Contacts of the strand formed by residues 121 - 126 (chain F) in PDB entry 2VLR
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 LYS 121 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117F ALA* 3.3 5.4 - - - -
118F TYR 3.1 34.2 + - - +
119F ASP* 3.5 6.7 - - - -
120F GLY* 1.3 75.6 - - - +
122F ASP* 1.3 71.5 + - - +
123F TYR* 3.3 0.7 + - - +
0G MET 3.4 31.7 + - - +
1G ILE* 4.2 28.7 - - + +
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Residues in contact with ASP 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F TYR 4.0 4.7 - - - -
120F GLY 4.3 0.8 + - - -
121F LYS* 1.3 78.0 - - - +
123F TYR* 1.3 60.1 + - - +
136F ALA* 3.4 23.4 - - + +
137F ASP* 5.7 0.5 - - - +
60G TRP* 2.7 39.2 + - - +
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Residues in contact with TYR 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F LEU* 3.6 20.5 - - + +
84F TYR* 3.4 16.1 - - - -
85F TYR* 3.6 27.1 - + - -
116F TYR* 2.8 26.3 + - + +
117F ALA 4.3 0.7 - - - -
118F TYR* 4.2 23.6 - - + +
121F LYS 3.3 0.6 + - - +
122F ASP* 1.3 73.3 - - - +
124F ILE* 1.3 70.2 + - + +
134F THR 4.6 0.4 - - - -
136F ALA* 3.1 27.0 + - - +
137F ASP* 4.8 1.8 - - - -
139F ALA 3.3 12.3 + - - -
140F ALA* 3.1 35.2 - - + +
143F THR* 2.9 29.9 + - - -
9H LEU* 3.9 23.7 - - + +
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Residues in contact with ILE 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F HIS 4.5 0.4 - - - +
115F GLN* 3.4 2.3 - - - +
116F TYR* 2.8 44.8 + - + +
122F ASP* 5.6 0.2 - - - +
123F TYR* 1.3 98.7 - - + +
125F ALA* 1.3 62.0 + - - +
133F TRP* 4.1 18.1 - - + -
134F THR 3.4 16.6 - - - +
135F ALA* 4.3 2.5 - - - -
140F ALA* 4.0 7.9 - - + +
143F THR* 3.9 20.4 - - + -
144F LYS* 4.0 26.2 - - + +
147F TRP* 3.8 32.1 - - + -
9H LEU* 4.5 0.4 - - + -
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Residues in contact with ALA 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F HIS 3.8 4.9 - - - -
115F GLN* 3.7 24.0 - - + +
124F ILE* 1.3 75.1 - - - +
126F LEU* 1.3 65.7 + - - +
127F LYS* 3.5 0.7 + - + -
133F TRP* 3.5 9.1 - - - -
134F THR* 3.0 42.3 + - - +
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Residues in contact with LEU 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F TYR* 5.3 3.0 - - - -
114F HIS* 3.0 35.1 + - + +
115F GLN* 4.8 6.6 + - - -
125F ALA* 1.3 77.6 - - - +
127F LYS* 1.3 68.2 + - - +
130F LEU* 3.6 43.4 - - + +
132F SER 3.7 15.0 - - - +
133F TRP* 3.5 21.9 - - + -
153F ALA* 4.0 26.9 - - + +
156F LEU* 4.7 12.6 - - + -
157F ARG 5.4 0.2 - - - +
160F LEU* 4.0 16.6 - - + -
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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