Contacts of the helix formed by residues 175 - 185 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLY* 4.2 0.4 - - - -
134A ARG* 3.7 8.1 - - + +
135A GLU* 3.3 31.0 - - + +
140A ILE* 4.6 0.4 - - - -
173A GLN 3.8 0.6 + - - +
174A ALA* 1.3 77.0 - - - +
176A HIS* 1.3 66.4 + - - +
177A ASP* 3.8 5.2 + - - +
178A GLN* 2.8 50.2 + - - +
179A ALA* 2.9 21.0 + - - +
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Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE* 3.5 36.9 - - + +
131A LYS* 4.0 3.9 - - - -
132A GLY 3.1 27.1 + - - +
133A GLY* 3.9 1.8 - - - -
135A GLU* 3.1 23.7 + - - +
140A ILE* 4.3 4.2 - - - +
175A THR* 1.3 74.9 - - - +
177A ASP* 1.3 72.1 + - - +
179A ALA* 3.1 2.9 + - - +
180A VAL* 2.9 37.4 + - + +
200B VAL* 3.6 30.8 + - + +
202B THR* 2.6 31.9 + - - -
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Residues in contact with ASP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 4.6 1.3 + - - -
175A THR* 3.3 5.7 + - - +
176A HIS* 1.3 91.6 - - - +
178A GLN* 1.3 57.9 + - + +
180A VAL* 3.4 8.2 + - - +
181A GLN* 3.0 36.7 + - + +
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 4.8 0.4 - - - -
173A GLN 4.2 2.9 - - - +
174A ALA* 3.5 14.7 - - + +
175A THR* 2.8 48.0 + - - +
177A ASP* 1.3 74.1 - - + +
179A ALA* 1.3 64.3 + - - +
181A GLN* 3.5 6.6 + - - +
182A ALA* 3.0 25.1 + - - +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE* 3.9 10.1 - - + -
140A ILE* 3.4 39.3 - - + -
171A LEU* 3.9 21.1 - - + -
174A ALA* 4.0 3.9 - - + +
175A THR 2.9 7.3 + - - +
176A HIS 3.5 5.2 - - - +
178A GLN* 1.3 73.6 - - - +
180A VAL* 1.3 68.8 + - - +
182A ALA* 3.2 1.4 + - - +
183A LEU* 3.1 30.4 + - - +
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ILE* 3.8 13.7 - - + -
176A HIS* 2.9 43.4 + - + +
177A ASP* 3.7 11.7 - - - +
178A GLN 3.3 0.4 - - - -
179A ALA* 1.3 75.2 - - - +
181A GLN* 1.3 65.9 + - - +
183A LEU* 3.4 1.6 + - - +
184A LYS* 2.9 58.3 + - + +
202B THR* 4.0 19.5 - - + -
204B VAL* 3.9 17.2 - - + +
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Residues in contact with GLN 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A ASP* 3.0 22.4 + - + +
178A GLN* 3.9 6.5 - - - +
179A ALA 3.2 0.2 - - - -
180A VAL* 1.3 87.1 - - - +
182A ALA* 1.3 58.2 + - - +
184A LYS* 3.4 12.5 + - - +
185A ARG* 3.0 48.7 + - + +
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Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A VAL* 4.1 7.4 - - + +
169A THR* 4.2 17.0 - - + -
171A LEU* 3.7 22.0 - - + -
178A GLN 3.0 17.1 + - - +
179A ALA 3.2 4.5 + - - +
181A GLN* 1.3 77.0 - - - +
183A LEU* 1.3 63.0 + - - +
185A ARG* 3.4 3.0 + - - -
186A ALA* 3.1 25.6 + - - +
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LYS* 3.0 24.8 + - - -
126A LEU* 3.7 27.8 - - + +
130A ILE* 4.0 23.3 - - + -
140A ILE* 5.3 0.4 - - + -
163A ILE* 4.3 18.4 - - + -
166A VAL* 3.9 13.9 - - + -
171A LEU* 4.3 14.8 - - + -
179A ALA 3.1 20.3 + - - +
180A VAL 3.9 2.0 - - - +
182A ALA* 1.3 73.8 - - - +
184A LYS* 1.3 63.0 + - - +
185A ARG 3.3 0.7 + - - -
186A ALA* 3.5 10.1 + - - +
190A VAL* 4.9 0.3 - - - +
192A LEU* 3.8 24.2 - - + -
204B VAL* 4.2 20.6 - - + -
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LYS* 3.5 14.0 + - - +
180A VAL* 2.9 42.7 + - + +
181A GLN* 3.9 16.5 - - - +
183A LEU* 1.3 75.9 - - - +
185A ARG* 1.3 68.3 + - + +
186A ALA 3.5 0.2 - - - -
187A GLY 4.8 0.3 + - - -
202B THR* 5.7 2.0 - - - +
203B VAL 4.3 16.1 + - - -
204B VAL* 4.6 16.6 - - + +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A GLN* 3.0 34.0 + - + +
182A ALA* 3.7 3.4 - - - +
183A LEU 3.2 0.2 - - - -
184A LYS* 1.3 83.7 + - + +
186A ALA* 1.3 61.6 + - - +
187A GLY* 3.1 7.2 + - - -
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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