Contacts of the helix formed by residues 175 - 185 (chain B) in PDB entry 2VRF
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 THR 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B GLY* 4.2 1.1 - - - -
134B ARG* 3.2 38.8 - - + +
135B GLU* 3.3 23.1 - - + +
140B ILE* 4.0 0.2 - - - +
173B GLN 3.6 0.4 + - - -
174B ALA* 1.3 80.4 - - - +
176B HIS* 1.3 65.5 + - - +
177B ASP* 3.5 8.2 + - - +
178B GLN* 2.9 37.3 + - - +
179B ALA* 3.1 17.5 + - - +
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Residues in contact with HIS 176 (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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200A VAL* 3.5 30.5 + - + +
202A THR* 2.6 30.2 + - - -
130B ILE* 3.3 35.4 - - + +
131B LYS* 3.9 5.5 + - - -
132B GLY 3.1 28.6 + - - +
133B GLY* 4.0 0.6 - - - -
135B GLU* 3.0 19.8 + - - +
136B ASN* 5.5 0.7 - - - +
140B ILE* 4.1 7.9 - - - +
175B THR* 1.3 74.2 - - - +
177B ASP* 1.3 59.7 + - - +
179B ALA* 3.1 5.7 + - - +
180B VAL* 2.8 37.4 + - + +
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 4.7 1.0 + - - +
175B THR* 3.5 7.4 + - - +
176B HIS* 1.3 81.6 - - - +
178B GLN* 1.3 57.0 + - + +
180B VAL* 3.2 8.4 + - - +
181B GLN* 2.9 39.3 + - + +
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Residues in contact with GLN 178 (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 ARG* 3.6 12.1 + - - +
171B LEU* 4.4 2.4 - - + +
173B GLN 4.0 0.3 - - - +
174B ALA* 3.3 15.1 - - + -
175B THR* 2.9 43.5 + - - +
177B ASP* 1.3 75.5 - - + +
179B ALA* 1.3 58.1 + - - +
181B GLN* 3.9 4.4 - - - +
182B ALA* 2.9 30.4 + - - +
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Residues in contact with ALA 179 (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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130B ILE* 4.1 3.8 - - + -
140B ILE* 3.6 42.6 - - + -
171B LEU* 3.7 22.0 - - + -
174B ALA* 4.1 1.0 - - + +
175B THR 3.1 7.8 + - - +
176B HIS 3.4 7.9 - - - +
178B GLN* 1.3 74.7 - - - +
180B VAL* 1.3 65.9 + - - +
182B ALA* 3.6 0.5 - - - +
183B LEU* 2.9 33.1 + - + +
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Residues in contact with VAL 180 (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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202A THR* 3.8 19.7 - - + +
204A VAL* 4.3 7.4 - - + -
130B ILE* 4.0 9.9 - - + -
176B HIS* 2.8 45.8 + - + +
177B ASP* 3.6 9.4 - - - +
179B ALA* 1.3 72.9 - - - +
181B GLN* 1.3 71.5 + - - +
183B LEU* 3.8 1.4 - - - +
184B LYS* 2.9 59.8 + - - +
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Residues in contact with GLN 181 (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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177B ASP* 2.9 21.9 + - + +
178B GLN* 4.0 4.7 - - - +
180B VAL* 1.3 87.5 - - - +
182B ALA* 1.3 67.1 + - - +
184B LYS* 4.5 12.5 - - - +
185B ARG* 2.9 76.2 + - - +
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Residues in contact with ALA 182 (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 VAL* 4.5 4.8 - - + +
169B THR* 4.0 18.1 + - + +
171B LEU* 3.9 22.7 - - + -
178B GLN 2.9 20.5 + - - +
179B ALA 3.2 4.5 + - - +
181B GLN* 1.3 77.1 - - - +
183B LEU* 1.3 63.3 + - - +
185B ARG* 3.8 3.8 - - - +
186B ALA* 3.4 20.4 + - - +
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Residues in contact with LEU 183 (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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204A VAL* 4.0 24.2 - - + -
120B LYS* 3.0 22.9 + - - -
126B LEU* 3.9 25.2 - - + +
130B ILE* 3.7 25.8 - - + -
140B ILE* 5.1 0.2 - - + -
163B ILE* 4.2 19.3 - - + -
166B VAL* 3.1 40.4 - - + -
171B LEU* 4.6 2.9 - - + -
179B ALA* 2.9 23.3 + - + +
180B VAL 3.9 3.1 - - - +
182B ALA* 1.3 76.4 - - - +
184B LYS* 1.3 58.3 + - - +
185B ARG 3.3 0.7 + - - -
186B ALA* 3.3 10.7 + - - +
190B VAL* 5.4 0.2 - - - +
192B LEU* 4.1 5.8 - - + -
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Residues in contact with LYS 184 (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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202A THR* 4.1 7.1 - - - +
203A VAL 3.7 24.1 + - - -
204A VAL* 4.0 17.9 - - + +
120B LYS* 3.8 10.3 + - - +
180B VAL* 2.9 41.9 + - + +
181B GLN* 4.1 14.4 - - - +
183B LEU* 1.3 75.7 - - - +
185B ARG* 1.3 62.4 + - + +
186B ALA 3.4 0.9 + - - -
187B GLY 4.7 1.0 + - - -
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Residues in contact with ARG 185 (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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181B GLN* 2.9 68.5 + - - +
182B ALA* 3.8 5.2 - - - +
183B LEU 3.2 0.2 - - - -
184B LYS* 1.3 77.8 - - + +
186B ALA* 1.3 60.4 + - - +
187B GLY 3.4 3.5 + - - -
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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