Contacts of the helix formed by residues 132 - 140 (chain C) in PDB entry 2VIG
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 SER 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C PHE 4.1 0.4 + - - -
131C GLY* 1.3 76.1 - - - -
133C LYS* 1.3 64.8 + - - +
134C GLU* 3.1 14.9 + - - +
135C GLN* 3.0 36.8 + - - +
136C LYS* 3.1 23.4 + - - +
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Residues in contact with LYS 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 5.5 0.2 - - - +
132C SER* 1.3 73.1 - - - +
134C GLU* 1.3 76.7 + - - +
136C LYS* 3.6 12.2 - - - +
137C GLN* 3.1 47.4 + - + +
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Residues in contact with GLU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C SER* 3.0 11.6 + - - +
133C LYS* 1.3 103.8 + - - +
135C GLN* 1.3 66.2 + - + +
136C LYS 3.2 0.2 - - - -
137C GLN* 3.3 15.7 + - - +
138C ALA* 3.0 25.6 + - - +
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Residues in contact with GLN 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ILE* 4.1 4.2 - - + +
130C PHE 4.6 0.9 - - - +
131C GLY* 3.5 12.4 - - - -
132C SER* 3.0 37.3 + - - +
134C GLU* 1.3 77.7 - - + +
136C LYS* 1.3 51.8 + - - +
138C ALA* 4.7 0.2 - - - -
139C TRP* 2.7 48.5 + - + +
214C LEU* 3.8 27.1 - - + +
251C ASP* 2.9 21.9 + - + +
252C SER 4.2 0.2 - - - -
253C ILE 2.8 31.1 + - - +
254C LEU* 3.9 5.6 - - - +
255C GLY 4.9 1.2 + - - -
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Residues in contact with LYS 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 3.9 31.4 - - + +
127C ILE* 3.8 14.4 - - - +
128C LEU* 3.2 33.3 + - - +
131C GLY 3.4 20.1 + - - -
132C SER 3.1 15.0 + - - +
133C LYS* 3.6 12.3 - - - +
135C GLN* 1.3 73.0 - - - +
137C GLN* 1.3 65.3 + - - +
140C VAL* 3.0 41.4 + - + +
141C THR* 3.3 3.5 + - - -
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Residues in contact with GLN 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LEU* 4.5 8.3 - - + -
133C LYS* 3.1 39.7 + - + +
134C GLU* 3.3 17.0 + - - +
136C LYS* 1.3 78.8 - - - +
138C ALA* 1.3 61.8 - - - +
141C THR* 3.5 14.9 - - - +
142C PRO* 3.5 15.4 - - - +
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Residues in contact with ALA 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C GLU 3.0 13.6 + - - +
137C GLN* 1.3 78.9 - - - +
139C TRP* 1.3 80.4 + - + +
140C VAL 3.8 0.4 - - - -
142C PRO* 3.3 19.8 - - - +
143C PHE* 4.5 4.0 - - - -
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Residues in contact with TRP 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C TYR* 2.9 50.7 + + - +
127C ILE* 3.8 14.2 - - + +
135C GLN* 2.7 36.6 + - - +
138C ALA* 1.3 91.2 - - + +
140C VAL* 1.3 60.5 - - - +
143C PHE* 3.3 12.2 - + - -
194C ALA* 3.6 20.6 - - + -
195C ALA 5.0 0.4 - - - -
214C LEU* 3.5 51.3 - - + +
215C VAL 3.7 10.3 - - - -
216C PRO* 3.5 31.6 - - + -
252C SER* 5.3 6.0 - - - +
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Residues in contact with VAL 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C VAL* 3.7 30.7 - - + -
88C LEU* 4.3 9.2 - - + -
124C LEU* 3.6 20.1 - - + +
127C ILE* 3.4 33.4 - - + -
128C LEU* 4.4 13.7 - - + -
136C LYS* 3.0 24.6 + - + +
139C TRP* 1.3 77.8 - - - +
141C THR* 1.3 59.2 + - - +
142C PRO 3.3 0.7 - - - -
143C PHE* 2.6 38.1 + - - +
144C THR* 3.5 6.8 + - + +
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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