Contacts of the strand formed by residues 128 - 133 (chain F) in PDB entry 1VHA
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 128 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E ALA* 4.6 2.2 - - - +
95F VAL* 3.6 15.9 - - + -
114F ARG* 2.5 59.4 + - + +
117F ILE* 3.9 41.7 - - + -
118F ALA* 4.4 7.2 - - + -
121F LEU* 4.9 0.9 - - + -
123F CYS* 3.8 24.9 - - - -
124F ASP 4.1 4.0 - - - +
125F ILE 3.5 6.0 + - - +
126F GLU 3.2 1.0 - - - -
127F GLN* 1.3 86.6 - - - +
129F ASN* 1.3 58.5 + - - +
130F VAL* 4.4 3.6 - - + -
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Residues in contact with ASN 129 (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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3E ARG* 6.2 0.2 - - - +
51E GLY* 3.2 29.8 - - - +
54E ALA* 3.3 14.5 - - + -
56E GLY* 3.0 45.9 + - - -
95F VAL 2.9 11.7 + - - +
96F ASP* 2.7 25.2 + - - +
97F ILE* 2.9 24.8 + - - +
114F ARG* 4.1 3.9 + - - +
128F VAL* 1.3 75.5 - - - +
130F VAL* 1.3 71.1 + - - +
131F LYS* 3.3 5.9 - - - +
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Residues in contact with VAL 130 (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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56E GLY* 4.9 6.1 - - - +
57E ASP* 4.9 2.3 - - - +
60E LYS* 5.9 1.7 - - - -
41F ALA* 6.2 0.4 - - + -
97F ILE* 3.5 16.8 - - + -
99F ILE* 3.8 21.8 - - + -
110F ILE* 3.4 49.1 - - + +
113F MSE 4.2 8.5 - - + -
114F ARG* 3.8 22.5 - - + +
117F ILE* 4.0 24.2 - - + -
128F VAL* 4.4 2.2 - - + -
129F ASN* 1.3 85.4 + - - +
131F LYS* 1.3 64.8 + - - +
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Residues in contact with LYS 131 (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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6E HIS 3.1 24.2 - - - +
7E GLY* 5.0 1.1 - - - -
8E PHE 5.5 0.2 - - - +
47E ASP* 3.3 36.7 + - + +
56E GLY 2.9 28.6 + - - +
57E ASP* 3.8 20.1 - - + +
96F ASP* 3.5 16.6 + - - -
97F ILE 2.7 15.5 + - - +
98F THR* 3.1 29.7 - - + +
99F ILE* 2.8 30.3 + - - +
110F ILE* 5.0 1.3 - - - -
129F ASN* 3.3 7.7 - - - +
130F VAL* 1.3 77.2 - - - +
132F ALA* 1.3 61.6 - - - +
133F THR* 6.1 0.7 - - + -
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Residues in contact with ALA 132 (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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57E ASP* 4.2 9.1 + - - +
99F ILE* 3.5 15.5 - - + +
106F MSE 4.9 15.0 - - + -
107F ARG* 3.1 35.3 + - - +
110F ILE* 4.6 15.1 - - + +
131F LYS* 1.3 78.0 - - - +
133F THR* 1.3 64.5 + - - +
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Residues in contact with THR 133 (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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8E PHE* 3.8 37.1 + - + +
9E ASP* 4.8 8.0 + - - -
47E ASP* 5.5 4.9 + - - -
98F THR* 4.0 16.4 - - + -
99F ILE 2.9 14.8 + - - +
100F ILE* 3.5 4.0 - - + -
101F ALA 3.1 26.2 + - - +
131F LYS* 6.3 0.4 - - - -
132F ALA* 1.3 77.8 - - - +
134F THR* 1.3 80.1 + - - +
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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