Contacts of the helix formed by residues 160 - 170 (chain B) in PDB entry 2VOO
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 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A SER* 4.7 19.5 - - - -
161A ILE 6.0 0.2 - - - -
162A GLU* 5.7 4.0 - - - -
111B ARG* 3.3 10.1 - - - +
158B PHE* 3.2 2.5 - - - +
159B ASP* 1.3 97.5 + - - +
161B ILE* 1.3 63.8 + - - +
162B GLU* 3.1 11.9 + - - +
163B SER* 3.1 19.8 + - - -
164B ALA* 3.1 20.6 + - - +
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Residues in contact with ILE 161 (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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161A ILE* 5.2 10.1 - - + +
162A GLU* 3.1 44.8 - - + +
165A LYS* 5.1 17.3 - - + +
107B ASP 5.3 0.2 - - - +
110B ASN* 4.1 28.3 - - + +
111B ARG* 3.3 23.2 - - + +
160B SER* 1.3 73.6 - - - +
162B GLU* 1.3 53.7 + - - +
164B ALA* 3.9 3.1 - - - -
165B LYS* 2.7 43.1 + - + +
184B PHE* 5.8 1.8 - - + -
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Residues in contact with GLU 162 (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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107A ASP* 4.6 17.0 - - - +
160A SER* 6.4 0.4 - - - -
161A ILE* 4.3 25.0 - - + +
160B SER* 3.7 11.6 - - - +
161B ILE* 1.3 79.6 - - - +
163B SER* 1.3 59.9 + - - +
165B LYS* 3.8 2.8 - - - +
166B LYS* 2.9 32.2 + - - +
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Residues in contact with SER 163 (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 LYS 3.9 20.9 - - - +
135B GLY* 4.0 9.0 - - - -
158B PHE* 3.4 12.2 - - - -
159B ASP* 3.1 22.5 + - - -
160B SER* 3.1 13.0 + - - -
162B GLU* 1.3 79.0 - - - +
164B ALA* 1.3 57.4 + - - +
166B LYS* 4.0 6.3 - - - +
167B PHE* 3.0 27.5 + - - +
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Residues in contact with ALA 164 (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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110B ASN 4.3 4.7 - - - +
111B ARG* 4.0 19.1 - - - +
113B VAL* 4.8 2.2 - - + -
158B PHE* 4.0 24.5 - - + -
160B SER 3.1 10.7 + - - +
161B ILE* 3.5 12.3 - - - +
162B GLU 3.0 0.8 - - - -
163B SER* 1.3 78.0 + - - +
165B LYS* 1.3 62.4 + - - +
167B PHE* 2.8 20.0 + - - +
168B VAL* 2.9 16.7 + - - +
184B PHE* 4.5 7.4 - - + -
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Residues in contact with LYS 165 (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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161B ILE* 2.7 30.1 + - + +
162B GLU* 3.8 3.1 - - - +
164B ALA* 1.3 72.9 - - - +
166B LYS* 1.3 56.1 + - - +
168B VAL* 3.3 1.2 + - - -
169B GLU* 2.8 71.1 + - + +
184B PHE* 4.3 17.2 - - + -
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Residues in contact with LYS 166 (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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103A GLU* 5.6 7.4 - - - +
162B GLU 2.9 19.7 + - - +
163B SER* 4.1 6.1 - - - +
165B LYS* 1.3 76.7 - - - +
167B PHE* 1.3 58.5 + - - +
169B GLU* 4.0 6.7 - - - -
170B THR* 2.5 36.5 + - - +
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Residues in contact with PHE 167 (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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113B VAL* 4.4 5.4 - - + -
115B ILE* 3.4 34.8 - - + -
130B TRP* 3.8 16.2 - + - -
131B LEU* 4.4 3.4 - - + -
134B LYS* 3.6 40.2 - - + +
158B PHE* 3.7 24.0 - + + -
163B SER 3.0 17.0 + - - +
164B ALA 2.8 13.1 + - - +
166B LYS* 1.3 80.1 - - - +
168B VAL* 1.3 60.0 + - - +
170B THR 3.5 6.9 + - - +
173B GLN* 2.9 44.2 + - - +
182B ILE* 3.7 34.2 - - + +
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Residues in contact with VAL 168 (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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113B VAL* 4.0 15.7 - - + -
164B ALA 2.9 14.0 + - - +
165B LYS 3.9 2.0 - - - +
167B PHE* 1.3 75.4 - - + +
169B GLU* 1.3 66.0 + - + +
170B THR 3.2 5.4 + - - +
182B ILE* 3.9 39.4 - - + +
183B LEU* 4.9 1.3 - - - -
184B PHE* 3.3 46.2 - - + +
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Residues in contact with GLU 169 (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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165B LYS* 2.8 51.5 + - + +
166B LYS* 4.5 4.8 + - - +
168B VAL* 1.3 76.4 - - + +
170B THR* 1.3 58.0 + - - +
171B PRO* 3.2 12.7 - - - +
184B PHE* 6.2 0.4 - - + -
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Residues in contact with THR 170 (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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166B LYS* 2.5 26.3 + - - +
167B PHE 3.6 5.9 - - - +
168B VAL 3.2 5.9 - - - +
169B GLU* 1.3 76.7 - - - +
171B PRO* 1.3 72.9 - - + +
173B GLN* 3.0 36.1 - - - +
182B ILE* 5.2 0.3 - - - +
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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