Contacts of the strand formed by residues 125 - 134 (chain A) in PDB entry 1VH7
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 125 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A VAL* 4.0 3.1 - - + +
102A ILE* 4.2 22.2 - - + -
113A ILE* 4.1 24.5 - - + +
116A ILE* 3.7 28.0 - - + -
117A ALA* 3.8 21.3 - - + +
121A GLY 3.9 10.5 - - - +
122A SER 2.9 8.4 + - - +
123A GLN 3.3 1.3 - - - -
124A ALA* 1.3 79.8 - - - +
126A VAL* 1.3 62.5 - - - +
127A VAL* 3.9 8.6 + - + -
165A ALA* 4.3 3.1 - - - -
166A GLY* 2.9 30.5 + - - +
167A GLU 3.3 6.4 + - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A THR* 4.2 9.4 - - + +
99A LYS* 3.8 23.3 - - + -
100A VAL 2.9 16.3 + - - +
101A SER* 3.2 15.0 - - - +
102A ILE* 3.0 26.9 + - - +
125A VAL* 1.3 73.2 - - - +
127A VAL* 1.3 63.5 + - - +
167A GLU* 3.4 36.6 - - + +
169A LEU* 3.8 33.0 - - + +
199A ILE* 4.6 7.2 - - + -
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Residues in contact with VAL 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.5 14.8 - - + +
103A ASN* 5.2 0.7 - - - +
106A ALA* 4.5 9.6 - - + -
113A ILE* 3.8 24.2 - - + -
125A VAL* 4.2 3.4 - - + -
126A VAL* 1.3 75.4 - - - +
128A ALA* 1.3 70.3 + - - +
129A ILE* 3.6 10.1 + - + -
156A TRP* 4.3 5.2 - - - +
160A VAL* 3.9 31.2 - - + -
165A ALA* 3.7 22.7 - - + -
167A GLU 2.9 11.4 + - - +
168A ILE* 3.4 7.5 - - + +
169A LEU 2.9 22.5 + - - -
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A SER* 3.5 20.4 - - - +
102A ILE 2.9 10.5 + - - +
103A ASN* 3.1 39.4 + - + +
126A VAL 3.7 1.8 + - - -
127A VAL* 1.3 74.0 - - - +
129A ILE* 1.3 61.7 + - - +
130A ASP* 5.1 4.0 - - - +
156A TRP* 5.2 1.0 + - - -
169A LEU* 3.3 24.0 - - + +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 4.8 1.1 - - - +
127A VAL* 4.0 11.2 - - + +
128A ALA* 1.3 75.8 - - - +
130A ASP* 1.3 70.9 + - - +
140A VAL* 4.3 7.2 - - + -
153A LEU* 3.7 24.7 - - + -
156A TRP* 3.7 36.6 - - + +
157A VAL* 4.1 20.9 - - + -
160A VAL* 4.4 11.2 - - + -
168A ILE* 3.8 23.3 - - + -
169A LEU 2.8 11.1 + - - +
170A LEU* 3.5 10.2 - - + +
171A THR 2.8 27.7 + - - +
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Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A ASN* 3.1 22.6 + - - +
128A ALA* 4.1 4.4 + - - +
129A ILE* 1.3 76.3 + - - +
131A ALA* 1.3 60.0 + - - +
140A VAL* 3.6 6.2 - - - +
141A PHE* 3.0 41.0 + - + +
142A THR* 5.9 0.2 - - - -
144A SER* 4.7 7.4 + - - -
145A GLY 4.5 11.0 + - - +
171A THR* 3.3 29.4 + - - +
173A ILE* 4.1 20.0 - - + -
264A PO4 5.5 0.7 + - - -
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A ILE* 4.8 1.8 - - + -
130A ASP* 1.3 75.2 - - - +
132A LYS* 1.3 62.2 + - - +
138A PHE* 5.2 0.4 - - + -
139A MET 3.2 15.5 - - - +
153A LEU* 4.0 31.6 - - + -
170A LEU* 4.9 1.1 - - + -
171A THR 2.9 7.6 + - - +
173A ILE* 2.8 29.4 + - - +
186A MET* 3.5 26.4 - - + +
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Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ALA* 1.3 78.1 - - - +
133A ARG* 1.3 74.0 + - - +
134A VAL* 3.6 2.7 + - - +
137A GLU 3.5 0.2 - - - +
138A PHE* 4.4 5.2 - - - -
139A MET* 2.9 33.3 + - - +
141A PHE* 3.4 40.7 - - + -
145A GLY 5.1 3.2 + - - -
173A ILE* 3.8 28.9 - - + +
174A ASP* 3.1 32.3 - - - +
186A MET* 4.5 2.0 - - - -
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Residues in contact with ARG 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS* 1.3 81.0 - - - +
134A VAL* 1.3 64.5 + - - +
135A ASP 4.2 0.7 - - - -
136A GLY* 5.3 6.3 - - - +
137A GLU 3.4 11.2 - - - +
138A PHE* 3.7 26.1 - - + +
174A ASP* 2.9 39.7 + - - +
175A ARG* 6.0 1.4 - - - +
183A ASP* 2.7 43.6 + - - -
185A GLU* 2.9 34.2 + - - +
186A MET* 4.5 0.4 - - - +
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Residues in contact with VAL 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS* 4.1 3.1 - - - +
133A ARG* 1.3 80.4 - - - +
135A ASP* 1.3 87.3 + - - +
136A GLY 3.2 0.2 - - - -
137A GLU* 2.8 26.9 + - - +
139A MET* 3.8 16.6 - - + +
141A PHE* 3.8 35.0 - - + -
148A ASN* 3.8 18.8 - - - +
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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