Contacts of the strand formed by residues 127 - 134 (chain B) 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 GLN 127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B GLN 3.7 1.2 - - - +
123B LEU* 3.6 2.0 - - - -
124B ARG* 2.8 54.4 + - + +
125B LEU 3.3 0.2 - - - -
126B ASP* 1.3 78.1 + - - +
128B GLY* 1.3 58.7 + - - +
129B ARG 4.0 0.2 + - - -
150B ASP* 2.5 32.3 - - - +
151B GLY* 2.8 30.0 + - - -
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B TYR* 3.8 9.6 - - - -
122B GLN 3.4 7.2 - - - -
123B LEU* 3.8 3.1 - - - +
126B ASP 3.6 4.0 + - - -
127B GLN* 1.3 72.5 - - - +
129B ARG* 1.3 61.2 + - - -
150B ASP* 3.4 1.4 - - - +
151B GLY 2.9 12.2 + - - -
152B ILE* 2.8 53.1 + - - +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU 3.7 0.5 - - - +
121B TYR* 3.4 5.9 - - - -
122B GLN* 2.9 50.9 + - + +
124B ARG* 2.8 49.8 - - - +
128B GLY* 1.3 72.3 - - - -
130B VAL* 1.3 65.5 + - - +
131B GLN* 3.7 27.7 + - + +
147B THR* 2.7 32.6 + - + +
149B MET 3.3 7.0 - - - +
150B ASP* 3.2 34.5 + - - +
152B ILE* 5.2 0.4 - - - -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE* 4.6 6.1 - - + -
119B LEU* 4.3 15.0 - - + -
120B LEU 3.2 11.2 - - - +
121B TYR* 3.9 20.6 - - + -
129B ARG* 1.3 78.1 - - - +
131B GLN* 1.3 69.7 + - - +
147B THR* 3.8 1.7 - - - -
148B LEU* 2.9 25.4 + - + +
149B MET 2.9 14.8 + - - +
152B ILE* 5.0 6.5 - - + -
158B PHE* 4.1 21.5 - - + -
174B VAL* 3.5 34.1 - - + -
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Residues in contact with GLN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 5.0 5.4 + - - +
118B LYS 3.6 1.0 - - - +
119B LEU* 3.6 3.8 - - - -
120B LEU* 2.8 51.7 + - + +
122B GLN* 3.3 28.3 + - - +
129B ARG* 3.7 23.4 + - + +
130B VAL* 1.3 80.9 - - - +
132B ALA* 1.3 60.3 + - - +
133B LEU* 3.9 12.0 - - + +
145B ALA* 3.6 20.6 - - - +
146B TYR 3.0 10.3 - - - +
147B THR* 3.7 22.1 + - - +
148B LEU* 5.0 1.1 - - - -
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B VAL* 4.2 12.6 - - + -
118B LYS 3.7 4.5 - - - -
119B LEU* 4.3 5.8 - - + -
131B GLN* 1.3 74.0 - - - +
133B LEU* 1.3 61.5 + - - +
134B VAL* 3.4 6.8 + - + -
144B ARG 3.3 5.0 - - - +
146B TYR* 2.7 35.3 + - - +
148B LEU* 3.9 13.2 - - + +
172B VAL* 3.9 27.1 - - + -
179B LEU* 4.7 4.3 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ILE* 5.2 2.5 - - + -
115B PRO 5.4 0.5 - - - +
116B LEU 3.8 0.5 - - - +
117B VAL* 3.3 4.7 - - - -
118B LYS* 2.9 67.6 + - + +
120B LEU* 4.3 27.4 - - + -
131B GLN* 4.4 11.7 - - + +
132B ALA* 1.3 70.5 - - - +
134B VAL* 1.3 62.0 + - - +
135B ARG 4.0 0.2 + - - -
143B THR* 3.7 20.0 - - - +
144B ARG 3.6 2.7 - - - -
145B ALA* 3.3 34.1 - - + +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.5 10.8 - - + +
117B VAL* 3.9 19.5 - - + -
132B ALA* 4.1 13.5 - - + +
133B LEU* 1.3 74.2 - - - +
135B ARG* 1.3 71.3 + - - +
136B GLU 3.7 2.1 + - - +
143B THR* 3.1 4.0 - - - -
144B ARG* 2.8 42.1 + - + +
146B TYR* 4.3 17.7 - - + -
170B LEU* 4.1 19.7 - - + -
172B VAL* 5.2 0.9 - - + -
179B LEU* 4.5 8.3 - - + -
181B GLN* 4.0 24.2 - - - +
183B LEU* 5.6 0.4 - - + -
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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