Contacts of the helix formed by residues 122 - 133 (chain G) in PDB entry 1V8O
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107G VAL* 4.0 4.0 - - - -
108G THR 3.3 15.3 - - - +
109G GLN* 3.5 8.7 - - - +
111G ARG* 3.8 21.9 + - - +
114G LEU* 3.9 12.6 - - + +
121G ILE* 1.3 80.6 - - - +
123G VAL* 1.3 63.3 + - - +
124G GLU* 3.0 12.3 + - - +
125G THR* 2.9 30.9 + - - -
126G LEU* 3.1 17.5 + - - +
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Residues in contact with VAL 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ALA* 3.5 35.7 - - + -
14G ALA* 3.9 14.8 - - + -
15G LEU* 3.5 32.3 - - + +
18G HIS* 5.0 2.0 - - + -
107G VAL* 4.1 7.2 - - + -
108G THR 5.0 0.2 - - - -
109G GLN* 3.3 30.5 + - - +
122G ASP* 1.3 74.1 - - - +
124G GLU* 1.3 65.3 + - - +
126G LEU* 3.2 2.1 + - - +
127G LEU* 3.0 31.3 + - + +
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Residues in contact with GLU 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G GLN* 5.0 0.6 + - - +
122G ASP* 3.0 12.6 + - - +
123G VAL* 1.3 77.9 - - - +
125G THR* 1.3 61.4 + - - +
127G LEU* 3.4 11.9 + - + +
128G VAL* 3.2 33.8 + - + +
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Residues in contact with THR 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121G ILE* 3.8 29.8 - - + +
122G ASP* 2.9 26.8 + - - -
124G GLU* 1.3 75.7 - - - +
126G LEU* 1.3 66.1 + - - +
128G VAL* 3.0 29.6 - - + +
129G ARG* 3.1 16.8 + - + +
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Residues in contact with LEU 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G TYR* 3.7 47.1 - - + +
7G VAL* 4.9 1.1 - - + -
15G LEU* 3.9 36.3 - - + -
29G LEU* 4.6 9.6 - - + -
107G VAL* 3.9 21.5 - - + -
121G ILE* 3.8 8.2 - - + +
122G ASP 3.1 13.1 + - - +
123G VAL 3.6 7.0 - - - +
125G THR* 1.3 77.8 - - - +
127G LEU* 1.3 62.0 + - - +
129G ARG* 3.2 3.5 + - - +
130G LEU* 3.0 45.3 + - + +
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Residues in contact with LEU 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G LEU* 4.0 22.4 - - + -
18G HIS* 3.3 38.6 - - + +
21G LYS* 4.1 36.9 - - + +
22G TRP* 4.6 7.9 - - + -
123G VAL* 3.0 22.2 + - + +
124G GLU* 3.6 13.0 - - + +
125G THR 3.2 0.2 - - - -
126G LEU* 1.3 77.6 - - - +
128G VAL* 1.3 57.8 + - + +
130G LEU* 3.9 8.0 - - + +
131G ALA* 3.0 27.9 + - - +
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Residues in contact with VAL 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G GLU* 3.2 22.2 - - + +
125G THR* 3.0 22.4 - - + +
127G LEU* 1.3 75.1 - - + +
129G ARG* 1.3 74.6 + - + +
131G ALA* 3.4 8.3 + - - +
132G ALA* 3.2 20.1 + - - +
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Residues in contact with ARG 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G GLU* 5.1 2.0 + - - -
5G TYR* 2.7 49.2 + - - +
105G VAL* 4.7 14.2 - - - +
119G GLY 5.7 0.4 + - - -
121G ILE* 3.8 37.9 - - - +
125G THR* 3.1 15.5 + - + +
126G LEU* 3.4 7.6 - - - +
128G VAL* 1.3 86.8 - - + +
130G LEU* 1.3 62.6 + - + +
132G ALA* 3.2 20.6 + - - +
133G GLN* 3.1 19.0 + - - +
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Residues in contact with LEU 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G TYR* 4.7 5.2 - - + +
21G LYS 4.8 5.4 - - - +
22G TRP* 3.8 30.3 - - + -
25G HIS* 3.0 60.0 + - + +
28G LYS* 4.1 11.4 - - + +
29G LEU* 4.9 6.7 - - + -
126G LEU* 3.0 46.5 + - + +
127G LEU* 4.0 8.5 - - + +
129G ARG* 1.3 73.6 - - - +
131G ALA* 1.3 65.2 + - - +
132G ALA 3.1 2.0 - - - -
133G GLN* 3.2 23.7 + - - +
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Residues in contact with ALA 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G LEU 3.0 20.1 + - - +
128G VAL* 3.7 9.4 - - - +
129G ARG 3.2 0.2 - - - -
130G LEU* 1.3 78.4 - - - +
132G ALA* 1.3 63.5 + - - +
133G GLN* 3.6 5.0 - - - +
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Residues in contact with ALA 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G VAL 3.2 11.0 + - - +
129G ARG* 3.2 13.9 + - - +
130G LEU 3.1 0.8 - - - -
131G ALA* 1.3 80.1 - - - +
133G GLN* 1.3 64.3 + - + +
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Residues in contact with GLN 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G GLU* 4.6 6.9 + - - +
5G TYR* 4.3 12.3 + - - -
25G HIS* 3.2 26.4 + - + -
28G LYS* 3.4 22.5 + - - +
129G ARG* 3.1 27.3 + - - +
130G LEU* 3.2 27.2 + - - +
131G ALA* 3.6 5.2 - - - +
132G ALA* 1.3 84.7 - - + +
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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