Contacts of the helix formed by residues 166 - 180 (chain A) in PDB entry 2OCA
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A VAL* 3.5 5.5 - - - +
165A PRO* 1.3 88.8 - - + +
167A THR* 1.3 62.6 + - - +
168A ALA* 3.5 10.1 + - - +
169A LEU* 3.3 28.6 + - + +
170A THR* 3.0 21.8 + - - -
211A THR* 3.5 6.1 - - - -
213A GLN* 5.4 0.7 - - - -
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Residues in contact with THR 167 (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 THR* 1.3 72.9 - - - +
168A ALA* 1.3 67.8 + - - +
170A THR* 3.0 25.3 - - - +
171A THR* 3.1 11.4 + - - -
193A GLY* 4.0 16.6 + - - +
194A GLY* 3.8 26.4 - - - +
211A THR* 4.4 12.3 - - + +
213A GLN* 6.0 0.2 - - - +
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Residues in contact with ALA 168 (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 THR* 3.2 9.5 + - - +
167A THR* 1.3 83.5 + - - +
169A LEU* 1.3 58.8 + - + +
171A THR* 3.1 10.1 + - - -
172A GLN* 2.9 26.6 + - - +
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Residues in contact with LEU 169 (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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164A VAL* 4.0 13.8 - - + +
165A PRO* 3.6 33.0 - - + -
166A THR* 3.3 23.8 + - + +
167A THR 3.2 0.2 - - - -
168A ALA* 1.3 77.1 - - + +
170A THR* 1.3 66.4 + - - +
172A GLN* 3.7 15.6 - - + +
173A MET* 2.8 27.4 + - - +
232A ASP* 6.0 1.3 - - - +
233A GLU* 5.5 4.7 - - + -
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Residues in contact with THR 170 (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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164A VAL* 3.3 17.1 - - - +
166A THR 3.0 16.0 + - - -
167A THR* 3.0 19.7 + - - -
169A LEU* 1.3 79.1 - - - +
171A THR* 1.3 59.4 + - - +
173A MET* 3.5 3.3 + - - +
174A ALA* 3.3 18.4 + - - +
190A LYS* 4.0 19.0 - - + +
191A ILE 4.5 2.9 + - - +
194A GLY* 4.2 12.1 - - - -
209A VAL* 3.7 36.9 - - + +
210A GLY* 4.2 4.1 - - - -
211A THR* 3.8 8.0 - - - +
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Residues in contact with THR 171 (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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167A THR 3.1 8.8 + - - -
168A ALA* 3.1 11.1 + - - -
170A THR* 1.3 77.1 - - - +
172A GLN* 1.3 66.3 - - - +
174A ALA* 3.2 2.3 + - - +
175A ASP* 2.9 42.0 + - - +
190A LYS* 4.2 14.5 - - + +
194A GLY* 3.9 16.1 + - - -
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Residues in contact with GLN 172 (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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168A ALA 2.9 16.7 + - - +
169A LEU* 3.2 19.7 + - + +
171A THR* 1.3 76.1 - - - +
173A MET* 1.3 57.4 + - - +
175A ASP* 3.3 9.3 + - - +
176A ASP* 2.8 65.3 + - - +
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Residues in contact with MET 173 (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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142A SER* 4.6 11.4 - - - -
145A GLN* 2.9 44.9 - - - +
162A ILE* 4.0 13.9 - - + -
164A VAL* 3.7 22.0 - - + -
169A LEU 2.8 18.0 + - - +
170A THR 3.6 5.4 - - - +
172A GLN* 1.3 77.7 - - - +
174A ALA* 1.3 63.3 + - - +
176A ASP* 3.3 4.6 + - - +
177A PHE* 3.0 58.8 + - + -
209A VAL* 4.4 15.7 - - + -
232A ASP* 4.1 7.2 - - - +
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Residues in contact with ALA 174 (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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170A THR 3.3 10.3 + - - +
171A THR 3.2 8.1 + - - +
173A MET* 1.3 79.3 - - - +
175A ASP* 1.3 65.3 + - - +
177A PHE* 3.0 13.6 + - - +
178A VAL* 3.1 16.6 + - - +
185A HIS* 4.1 15.7 - - + +
188A ILE* 3.9 29.7 - - + +
190A LYS* 3.9 21.1 - - + +
209A VAL* 5.4 1.5 - - + +
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Residues in contact with ASP 175 (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 THR* 2.9 35.2 + - - +
172A GLN* 3.8 11.4 - - - +
174A ALA* 1.3 74.7 - - - +
176A ASP* 1.3 58.7 + - - +
178A VAL* 3.2 7.0 - - - +
179A ASP* 3.0 26.3 + - - +
185A HIS* 3.2 27.0 + - - -
190A LYS* 5.9 0.7 - - - +
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Residues in contact with ASP 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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142A SER* 3.2 32.8 + - - +
172A GLN* 2.8 49.4 + - - +
173A MET* 3.7 5.0 + - - +
175A ASP* 1.3 74.3 - - - +
177A PHE* 1.3 67.3 + - - +
179A ASP* 3.1 10.4 + - - +
180A TYR* 3.0 36.9 + - + -
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Residues in contact with PHE 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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142A SER 3.7 9.6 - - - -
145A GLN* 3.8 4.5 - - + -
146A ALA* 3.4 43.3 - - + -
149A ALA* 4.2 4.9 - - + -
162A ILE* 3.6 33.0 - - + -
173A MET* 3.0 35.1 + - + +
174A ALA 3.0 9.8 + - - +
176A ASP* 1.3 81.0 - - + +
178A VAL* 1.3 60.8 + - - +
180A TYR* 3.7 7.5 + + - +
181A ARG 3.6 1.4 + - - -
182A LEU* 3.5 21.3 + - - +
183A PHE* 3.5 33.6 + + + -
188A ILE* 3.4 25.4 - - + -
207A VAL* 4.5 6.5 - - + -
209A VAL* 6.0 1.3 - - + -
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Residues in contact with VAL 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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174A ALA 3.1 15.1 + - - +
175A ASP* 3.2 11.4 - - - +
177A PHE* 1.3 74.8 - - - +
179A ASP* 1.3 64.5 + - - +
181A ARG* 2.6 30.3 + - - +
183A PHE 3.2 14.9 - - - +
184A SER* 4.1 2.5 - - - -
185A HIS* 3.5 55.4 - - + +
188A ILE* 4.4 3.6 - - + -
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Residues in contact with ASP 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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106A TYR* 3.6 10.7 - - - +
107A SER* 3.5 12.6 + - - -
108A GLY* 3.4 31.9 + - - +
175A ASP 3.0 11.1 + - - +
176A ASP* 3.1 15.6 + - - +
178A VAL* 1.3 86.7 - - - +
180A TYR* 1.3 67.1 + - + +
181A ARG* 2.9 12.8 + - - +
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Residues in contact with TYR 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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104A GLU 3.6 0.2 - - - +
105A ILE* 3.5 19.9 - - + -
106A TYR 2.9 36.9 + - - -
107A SER* 5.9 1.3 - - - -
112A ILE* 4.7 10.3 - - + -
140A GLY* 5.3 2.4 + - - -
142A SER* 3.2 29.1 + - - -
143A LEU* 3.2 57.0 + - + +
146A ALA* 4.0 13.0 - - + -
176A ASP* 3.0 34.8 + - + +
177A PHE* 3.9 7.0 - - - +
178A VAL 3.2 0.2 - - - -
179A ASP* 1.3 79.5 - - - +
181A ARG* 1.3 67.8 + - - +
182A LEU* 4.2 10.7 - - + +
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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