A PRO* 3.7 0.5 - - - +
143A ALA* 3.1 22.0 + - - +
144A CYS 3.1 11.4 + - - +
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Residues in contact with ILE 86 (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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76A LEU* 4.0 42.6 - - + -
80A THR* 4.0 17.7 - - + -
85A ASN* 1.3 74.0 - - - +
87A TYR* 1.3 65.7 + - - +
88A CYS* 3.7 1.0 + - - -
94A ILE* 4.1 21.8 - - + -
102A PRO* 4.6 6.1 - - + -
106A SER* 4.9 3.8 - - - +
109A ALA* 4.1 15.3 - - + -
110A LYS 2.9 11.0 + - - +
111A LEU* 3.3 24.0 - - + +
112A MET 2.9 22.6 + - - -
144A CYS* 3.5 21.8 - - - +
146A SER* 4.6 2.0 - - - -
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Residues in contact with TYR 87 (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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85A ASN* 3.3 25.6 + - + -
86A ILE* 1.3 69.4 - - - +
88A CYS* 1.3 63.5 + - - +
112A MET* 3.2 34.3 - - + +
114A VAL* 4.1 7.2 - - + -
121A LEU* 4.7 0.7 - - - -
126A LEU* 4.0 16.8 - - + -
129A ARG* 3.5 39.6 + - + -
130A THR* 4.0 17.3 - - + -
132A GLU* 5.1 1.6 + - - +
142A PRO* 3.1 48.1 - - + +
143A ALA 4.2 0.9 - - - -
144A CYS 3.0 20.9 + - - +
145A VAL* 3.5 8.6 - - + +
146A SER* 2.8 30.5 + - - +
174A LEU* 4.8 1.1 - - + -
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Residues in contact with CYS 88 (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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86A ILE 4.0 9.6 - - - -
87A TYR* 1.3 76.3 - - - +
89A HIS* 1.3 64.2 + - - +
92A SER* 3.6 22.4 - - - +
94A ILE* 3.7 26.0 - - + -
95A ASN* 4.2 4.7 - - - -
111A LEU* 4.1 19.5 - - - -
112A MET 3.1 8.8 + - - -
113A THR* 3.0 13.3 - - - -
114A VAL 2.8 23.8 + - - +
121A LEU* 4.2 8.0 - - - +
146A SER 3.8 12.6 - - - +
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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