Contacts of the helix formed by residues 132 - 140 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E PHE 4.1 0.4 + - - -
131E GLY* 1.3 77.1 - - - -
133E LYS* 1.3 64.7 + - - +
134E GLU* 3.6 15.6 + - - +
135E GLN* 3.0 35.6 + - - +
136E LYS* 3.1 23.8 + - - +
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Residues in contact with LYS 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E SER* 1.3 72.9 - - - +
134E GLU* 1.3 76.6 + - - +
136E LYS* 3.4 11.4 + - - +
137E GLN* 3.1 36.8 + - - +
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Residues in contact with GLU 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E SER* 3.6 19.5 + - - +
133E LYS* 1.3 89.0 + - - +
135E GLN* 1.3 57.8 + - + +
137E GLN* 3.1 15.3 + - - +
138E ALA* 2.9 30.8 + - - +
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Residues in contact with GLN 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E ILE* 4.3 3.8 - - + -
130E PHE 4.5 1.2 - - - +
131E GLY* 3.4 12.6 - - - -
132E SER* 3.0 36.6 + - - +
134E GLU* 1.3 80.1 - - + +
136E LYS* 1.3 51.0 + - - +
138E ALA* 4.5 0.2 - - - -
139E TRP* 2.6 49.5 + - + +
214E LEU* 3.9 27.8 - - + +
251E ASP 3.1 21.3 + - - +
253E ILE 2.9 30.0 + - - +
254E LEU* 3.9 5.3 - - - +
255E GLY 5.2 0.7 + - - -
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Residues in contact with LYS 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 3.8 34.0 - - + +
127E ILE* 3.8 16.2 - - + +
128E LEU* 3.7 26.9 + - + +
131E GLY 3.4 22.4 + - - -
132E SER 3.1 12.9 + - - +
133E LYS* 3.6 11.1 - - - +
135E GLN* 1.3 72.0 - - - +
137E GLN* 1.3 62.0 + - - +
140E VAL* 2.9 45.6 + - + +
141E THR* 3.1 5.4 + - - -
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Residues in contact with GLN 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E LEU* 4.6 11.0 - - + -
133E LYS* 3.1 24.9 + - - +
134E GLU* 3.6 13.7 - - - +
136E LYS* 1.3 77.8 - - - +
138E ALA* 1.3 60.9 + - - +
141E THR* 3.6 14.4 - - - +
142E PRO* 3.5 16.1 - - - +
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Residues in contact with ALA 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E GLU 2.9 14.6 + - - +
135E GLN* 4.5 0.2 - - - -
137E GLN* 1.3 79.8 - - - +
139E TRP* 1.3 81.8 + - + +
142E PRO* 3.4 18.3 - - - +
143E PHE* 4.5 4.3 - - - -
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Residues in contact with TRP 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E TYR* 2.9 46.2 + + - +
127E ILE* 3.9 13.6 - - + +
135E GLN* 2.6 37.2 + - - +
138E ALA* 1.3 91.7 - - + +
140E VAL* 1.3 59.8 + - - +
143E PHE* 3.3 17.1 - + - -
193E SER 5.3 0.2 - - - -
194E ALA* 3.6 20.2 - - + -
195E ALA 5.1 0.2 - - - -
214E LEU* 3.7 47.1 - - + +
215E VAL 3.8 13.9 - - - -
216E PRO* 3.7 30.7 - - + -
249E PRO* 6.5 0.4 - - + -
251E ASP 6.0 0.2 + - - -
252E SER* 5.3 6.5 - - - +
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Residues in contact with VAL 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E VAL* 3.8 28.0 - - + -
88E LEU* 4.1 12.6 - - + -
124E LEU* 3.7 21.8 - - + +
127E ILE* 3.8 31.6 - - + -
128E LEU* 4.3 13.2 - - + -
136E LYS* 2.9 26.1 + - + +
139E TRP* 1.3 77.9 - - - +
141E THR* 1.3 56.8 + - - +
142E PRO 3.4 0.2 - - - -
143E PHE* 2.7 30.7 + - - +
144E THR* 3.3 13.4 - - + +
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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