Contacts of the strand formed by residues 132 - 135 (chain A) in PDB entry 3V4P
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 CYS 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 4.0 10.8 - - + -
110A THR 3.3 4.9 - - - +
111A CYS* 2.0 46.2 - - - +
131A GLY* 1.3 75.3 - - - -
133A TYR* 1.3 66.6 + - - +
146A ARG* 3.4 13.1 - - - +
147A ILE* 2.9 39.8 + - + +
167A ALA* 4.6 0.9 - - - -
168A GLY* 3.8 10.1 - - - -
180A MET* 3.7 28.9 - - - -
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A TRP* 6.0 1.4 - - - -
73A LEU* 3.8 45.5 + - + -
74A GLY* 4.3 20.1 - - - -
87A GLU* 5.0 6.9 + - - -
89A ARG* 5.9 1.6 - - - -
92A GLN* 5.3 7.7 + - - -
94A LEU* 3.9 31.4 - - + -
108A ILE 3.7 0.2 - - - +
109A VAL* 3.2 9.0 - - - -
110A THR* 2.8 32.9 + - - +
115A TRP* 5.8 1.0 + - - -
131A GLY 5.4 0.2 - - - -
132A CYS* 1.3 77.8 - - - +
134A GLY* 1.3 61.4 + - - +
135A VAL* 4.1 1.8 + - + +
144A SER* 4.4 8.7 - - - -
145A LYS 3.4 6.3 - - - -
146A ARG* 3.4 53.6 + - + -
147A ILE* 4.4 0.9 - - - -
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Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 6.3 0.2 - - - -
108A ILE 3.4 7.0 - - - -
109A VAL* 4.6 2.0 - - - -
133A TYR* 1.3 72.8 - - - +
135A VAL* 1.3 60.2 + - - -
136A PRO* 4.3 0.4 - - - +
144A SER* 3.2 8.7 - - - -
145A LYS* 2.8 39.4 + - - -
147A ILE* 4.0 13.2 - - - +
173A TYR* 6.1 0.9 - - - -
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 5.6 4.5 - - + -
73A LEU* 3.7 31.4 - - + -
107A SER* 3.6 6.7 - - - -
108A ILE* 2.8 48.3 + - + +
110A THR* 5.4 3.4 - - + -
133A TYR 4.4 7.0 - - - +
134A GLY* 1.3 79.3 - - - +
136A PRO* 1.3 84.0 - - + +
139A LEU* 4.1 26.9 - - + -
140A ARG 4.8 0.9 - - - +
141A THR* 4.7 10.1 - - + -
144A SER* 4.3 1.8 - - - -
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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
------------------------------------------------------------
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