Contacts of the strand formed by residues 144 - 152 (chain A) in PDB entry 1VAV
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 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A ALA 3.3 3.6 - - - +
133A LEU* 3.3 2.2 - - - -
134A VAL* 2.7 38.2 + - + +
136A GLU* 4.0 35.6 - - - +
140A ASP* 4.8 4.0 + - - -
142A GLY 5.2 3.8 + - - -
143A THR* 1.3 77.6 - - - +
145A ALA* 1.3 59.9 + - - +
146A TYR* 3.5 32.5 - - + -
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Residues in contact with ALA 145 (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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131A GLN* 4.1 19.5 - - - +
132A ALA 3.4 3.8 - - - -
133A LEU* 3.3 24.2 - - + -
143A THR* 4.2 0.8 + - - -
144A ARG* 1.3 73.3 - - - +
146A TYR* 1.3 66.4 + - - +
147A THR 4.3 0.4 + - - -
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Residues in contact with TYR 146 (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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131A GLN* 3.1 4.3 - - - -
132A ALA* 2.8 45.6 + - + +
134A VAL* 3.6 21.6 - - + +
144A ARG* 3.5 41.5 - - + -
145A ALA* 1.3 79.5 - - - +
147A THR* 1.3 63.4 + - - +
148A LEU* 3.4 8.8 + - + -
179A LEU* 3.4 44.9 - - + -
181A GLN* 5.8 1.9 + - - -
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Residues in contact with THR 147 (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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129A ARG* 3.5 28.0 + - + +
130A VAL 3.8 5.8 - - - +
131A GLN* 3.4 20.5 + - - +
145A ALA 4.3 0.2 - - - -
146A TYR* 1.3 71.5 - - - +
148A LEU* 1.3 64.5 + - - +
149A MET 3.8 23.6 - - - +
150A ASP* 4.8 6.7 - - + +
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Residues in contact with LEU 148 (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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119A LEU* 4.2 3.1 - - + -
130A VAL 3.0 8.6 + - - +
132A ALA* 3.9 10.1 - - + +
146A TYR* 4.1 15.7 - - + +
147A THR* 1.3 78.5 - - - +
149A MET* 1.3 61.7 - - - +
172A VAL* 3.7 31.0 - - + +
173A SER* 3.8 8.7 - - - -
174A VAL* 3.8 30.3 - - + -
177A SER* 2.7 47.4 + - - +
178A ALA 4.2 4.9 - - - -
179A LEU* 4.1 25.8 - - + -
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Residues in contact with MET 149 (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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129A ARG* 3.1 4.5 - - - +
130A VAL 2.8 33.1 + - - +
147A THR* 3.5 5.1 - - - +
148A LEU* 1.3 83.7 - - - +
150A ASP* 1.3 66.1 + - - +
152A ILE* 3.6 22.6 - - + +
174A VAL* 3.7 26.9 - - + +
175A ASN* 3.8 16.4 - - + +
177A SER* 3.6 27.1 - - - -
20B ILE* 5.5 1.1 - - + -
24B GLN* 3.5 36.3 - - - +
27B ARG* 5.6 0.2 - - - -
29B TYR* 3.7 21.5 - - + -
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Residues in contact with ASP 150 (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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124A ARG* 2.8 30.5 + - - -
127A GLN* 4.1 11.4 - - - +
128A GLY 3.5 11.5 - - - +
129A ARG* 3.5 14.5 - - + +
147A THR* 4.8 6.6 - - + +
149A MET* 1.3 77.4 - - - +
151A GLY* 1.3 75.9 + - - +
152A ILE* 3.3 3.1 - - - -
24B GLN* 2.9 24.6 + - - +
27B ARG* 3.0 27.9 + - - +
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Residues in contact with GLY 151 (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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127A GLN* 3.0 28.2 - - - +
128A GLY 3.2 0.2 + - - -
150A ASP* 1.3 91.3 + - - +
152A ILE* 1.3 57.2 + - - +
153A PRO* 3.2 11.1 - - - +
156A GLN* 5.5 0.9 - - - +
21B SER* 5.0 3.5 + - - -
24B GLN* 3.5 12.9 + - - +
27B ARG* 3.2 18.1 - - - +
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Residues in contact with ILE 152 (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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121A TYR* 2.8 17.6 + - + -
128A GLY 2.7 40.1 + - - +
130A VAL* 4.0 26.2 - - + -
149A MET* 3.6 24.0 - - + +
150A ASP 3.8 1.8 - - - +
151A GLY* 1.3 72.0 - - - +
153A PRO* 1.3 62.7 - - - +
156A GLN* 3.6 22.2 - - + +
158A PHE* 3.5 45.8 - - + -
174A VAL* 4.4 0.7 - - + -
175A ASN* 4.5 1.3 - - - +
24B GLN* 3.7 17.5 - - - +
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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