Contacts of the helix formed by residues 122 - 132 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 4.0 3.4 - - - -
108B THR 3.3 11.0 - - - +
109B GLN* 3.2 14.8 - - - +
111B ARG* 4.1 22.0 + - - +
114B LEU* 3.7 5.6 - - + +
121B ILE* 1.3 81.6 - - - +
123B VAL* 1.3 59.6 + - - +
124B GLU* 3.1 17.3 + - - +
125B THR* 2.8 41.5 + - - -
126B LEU* 2.9 23.4 + - - +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B ALA* 3.7 37.0 - - + +
14B ALA* 4.3 8.7 - - + -
15B LEU* 3.5 28.5 - - + +
18B HIS* 4.8 6.1 - - + -
107B VAL* 4.1 8.3 - - + -
108B THR 5.3 0.2 - - - +
109B GLN* 3.2 30.6 + - - +
122B ASP* 1.3 72.0 - - - +
124B GLU* 1.3 66.1 + - - +
126B LEU* 3.2 3.2 + - - +
127B LEU* 2.9 33.2 + - + +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLN* 5.0 0.6 + - - +
122B ASP* 3.1 13.2 + - - +
123B VAL* 1.3 77.5 - - - +
125B THR* 1.3 65.1 + - - +
127B LEU* 3.1 10.9 + - - +
128B VAL* 3.1 35.7 + - + +
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ILE* 3.8 24.8 - - + +
122B ASP* 2.8 31.8 + - - -
124B GLU* 1.3 74.7 + - - +
126B LEU* 1.3 61.2 + - - +
128B VAL* 3.2 17.3 - - + +
129B ARG* 3.2 32.8 - - + +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B TYR* 3.7 37.7 - - + -
7B VAL* 4.8 1.1 - - + -
15B LEU* 4.3 27.4 - - + -
22B TRP* 5.8 0.2 - - + -
29B LEU* 4.7 13.0 - - + -
107B VAL* 3.9 27.8 - - + -
121B ILE* 4.5 4.9 - - + -
122B ASP 2.9 12.3 + - - +
123B VAL* 3.4 10.1 - - - +
124B GLU 3.1 0.2 - - - -
125B THR* 1.3 75.6 - - - +
127B LEU* 1.3 67.2 + - + +
129B ARG* 3.3 4.8 + - - +
130B LEU* 3.1 45.5 + - + +
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Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 4.5 6.7 - - + -
18B HIS* 3.9 33.0 - - + +
21B LYS* 3.8 39.7 - - + +
22B TRP* 4.4 16.6 - - + -
123B VAL* 2.9 25.7 + - + +
124B GLU* 3.1 10.3 + - - +
126B LEU* 1.3 75.9 - - + +
128B VAL* 1.3 66.3 - - + +
130B LEU* 3.1 13.1 + - + +
131B ALA* 2.8 24.3 + - - +
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLU* 3.1 22.6 + - + +
125B THR* 3.2 22.9 - - + +
127B LEU* 1.3 75.9 - - + +
129B ARG* 1.3 71.7 + - + +
131B ALA* 3.1 21.3 + - - +
132B ALA* 3.3 9.0 + - - +
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Residues in contact with ARG 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 3.4 33.5 + - + +
105B VAL* 4.1 22.4 - - - +
119B GLY 5.1 1.2 + - - -
121B ILE* 3.7 24.7 - - - +
125B THR* 3.2 25.5 - - + +
126B LEU* 3.3 8.5 + - - +
127B LEU 3.1 0.6 - - - -
128B VAL* 1.3 82.6 - - + +
130B LEU* 1.3 65.4 + - - +
131B ALA 3.0 1.3 - - - -
132B ALA* 3.0 15.5 + - - +
133B GLN* 3.0 24.8 + - - +
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Residues in contact with LEU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TYR* 4.2 17.9 - - + +
21B LYS 4.2 5.6 - - - +
22B TRP* 3.7 30.1 - - + -
25B HIS* 3.5 54.1 + - + +
28B LYS* 4.7 8.3 - - - +
29B LEU* 5.0 6.1 - - + -
126B LEU* 3.1 41.6 + - + +
127B LEU* 3.7 9.9 - - + +
129B ARG* 1.3 79.5 - - - +
131B ALA* 1.3 61.8 + - - +
133B GLN* 3.1 19.7 + - - +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LEU 2.8 12.9 + - - +
128B VAL* 3.1 19.7 - - - +
129B ARG 3.0 0.4 - - - -
130B LEU* 1.3 78.3 - - - +
132B ALA* 1.3 54.8 + - - +
133B GLN* 3.0 10.7 + - - +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B VAL 3.3 6.7 + - - +
129B ARG* 3.0 13.4 + - - +
131B ALA* 1.3 78.2 - - - +
133B GLN* 1.3 71.8 + - - +
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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