Contacts of the helix formed by residues 187 - 196 (chain A) in PDB entry 2O07
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 GLU 187 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A SER* 1.3 68.3 + - - +
189A TYR* 3.1 7.1 - - - +
190A TYR* 3.1 23.4 + - - +
191A GLN 3.5 2.6 + - - -
219A GLU* 4.8 8.1 - - - +
220A MET* 3.6 25.3 - - + +
223A PHE* 3.2 66.0 - - + +
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Residues in contact with SER 188 (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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157A PHE* 3.6 22.4 - - - -
187A GLU* 1.3 78.5 + - - +
189A TYR* 1.3 62.9 + - - +
191A GLN* 3.1 13.3 + - - +
192A LEU* 3.0 28.2 + - - +
223A PHE* 4.7 0.9 - - - -
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Residues in contact with TYR 189 (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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100A ILE* 3.4 23.6 - - + +
156A GLY 3.9 14.4 - - - -
157A PHE* 3.8 37.6 - + + -
160A MET* 3.6 25.1 - - + +
172A THR* 2.7 42.0 + - + +
187A GLU 3.1 4.8 - - - +
188A SER* 1.3 80.6 + - - +
190A TYR* 1.3 67.0 + + + +
192A LEU* 3.1 6.2 + - + +
193A MET* 2.9 55.1 + - + +
205A CYS* 4.6 1.8 - - - -
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Residues in contact with TYR 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLU* 3.1 19.3 + - - +
189A TYR* 1.3 88.0 - + + +
191A GLN* 1.3 55.4 + - - +
193A MET* 3.5 25.8 + - + +
194A LYS* 3.0 26.2 + - - +
203A LEU* 3.9 13.7 - - + -
205A CYS* 3.1 33.6 - - - +
206A GLN 4.7 2.8 + - - -
207A GLY* 5.9 0.2 - - - -
220A MET* 4.2 25.7 - - + +
223A PHE* 4.1 11.0 - - + -
224A CYS* 3.5 26.7 - - - -
227A LEU* 4.1 8.1 - - + -
228A PHE* 3.7 7.9 - + + -
249A MET* 3.7 22.3 - - + +
251A CYS* 4.4 2.2 - - - -
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Residues in contact with GLN 191 (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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187A GLU 3.5 3.0 + - - +
188A SER* 3.1 18.6 + - - +
190A TYR* 1.3 77.9 - - - +
192A LEU* 1.3 80.9 + - - +
194A LYS* 3.2 10.2 + - + +
195A THR* 3.1 39.4 + - - -
223A PHE* 5.6 1.8 - - + -
227A LEU* 3.9 26.8 - - + +
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Residues in contact with LEU 192 (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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157A PHE* 3.6 55.9 - - + +
160A MET* 3.5 20.1 - - + +
161A LYS* 3.9 29.6 - - + -
163A ASN 4.9 0.2 - - - +
188A SER* 3.0 16.7 + - - +
189A TYR* 3.1 7.2 + - - +
191A GLN* 1.3 89.8 - - - +
193A MET* 1.3 55.9 - - - +
195A THR* 3.3 8.2 + - - +
196A ALA* 3.0 27.7 + - - +
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Residues in contact with MET 193 (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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160A MET* 3.8 24.2 - - + -
170A ILE* 3.7 23.5 - - + +
172A THR* 3.7 11.9 - - - -
189A TYR* 2.9 42.3 + - + +
190A TYR* 3.6 32.1 - - + +
192A LEU* 1.3 73.2 - - - +
194A LYS* 1.3 64.3 + - - +
196A ALA* 3.2 1.9 + - - +
197A LEU* 2.9 29.6 + - - +
203A LEU* 3.7 19.3 - - + -
205A CYS* 3.4 27.8 - - - -
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Residues in contact with LYS 194 (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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190A TYR 3.0 15.8 + - - +
191A GLN* 3.2 14.3 + - + +
193A MET* 1.3 76.9 - - - +
195A THR* 1.3 62.1 + - - +
197A LEU* 3.5 2.1 + - - -
226A SER 5.4 0.2 + - - -
227A LEU* 2.7 49.8 + - + +
228A PHE* 3.7 26.8 - - + -
229A PRO* 6.2 1.1 - - - -
253A LYS* 2.8 48.8 + - + +
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Residues in contact with THR 195 (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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163A ASN 4.2 4.9 - - - +
164A GLN* 3.4 35.2 - - + +
165A ASP* 2.9 21.4 + - - +
191A GLN* 3.1 28.5 + - - -
192A LEU* 3.6 11.7 - - - -
193A MET 3.3 0.2 - - - -
194A LYS* 1.3 75.8 - - - +
196A ALA* 1.3 59.5 + - - +
197A LEU 3.4 5.0 + - - +
253A LYS* 4.7 1.2 + - - +
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Residues in contact with ALA 196 (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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160A MET* 3.7 24.5 - - - +
163A ASN* 3.5 29.3 + - + +
165A ASP 3.7 1.8 - - - +
166A ALA* 2.8 26.5 + - - +
167A PHE* 3.1 11.2 + - + -
170A ILE* 3.9 7.0 - - + -
192A LEU 3.0 16.6 + - - +
193A MET 3.2 4.5 + - - +
195A THR* 1.3 76.0 - - - +
197A LEU* 1.3 57.5 + - - +
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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