Contacts of the helix formed by residues 122 - 132 (chain J) in PDB entry 1V8P
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 ASP 122 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107J VAL* 3.9 3.6 - - - -
108J THR 3.2 14.1 - - - +
109J GLN* 3.0 15.5 - - - +
111J ARG* 4.0 21.8 + - - +
114J LEU* 3.9 8.2 - - + +
121J ILE* 1.3 78.4 - - - +
123J VAL* 1.3 66.0 + - - +
124J GLU* 3.1 18.0 + - - +
125J THR* 3.0 27.0 + - - -
126J LEU* 2.9 20.1 + - - +
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Residues in contact with VAL 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ALA* 3.6 33.7 - - + +
14J ALA* 3.8 14.4 - - + +
15J LEU* 3.6 33.7 - - + +
18J HIS* 5.0 2.9 - - + +
107J VAL* 4.0 3.1 - - + +
109J GLN* 2.9 35.9 + - - +
122J ASP* 1.3 68.2 - - - +
124J GLU* 1.3 69.6 + - - +
126J LEU* 3.2 7.2 + - - +
127J LEU* 3.1 30.6 + - + +
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Residues in contact with GLU 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109J GLN* 4.6 1.8 + - - +
122J ASP* 3.1 16.5 + - - +
123J VAL* 1.3 80.8 - - - +
125J THR* 1.3 63.8 + - - +
127J LEU* 3.3 9.3 + - - +
128J VAL* 3.3 28.0 + - + +
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Residues in contact with THR 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J ILE* 3.7 25.9 - - + +
122J ASP* 3.0 20.2 + - - -
124J GLU* 1.3 74.8 - - - +
126J LEU* 1.3 66.3 + - - +
128J VAL* 2.8 33.7 - - + +
129J ARG* 2.9 22.0 + - + +
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Residues in contact with LEU 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J TYR* 3.8 40.8 - - + -
7J VAL* 5.1 2.5 - - + -
15J LEU* 3.8 34.8 - - + -
29J LEU* 4.9 9.6 - - + -
107J VAL* 3.8 26.5 - - + -
121J ILE* 3.9 6.2 - - + +
122J ASP 2.9 14.8 + - - +
123J VAL* 3.2 8.0 + - - +
125J THR* 1.3 74.6 - - - +
127J LEU* 1.3 58.0 + - - +
129J ARG* 3.0 9.0 + - - +
130J LEU* 2.9 52.9 + - + +
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Residues in contact with LEU 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15J LEU* 4.1 20.2 - - + -
18J HIS* 4.0 31.4 - - + +
21J LYS* 3.6 39.4 - - + +
22J TRP* 4.3 7.2 - - + -
123J VAL* 3.1 21.9 + - + +
124J GLU* 3.6 9.4 - - - +
125J THR 3.2 0.2 - - - -
126J LEU* 1.3 79.2 - - - +
128J VAL* 1.3 59.2 + - + +
130J LEU* 2.8 16.4 + - + +
131J ALA* 2.8 28.7 + - - +
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Residues in contact with VAL 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J GLU* 3.3 15.8 + - + +
125J THR* 2.8 39.0 + - + +
127J LEU* 1.3 75.7 - - + +
129J ARG* 1.3 63.2 + - + +
131J ALA* 3.4 20.3 + - - +
132J ALA* 3.5 10.2 + - - +
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Residues in contact with ARG 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J TYR* 3.3 42.2 + - + +
105J VAL* 4.2 16.5 - - - +
119J GLY 4.9 2.2 + - - -
121J ILE* 3.6 26.1 - - - +
125J THR* 2.9 30.5 + - + +
126J LEU* 3.2 11.4 - - - +
127J LEU 3.0 0.2 - - - -
128J VAL* 1.3 81.4 - - + +
130J LEU* 1.3 61.5 + - + +
131J ALA 3.4 0.3 + - - -
132J ALA* 3.7 7.9 + - - +
133J GLN* 3.0 28.6 + - - +
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Residues in contact with LEU 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5J TYR* 5.1 6.3 - - + +
21J LYS 4.1 7.4 - - - +
22J TRP* 3.6 31.9 - - + -
25J HIS* 3.1 51.9 + - + +
28J LYS* 4.6 9.2 - - - +
29J LEU* 4.9 9.2 - - + -
126J LEU* 2.9 43.0 + - + +
127J LEU* 2.8 16.4 + - + +
129J ARG* 1.3 75.3 - - - +
131J ALA* 1.3 58.9 + - - +
133J GLN* 3.0 26.9 + - - +
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Residues in contact with ALA 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J LEU 2.8 11.1 + - - +
128J VAL* 3.4 15.5 - - - +
129J ARG 3.2 0.2 - - - -
130J LEU* 1.3 72.4 - - - +
132J ALA* 1.3 53.7 + - - +
133J GLN* 2.5 27.0 + - - +
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Residues in contact with ALA 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128J VAL 3.5 10.1 + - - +
129J ARG* 3.7 6.2 + - - +
130J LEU 3.5 0.2 - - - -
131J ALA* 1.3 75.9 - - - +
133J GLN* 1.3 65.2 + - + +
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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