Contacts of the helix formed by residues 123 - 131 (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 TYR 123 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E VAL 2.9 11.5 + - - +
119E ASN* 3.6 14.1 - - - +
122E LEU* 1.3 76.2 - - - +
124E LEU* 1.3 82.2 + - + +
126E PRO* 3.3 11.6 - - - +
127E ILE* 3.4 31.8 - - + +
139E TRP* 2.9 43.2 + + - +
143E PHE* 3.7 20.4 - + + -
150E GLY* 3.6 13.0 - - - -
151E CYS 3.6 32.8 - - - +
194E ALA* 3.2 38.7 - - + +
195E ALA 4.2 3.8 - - - -
196E VAL* 4.0 11.5 - - + +
214E LEU* 5.1 0.4 - - + -
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Residues in contact with LEU 124 (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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80E LEU 3.4 25.8 - - - +
81E ALA* 3.6 20.4 - - + -
84E VAL* 3.8 16.4 - - + -
119E ASN* 3.0 21.1 + - - +
120E ASN* 3.6 6.3 - - - +
123E TYR* 1.3 98.5 - - + +
125E GLY* 1.3 65.3 + - - +
127E ILE* 3.0 8.0 + - - +
128E LEU* 2.9 26.5 + - + +
140E VAL* 3.7 46.2 - - + +
143E PHE* 4.1 7.0 - - + +
144E THR* 4.6 0.2 - - + -
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Residues in contact with GLY 125 (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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95E TYR* 5.8 0.2 - - - -
120E ASN 3.2 14.9 + - - -
121E SER* 3.4 11.4 + - - -
124E LEU* 1.3 75.0 - - - +
126E PRO* 1.3 63.5 - - - +
128E LEU* 3.3 9.4 + - - +
129E LYS* 3.0 28.6 + - - +
270E MET* 4.1 17.7 - - - +
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Residues in contact with PRO 126 (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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121E SER 3.5 7.9 - - - +
122E LEU 3.1 28.0 - - - +
123E TYR 3.3 9.4 - - - +
125E GLY* 1.3 88.7 - - - +
127E ILE* 1.3 55.5 + - - +
129E LYS* 4.4 1.6 - - + -
130E PHE* 2.9 39.5 + - + +
152E PHE* 5.0 1.1 - - + -
196E VAL* 4.2 15.3 - - + -
254E LEU* 3.7 10.1 - - + +
263E ILE* 4.1 15.9 - - + -
267E THR* 3.4 26.5 - - + +
270E MET* 4.4 1.3 - - + -
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Residues in contact with ILE 127 (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* 3.4 57.7 - - + +
124E LEU* 3.0 5.6 + - - +
126E PRO* 1.3 73.9 - - - +
128E LEU* 1.3 63.4 + - - +
131E GLY* 2.8 34.8 + - - -
135E GLN* 4.1 25.6 - - + +
136E LYS* 3.8 7.2 - - + +
139E TRP* 3.9 15.9 - - + +
140E VAL* 3.8 19.3 - - + -
196E VAL* 4.4 3.8 - - + -
214E LEU* 3.8 23.1 - - + -
254E LEU* 4.2 7.0 - - + -
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Residues in contact with LEU 128 (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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83E ASP* 4.1 10.8 - - + +
84E VAL* 3.4 37.5 - - + -
85E PRO* 3.6 25.6 - - + -
88E LEU* 3.6 22.9 - - + -
124E LEU* 2.9 21.0 + - + +
125E GLY* 3.7 9.2 - - - +
127E ILE* 1.3 78.7 - - - +
129E LYS* 1.3 60.1 + - - +
136E LYS* 3.7 25.3 + - + +
140E VAL* 4.3 8.7 - - + +
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Residues in contact with LYS 129 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125E GLY 3.0 17.3 + - - +
126E PRO* 4.4 0.7 - - + -
128E LEU* 1.3 78.2 - - - +
130E PHE* 1.3 89.1 - - + +
131E GLY 3.7 1.4 - - - +
266E GLN* 2.7 34.5 + - + +
270E MET* 4.5 19.7 - - + -
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Residues in contact with PHE 130 (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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126E PRO* 2.9 26.3 + - + +
129E LYS* 1.3 101.8 - - + +
131E GLY* 1.3 63.2 + - - +
132E SER 4.1 0.2 + - - -
135E GLN* 4.5 0.3 - - - +
254E LEU* 3.8 17.5 - - + +
255E GLY* 3.9 14.5 + - - +
259E MET* 3.7 30.5 - - + -
262E LYS 5.2 0.2 - - - -
263E ILE* 3.7 47.6 - - + -
266E GLN* 3.2 26.7 - - + -
267E THR* 5.1 0.7 - - - -
270E MET* 6.2 0.2 - - + -
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Residues in contact with GLY 131 (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* 2.8 25.9 + - - -
129E LYS 3.7 1.3 - - - +
130E PHE* 1.3 75.9 - - - +
132E SER* 1.3 66.5 + - - -
135E GLN* 3.4 15.9 - - - -
136E LYS* 3.4 15.1 + - - -
254E LEU* 3.6 8.6 - - - +
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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