Contacts of the helix formed by residues 132 - 140 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B PHE 4.1 0.2 + - - -
131B GLY* 1.3 76.6 - - - -
133B LYS* 1.3 64.7 + - - +
134B GLU* 3.4 23.0 + - - +
135B GLN* 3.0 37.6 + - - +
136B LYS* 2.9 24.5 + - - +
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Residues in contact with LYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B SER* 1.3 72.0 - - - +
134B GLU* 1.3 73.0 + - + +
136B LYS* 3.1 17.0 + - - +
137B GLN* 3.1 34.2 + - - +
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Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B SER* 3.5 18.4 + - - +
133B LYS* 1.3 88.7 + - + +
135B GLN* 1.3 58.9 + - + +
137B GLN* 3.3 15.5 + - - +
138B ALA* 2.9 31.3 + - - +
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Residues in contact with GLN 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ILE* 4.1 3.5 - - + +
130B PHE 4.6 0.5 - - - +
131B GLY* 3.3 12.9 - - - -
132B SER* 3.0 39.6 + - - +
134B GLU* 1.3 77.8 - - + +
136B LYS* 1.3 56.1 + - - +
138B ALA* 4.6 0.4 - - - -
139B TRP* 2.9 45.6 + - + +
214B LEU* 4.1 26.3 - - + +
251B ASP 3.1 20.9 + - - +
252B SER 4.1 0.4 + - - -
253B ILE 2.8 31.0 + - - +
254B LEU* 3.6 7.0 - - - +
255B GLY 4.9 1.2 + - - -
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 4.1 30.1 - - + -
127B ILE* 3.9 12.8 - - - +
128B LEU* 3.4 32.8 + - + +
131B GLY 3.4 21.6 + - - -
132B SER 2.9 18.2 + - - +
133B LYS* 3.1 13.1 + - - +
135B GLN* 1.3 75.3 - - - +
137B GLN* 1.3 58.9 + - - +
140B VAL* 2.8 44.0 + - + +
141B THR* 3.1 6.2 + - - -
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Residues in contact with GLN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B LEU* 4.4 13.7 - - + -
133B LYS* 3.1 20.7 + - - +
134B GLU* 3.3 17.1 + - - +
136B LYS* 1.3 77.3 - - - +
138B ALA* 1.3 60.1 + - - +
141B THR* 3.6 13.8 - - - +
142B PRO* 3.4 17.0 - - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLU 2.9 15.5 + - - +
135B GLN* 4.6 0.2 - - - -
137B GLN* 1.3 78.8 - - - +
139B TRP* 1.3 83.5 + - + +
142B PRO* 3.2 19.6 - - - +
143B PHE* 4.5 3.8 - - - -
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Residues in contact with TRP 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TYR* 2.8 45.6 + + - +
127B ILE* 4.0 13.5 - - + -
135B GLN* 2.9 33.3 + - - +
138B ALA* 1.3 95.2 - - + +
140B VAL* 1.3 61.6 + - - +
143B PHE* 3.1 17.9 - + - -
193B SER 5.3 0.2 - - - -
194B ALA* 3.7 20.4 - - + -
195B ALA 5.2 0.2 - - - -
214B LEU* 3.5 58.2 - - + +
215B VAL 4.0 8.5 - - - -
216B PRO* 3.9 23.1 - - + -
249B PRO* 6.5 0.7 - - + -
251B ASP* 5.9 1.2 + - - -
252B SER* 5.1 8.0 - - - +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B VAL* 3.8 29.2 - - + -
88B LEU* 4.4 9.9 - - + -
124B LEU* 3.7 26.5 - - + +
127B ILE* 3.5 33.7 - - + -
128B LEU* 4.6 7.0 - - + +
136B LYS* 2.8 30.7 + - + +
139B TRP* 1.3 70.9 - - - +
141B THR* 1.3 57.1 + - - +
142B PRO* 3.2 2.2 - - - -
143B PHE* 2.6 32.2 + - - +
144B THR* 3.3 12.4 - - + +
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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