Contacts of the strand formed by residues 128 - 133 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D ALA* 4.5 2.3 - - - +
95E VAL* 3.7 16.8 - - + -
114E ARG* 2.8 48.6 + - + +
117E ILE* 3.7 36.8 - - + -
118E ALA* 4.1 13.5 - - + -
121E LEU* 4.9 0.7 - - + -
123E CYS* 3.8 24.5 - - - -
124E ASP 3.9 4.5 - - - +
125E ILE 3.2 9.4 + - - +
126E GLU 3.3 1.0 - - - -
127E GLN* 1.3 84.2 - - - +
129E ASN* 1.3 66.0 + - - +
130E VAL* 4.5 0.7 - - + -
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Residues in contact with ASN 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ARG* 6.0 0.2 - - - +
51D GLY* 3.2 30.4 - - - +
54D ALA* 3.2 16.4 - - + +
56D GLY* 2.9 48.0 + - - -
95E VAL 3.0 11.1 + - - +
96E ASP* 2.9 23.7 + - - +
97E ILE* 3.0 23.7 + - - +
114E ARG* 4.5 4.3 - - - +
128E VAL* 1.3 74.6 - - - +
130E VAL* 1.3 73.4 + - - +
131E LYS* 4.0 4.2 - - - +
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Residues in contact with VAL 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D GLY* 4.7 6.9 - - - +
57D ASP* 5.1 0.3 - - - +
60D LYS* 5.5 0.7 + - - -
97E ILE* 3.5 31.0 - - + +
99E ILE* 4.0 19.7 - - + -
110E ILE* 3.4 48.4 - - + +
113E MSE 4.4 12.1 - - + -
114E ARG* 4.2 15.4 - - + +
117E ILE* 4.0 15.7 - - + -
128E VAL* 4.5 1.8 - - + -
129E ASN* 1.3 86.6 + - - +
131E LYS* 1.3 65.7 + - - +
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Residues in contact with LYS 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D HIS 2.9 23.3 + - - +
7D GLY* 5.3 1.1 - - - -
8D PHE 5.6 0.7 - - - +
47D ASP* 3.4 40.4 - - + +
56D GLY 3.7 13.9 - - - +
57D ASP* 3.6 31.6 - - + +
96E ASP* 2.9 27.5 + - - -
97E ILE 2.9 10.0 + - - +
98E THR* 3.1 24.9 + - + +
99E ILE* 2.9 27.5 + - - +
110E ILE* 4.9 2.9 - - - -
129E ASN* 4.1 1.3 - - - +
130E VAL* 1.3 77.5 - - - +
132E ALA* 1.3 64.8 + - - +
133E THR* 5.9 2.5 - - - -
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Residues in contact with ALA 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ASP* 4.2 11.4 + - - +
99E ILE* 3.3 24.7 - - + +
104E PRO 5.9 2.5 - - - +
106E MSE 4.8 19.1 - - + -
107E ARG 6.0 0.4 - - - +
110E ILE* 5.0 6.4 - - + +
131E LYS* 1.3 78.7 - - - +
133E THR* 1.3 61.9 + - - +
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Residues in contact with THR 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PHE* 3.5 39.1 + - + +
9D ASP* 4.0 12.0 + - - -
47D ASP* 5.2 6.1 + - - -
98E THR* 4.1 14.8 - - + -
99E ILE 2.8 14.8 + - - +
100E ILE* 3.5 4.7 - - + -
101E ALA 3.1 25.5 + - - +
131E LYS* 5.8 2.7 - - - -
132E ALA* 1.3 76.4 - - - +
134E THR* 1.3 80.4 + - - +
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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