Contacts of the helix formed by residues 182 - 192 (chain B) in PDB entry 2V1C
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 ASP 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A PRO* 6.1 0.8 - - + +
174A VAL* 3.8 24.6 - - - +
180B TYR 3.9 2.6 + - - -
181B THR* 1.3 78.5 - - - +
183B GLU* 1.3 80.8 + - - +
184B VAL* 2.7 42.1 + - - +
185B THR* 3.2 10.2 + - - +
186B LEU* 3.1 19.4 + - - +
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Residues in contact with GLU 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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96A ARG 4.8 13.0 - - - +
97A SER* 4.3 11.8 + - - +
181B THR 4.1 5.2 - - - +
182B ASP* 1.3 91.9 + - - +
184B VAL* 1.3 67.1 + - + +
186B LEU* 3.2 10.8 + - - +
187B GLY* 3.0 20.1 + - - -
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Residues in contact with VAL 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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174A VAL* 2.9 20.4 - - + -
182B ASP* 2.7 17.6 + - - +
183B GLU* 1.3 74.7 - - + +
185B THR* 1.3 64.1 + - - +
187B GLY* 3.6 2.4 + - - +
188B ARG* 3.1 44.2 + - + +
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Residues in contact with THR 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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172A VAL 4.4 0.4 - - - +
173A PRO* 3.8 2.0 - - + -
174A VAL* 1.7 80.1 + - + +
171B GLY* 3.6 27.1 - - - +
172B VAL* 3.8 4.3 - - + +
181B THR* 3.4 22.7 - - + -
182B ASP* 3.2 11.8 + - - +
183B GLU 3.1 0.6 - - - -
184B VAL* 1.3 72.5 - - - +
186B LEU* 1.3 51.3 + - - +
188B ARG* 2.7 24.8 + - - +
189B ALA 2.7 15.2 + - - -
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Residues in contact with LEU 186 (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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93A ALA* 3.8 19.1 - - + +
94A LEU* 3.9 16.4 - - + -
97A SER* 3.4 25.4 - - - +
99A GLU* 4.0 0.2 - - - -
172B VAL* 4.0 13.0 - - + -
178B LEU* 3.7 43.7 - - + +
181B THR* 4.2 13.9 - - + +
182B ASP 3.1 9.1 + - - +
183B GLU* 3.5 7.9 - - - +
185B THR* 1.3 79.6 - - - +
187B GLY* 1.3 58.0 + - - +
189B ALA* 3.1 6.2 + - + +
190B LEU* 2.8 33.1 + - - +
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Residues in contact with GLY 187 (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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97A SER* 4.2 2.6 + - - -
99A GLU* 2.2 45.4 - - - +
183B GLU 3.0 14.9 + - - -
184B VAL* 4.0 3.6 - - - -
185B THR 3.2 0.2 - - - -
186B LEU* 1.3 75.0 - - - +
188B ARG* 1.3 57.9 - - - +
191B THR* 3.0 27.7 + - - +
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Residues in contact with ARG 188 (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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174A VAL* 4.8 1.1 - - + -
194A GLN* 5.3 4.6 + - - +
148B ASP* 4.3 15.0 + - - -
170B TYR* 3.7 61.0 - - + +
184B VAL* 3.1 29.4 + - + +
185B THR* 2.7 16.8 + - - +
187B GLY* 1.3 70.3 - - - +
189B ALA* 1.3 59.5 + - - +
190B LEU 3.0 2.0 - - - -
191B THR* 3.5 7.9 + - - -
192B GLY* 2.9 28.9 + - - -
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Residues in contact with ALA 189 (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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168A ILE* 4.8 5.1 - - + +
169A ALA* 3.5 33.4 + - + +
170B TYR 4.4 0.8 + - - -
171B GLY* 4.0 4.5 - - - -
172B VAL* 3.5 42.0 - - + +
185B THR 2.7 13.0 + - - +
186B LEU* 3.7 8.3 - - + +
188B ARG* 1.3 73.3 - - - +
190B LEU* 1.3 60.0 + - - +
192B GLY 4.0 0.2 - - - -
193B ARG* 3.5 14.7 + - - +
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Residues in contact with LEU 190 (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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94A LEU* 6.0 2.5 - - + +
97A SER* 5.5 4.5 - - - +
99A GLU* 3.1 48.2 - - + +
100A TYR* 4.1 14.6 - - + -
138A ILE* 5.1 13.9 - - + -
168A ILE* 6.2 6.7 - - + -
186B LEU 2.8 17.2 + - - +
189B ALA* 1.3 76.2 - - - +
191B THR* 1.3 61.6 + - + +
192B GLY 3.0 0.9 - - - -
193B ARG* 2.8 62.2 + - + +
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Residues in contact with THR 191 (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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99A GLU* 4.1 15.0 - - - +
194A GLN* 5.3 0.7 + - - -
187B GLY 3.0 19.3 + - - +
188B ARG* 3.5 11.3 + - - +
190B LEU* 1.3 76.5 - - + +
192B GLY* 1.3 60.2 + - - +
193B ARG* 3.2 12.6 + - - +
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Residues in contact with GLY 192 (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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169A ALA* 4.2 10.1 - - - +
192A GLY 5.8 0.2 - - - +
194A GLN* 3.8 29.7 - - - +
170B TYR 5.9 0.4 - - - -
188B ARG 2.9 17.6 + - - -
189B ALA 3.9 4.9 - - - -
191B THR* 1.3 79.0 + - - +
193B ARG* 1.3 65.0 + - - +
194B GLN* 3.5 5.9 + - - +
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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