Contacts of the helix formed by residues 132 - 140 (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 SER 132 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130H PHE 4.0 0.6 + - - -
131H GLY* 1.3 76.6 - - - -
133H LYS* 1.3 65.3 + - - +
134H GLU* 3.6 16.3 + - - +
135H GLN* 3.1 44.4 + - - +
136H LYS* 3.2 14.7 + - - +
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Residues in contact with LYS 133 (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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88H LEU* 5.4 0.3 - - - +
132H SER* 1.3 73.4 - - - +
134H GLU* 1.3 76.3 + - - +
136H LYS* 3.8 13.2 + - + +
137H GLN* 3.4 32.1 + - - +
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Residues in contact with GLU 134 (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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132H SER* 3.6 18.7 - - - +
133H LYS* 1.3 91.0 + - - +
135H GLN* 1.3 61.1 + - + +
137H GLN* 3.3 9.9 + - - +
138H ALA* 3.0 29.7 + - - +
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Residues in contact with GLN 135 (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* 4.3 3.6 - - + -
130H PHE 4.7 0.9 - - - +
131H GLY* 3.4 12.8 - - - -
132H SER* 3.1 40.8 + - - +
134H GLU* 1.3 79.6 - - + +
136H LYS* 1.3 52.6 + - - +
138H ALA* 4.7 0.4 - - - -
139H TRP* 2.7 52.2 + - + +
214H LEU* 3.7 26.6 - - + +
251H ASP* 2.8 28.7 + - + +
253H ILE 3.0 21.1 + - - +
254H LEU* 3.8 5.9 - - - +
255H GLY 5.0 0.9 + - - -
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Residues in contact with LYS 136 (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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88H LEU* 4.0 32.8 - - + +
127H ILE* 3.8 18.2 - - + +
128H LEU* 3.3 33.5 + - + +
131H GLY 3.5 20.5 + - - -
132H SER 3.2 14.5 + - - +
133H LYS* 4.0 10.3 - - - +
135H GLN* 1.3 73.5 - - - +
137H GLN* 1.3 62.2 + - - +
140H VAL* 2.7 44.5 + - + +
141H THR* 3.2 4.3 + - - -
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Residues in contact with GLN 137 (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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88H LEU* 4.4 15.0 - - + +
133H LYS* 3.4 18.4 + - - +
134H GLU* 3.3 12.1 + - - +
136H LYS* 1.3 79.5 - - - +
138H ALA* 1.3 60.5 + - - +
141H THR* 3.7 13.6 - - - +
142H PRO* 3.6 14.0 - - - +
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Residues in contact with ALA 138 (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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134H GLU 3.0 17.2 + - - +
135H GLN* 4.7 0.2 - - - -
137H GLN* 1.3 77.7 - - - +
139H TRP* 1.3 80.3 - - + +
142H PRO* 3.3 19.3 - - - +
143H PHE* 4.5 4.2 - - - -
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Residues in contact with TRP 139 (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* 3.0 44.1 + + - +
127H ILE* 4.3 14.6 - - + -
135H GLN* 2.7 36.1 + - - +
138H ALA* 1.3 92.3 - - + +
140H VAL* 1.3 60.4 + - - +
142H PRO* 4.4 0.2 - - - -
143H PHE* 3.2 17.5 - + - -
194H ALA* 3.5 22.7 - - + -
195H ALA 5.1 0.4 - - - -
214H LEU* 3.6 53.9 - - + +
215H VAL 3.8 7.2 - - - -
216H PRO* 3.7 31.4 - - + -
249H PRO* 6.5 0.2 - - + -
251H ASP 5.8 1.0 + - - -
252H SER* 4.8 7.7 - - - +
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Residues in contact with VAL 140 (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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84H VAL* 3.7 31.2 - - + -
88H LEU* 4.1 13.2 - - + -
124H LEU* 3.8 16.9 - - + +
127H ILE* 3.5 33.4 - - + -
128H LEU* 4.3 14.1 - - + -
136H LYS* 2.7 31.1 + - + +
139H TRP* 1.3 73.0 - - - +
141H THR* 1.3 57.6 + - - +
142H PRO 3.4 0.4 - - - -
143H PHE* 2.8 26.9 + - - +
144H THR* 3.4 15.2 - - + +
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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