Contacts of the strand formed by residues 117 - 124 (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 VAL 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLN* 3.3 7.4 - - - +
103B ILE* 3.1 36.3 + - + +
115B PRO* 4.2 1.0 - - - +
116B LEU* 1.3 93.8 - - + +
118B LYS* 1.3 77.0 + - - +
119B LEU* 4.7 4.7 - - + +
132B ALA* 4.2 8.7 - - + -
133B LEU 3.3 9.9 - - - +
134B VAL* 3.9 12.3 - - + -
162B ILE* 5.3 3.6 - - + -
170B LEU* 3.5 39.5 - - + -
172B VAL* 4.0 19.7 - - + -
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Residues in contact with LYS 118 (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* 4.1 24.6 - - + +
101B GLY 3.8 4.5 - - - -
102B GLN* 3.7 14.8 - - - +
115B PRO* 3.6 32.9 - - + +
117B VAL* 1.3 76.7 - - - +
119B LEU* 1.3 62.4 + - - +
120B LEU 3.5 2.6 + - - -
131B GLN 3.6 0.2 - - - +
132B ALA* 3.7 0.5 - - - -
133B LEU* 2.9 64.5 + - + +
135B ARG* 5.3 4.5 - - - +
143B THR* 5.1 12.8 + - - +
199B TYR* 5.9 4.5 - - + -
201B GLN* 5.1 10.1 - - - +
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Residues in contact with LEU 119 (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* 3.3 6.5 - - - +
100B ILE* 2.9 34.0 + - + -
101B GLY 2.8 22.9 + - - +
117B VAL* 4.2 4.2 - - + -
118B LYS* 1.3 71.4 - - - +
120B LEU* 1.3 59.0 + - - +
130B VAL* 4.3 12.3 - - + -
131B GLN 3.6 3.1 - - - +
132B ALA* 4.3 22.0 - - + -
148B LEU* 4.5 12.1 - - + -
160B TYR* 3.2 59.2 - - + -
162B ILE* 3.7 26.0 - - + +
172B VAL* 4.8 0.2 - - + -
173B SER 5.6 0.2 - - - +
174B VAL* 5.1 1.1 - - + -
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Residues in contact with LEU 120 (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* 4.0 37.7 - - + +
98B MET 3.1 42.0 - - - +
99B ILE* 3.6 15.9 - - + -
100B ILE* 5.1 0.7 - - - -
118B LYS 3.5 3.3 + - - +
119B LEU* 1.3 73.9 - - - +
121B TYR* 1.3 65.3 + - - +
122B GLN* 4.0 1.5 + - + +
129B ARG 3.7 0.5 - - - +
130B VAL* 3.2 7.8 - - - +
131B GLN* 2.8 63.3 + - - +
133B LEU* 4.3 22.7 - - + -
201B GLN* 4.8 3.8 - - + -
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Residues in contact with TYR 121 (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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89B ILE* 3.7 42.8 - - + -
92B VAL* 4.0 16.8 - - + -
97B ARG* 3.5 4.0 - - - -
98B MET* 2.8 38.4 + - + +
100B ILE* 4.2 22.8 - - + +
119B LEU 4.3 0.4 + - - -
120B LEU* 1.3 74.5 - - - +
122B GLN* 1.3 61.8 + - - +
123B LEU* 3.6 24.3 - - + +
128B GLY* 4.1 9.6 - - - -
129B ARG 3.4 9.9 - - - -
130B VAL* 3.9 12.8 - - + +
152B ILE* 2.8 44.0 + - + -
153B PRO 3.8 9.6 - - - -
154B LEU* 3.9 5.5 + - + +
158B PHE* 4.5 3.8 - + - -
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Residues in contact with GLN 122 (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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95B THR 5.1 2.4 + - - -
96B ARG* 3.1 13.0 - - + +
97B ARG* 2.7 45.2 + - + +
120B LEU* 4.0 2.2 + - + -
121B TYR* 1.3 77.9 - - - +
123B LEU* 1.3 63.7 + - - +
124B ARG* 3.9 22.3 + - + +
127B GLN 3.7 1.7 - - - +
128B GLY* 3.4 1.4 - - - -
129B ARG* 2.9 56.0 + - + +
131B GLN* 3.3 23.3 + - - +
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Residues in contact with LEU 123 (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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92B VAL* 4.0 18.2 - - + -
96B ARG* 3.0 69.1 + - - +
121B TYR* 3.6 29.1 - - + +
122B GLN* 1.3 72.2 - - - +
124B ARG* 1.3 60.2 + - - +
125B LEU 3.1 14.6 - - - +
126B ASP* 3.7 23.3 - - - +
127B GLN 3.6 0.7 - - - -
128B GLY 3.8 7.9 - - - +
152B ILE 4.6 0.9 - - - +
154B LEU* 4.0 28.0 - - + +
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Residues in contact with ARG 124 (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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122B GLN* 4.3 27.1 - - + +
123B LEU* 1.3 71.0 - - - +
125B LEU* 1.3 69.0 + - + +
127B GLN* 2.8 49.7 + - + +
129B ARG* 2.8 50.1 - - - +
150B ASP* 3.5 16.8 + - - -
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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
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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