Contacts of the helix formed by residues 123 - 131 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118H VAL 2.8 14.5 + - - +
119H ASN* 3.7 19.5 - - - +
122H LEU* 1.3 72.5 - - - +
124H LEU* 1.3 79.1 + - + +
125H GLY 3.3 0.7 - - - -
126H PRO* 3.2 12.1 - - - +
127H ILE* 3.1 34.5 - - + +
139H TRP* 3.0 41.2 + + - -
143H PHE* 3.7 22.4 - + + -
150H GLY* 3.6 20.6 - - - -
151H CYS 3.6 20.4 - - - +
194H ALA* 3.2 39.3 - - + +
195H ALA 4.3 1.8 - - - -
196H VAL* 3.8 13.8 - - + +
214H LEU* 5.0 0.7 - - + -
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Residues in contact with LEU 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80H LEU 3.2 27.1 - - - +
81H ALA* 3.9 8.5 - - + -
84H VAL* 3.8 28.9 - - + -
119H ASN* 2.9 29.6 + - - +
120H ASN* 3.7 6.3 - - - +
123H TYR* 1.3 92.1 - - + +
125H GLY* 1.3 65.3 + - - +
127H ILE* 3.2 6.9 + - - +
128H LEU* 2.9 28.7 + - + +
140H VAL* 3.8 41.9 - - + +
143H PHE* 3.9 7.2 - - + +
144H THR* 4.6 1.1 - - + -
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Residues in contact with GLY 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H TYR* 5.9 0.2 - - - -
120H ASN 3.0 14.3 + - - -
121H SER* 3.4 11.4 + - - -
123H TYR 3.3 0.2 - - - -
124H LEU* 1.3 75.2 - - - +
126H PRO* 1.3 63.2 - - - +
128H LEU* 3.4 8.5 + - - +
129H LYS* 3.0 28.1 + - - +
270H MET* 3.8 17.5 - - - +
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Residues in contact with PRO 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121H SER 3.5 6.5 - - - +
122H LEU 3.3 23.8 - - - +
123H TYR 3.2 11.9 - - - +
125H GLY* 1.3 86.2 - - - +
127H ILE* 1.3 57.8 + - - +
129H LYS* 4.5 0.2 - - + -
130H PHE* 2.7 48.7 + - + +
152H PHE* 5.1 0.9 - - + -
196H VAL* 4.4 15.3 - - + -
254H LEU* 3.8 14.3 - - + +
263H ILE* 4.0 11.2 - - + -
267H THR* 3.5 25.1 - - + +
270H MET* 4.2 1.5 - - + -
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Residues in contact with ILE 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H TYR* 3.1 59.9 - - + +
124H LEU* 3.2 6.8 + - - +
126H PRO* 1.3 77.5 - - - +
128H LEU* 1.3 57.8 + - - +
131H GLY* 2.8 32.4 + - - -
135H GLN* 4.2 20.4 - - + +
136H LYS* 3.8 10.7 - - + +
139H TRP* 4.1 9.0 - - + +
140H VAL* 3.5 20.9 - - + -
196H VAL* 4.4 4.7 - - + -
214H LEU* 3.7 24.2 - - + -
254H LEU* 4.1 10.5 - - + -
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Residues in contact with LEU 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H ASP* 4.3 9.4 - - + +
84H VAL* 3.4 39.0 - - + -
85H PRO* 3.7 14.8 - - + -
88H LEU* 3.6 30.1 - - + -
120H ASN 6.0 0.2 - - - +
124H LEU* 2.9 22.5 + - + +
125H GLY* 3.7 7.4 - - - +
127H ILE* 1.3 77.2 - - - +
129H LYS* 1.3 59.9 + - - +
136H LYS* 3.3 30.8 + - + +
140H VAL* 4.3 9.6 - - + -
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Residues in contact with LYS 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125H GLY 3.0 17.2 + - - +
126H PRO* 3.3 0.4 + - + -
128H LEU* 1.3 78.2 - - - +
130H PHE* 1.3 90.4 + - + +
131H GLY 5.4 0.2 - - - -
266H GLN* 3.1 30.9 + - + +
270H MET* 5.2 15.5 - - + -
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Residues in contact with PHE 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H PRO* 2.7 33.1 + - + +
129H LYS* 1.3 102.3 - - + +
131H GLY* 1.3 63.9 + - - +
132H SER 4.0 0.2 + - - -
135H GLN* 4.7 0.3 - - - +
254H LEU* 3.8 15.9 - - + -
255H GLY* 4.0 16.4 + - - +
259H MET* 3.8 24.9 - - + -
262H LYS* 4.7 1.1 - - + -
263H ILE* 3.8 49.8 - - + -
266H GLN* 3.4 33.7 - - + -
267H THR* 4.9 1.3 - - - -
270H MET* 6.3 0.9 - - + -
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Residues in contact with GLY 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127H ILE* 2.8 25.9 + - - -
128H LEU 5.0 0.2 - - - +
130H PHE* 1.3 76.6 - - - +
132H SER* 1.3 67.8 + - - +
135H GLN* 3.4 16.6 - - - -
136H LYS* 3.5 13.8 + - - -
254H LEU* 3.5 9.7 - - - +
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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