Contacts of the helix formed by residues 186 - 196 (chain B) 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 LYS 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157B PHE* 4.2 17.7 - - + -
182B GLU* 4.1 13.4 + - - +
183B SER* 3.2 43.4 + - - +
185B PHE* 1.3 79.2 - - - +
187B GLU* 1.3 64.0 + - - +
188B SER* 4.1 13.0 - - - +
189B TYR* 2.9 26.0 + - - +
190B TYR* 3.8 5.4 + - - -
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Residues in contact with GLU 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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185B PHE 4.4 7.0 - - - +
186B LYS* 1.3 75.8 - - - +
188B SER* 1.3 61.3 + - - +
190B TYR* 3.1 14.5 + - + +
191B GLN 3.6 1.9 + - - -
219B GLU* 5.4 6.8 - - - +
220B MET* 6.4 1.3 - - - -
223B PHE* 3.0 65.8 - - + -
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Residues in contact with SER 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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157B PHE* 3.3 23.8 - - - -
186B LYS* 4.1 6.3 - - - +
187B GLU* 1.3 76.6 - - - +
189B TYR* 1.3 52.4 + - - +
191B GLN* 3.2 13.3 + - - +
192B LEU* 2.7 41.2 + - - +
223B PHE* 5.2 1.3 - - - -
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Residues in contact with TYR 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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100B ILE* 3.3 25.1 - - - +
156B GLY 3.8 11.7 - - - -
157B PHE* 3.6 27.0 - + + -
160B MET* 3.5 28.7 - - + +
172B THR* 2.9 33.4 + - + +
183B SER 3.8 11.4 - - - +
184B LEU* 3.2 39.3 - - + +
186B LYS 2.9 15.8 + - - +
188B SER* 1.3 81.5 + - - +
190B TYR* 1.3 58.4 + + - +
192B LEU* 3.2 5.2 + - + +
193B MET* 2.9 49.2 + - + +
205B CYS* 4.6 1.3 - - - -
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Residues in contact with TYR 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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184B LEU 4.4 15.2 + - - -
185B PHE* 5.4 4.3 - + - -
186B LYS 4.2 10.3 - - - -
187B GLU* 3.1 14.9 + - + +
189B TYR* 1.3 77.5 - + - +
191B GLN* 1.3 57.9 + - - +
193B MET* 3.4 24.4 + - + +
194B LYS* 3.0 26.5 + - - +
203B LEU* 4.0 12.1 - - + -
205B CYS* 3.1 30.4 - - - +
220B MET* 2.8 36.4 - - + +
223B PHE* 4.1 12.8 - + + -
224B CYS* 3.3 29.6 - - - -
227B LEU* 4.2 7.9 - - + -
228B PHE* 3.8 8.0 - + + -
249B MET* 3.8 13.9 - - + +
251B CYS* 4.6 2.2 - - - -
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Residues in contact with GLN 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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187B GLU 3.6 3.1 + - - +
188B SER* 3.2 17.4 + - - +
190B TYR* 1.3 75.4 - - - +
192B LEU* 1.3 80.6 + - - +
194B LYS* 3.3 9.7 + - + +
195B THR* 3.0 45.4 + - - -
223B PHE* 5.3 2.9 - - + -
227B LEU* 4.0 28.1 - - + +
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Residues in contact with LEU 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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157B PHE* 3.7 56.3 - - + +
160B MET* 3.5 20.7 - - + +
161B LYS* 3.8 32.8 - - + -
188B SER* 2.7 21.4 + - - +
189B TYR* 3.2 7.4 + - - +
191B GLN* 1.3 86.9 - - - +
193B MET* 1.3 57.1 + - - +
195B THR* 3.3 8.2 + - - -
196B ALA* 3.0 27.0 + - - +
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Residues in contact with MET 193 (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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160B MET* 3.8 25.8 - - + -
170B ILE* 3.6 21.1 - - + +
172B THR* 3.6 13.0 - - - -
189B TYR* 2.9 44.2 + - + +
190B TYR* 3.5 39.5 - - + +
192B LEU* 1.3 73.2 - - - +
194B LYS* 1.3 66.6 + - - +
196B ALA* 3.3 2.4 + - - -
197B LEU* 3.0 30.5 + - - +
203B LEU* 3.8 18.4 - - + -
205B CYS* 3.6 16.2 - - - -
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Residues in contact with LYS 194 (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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190B TYR 3.0 8.9 + - - +
191B GLN* 3.3 13.9 + - + +
193B MET* 1.3 76.4 - - - +
195B THR* 1.3 58.9 + - - +
197B LEU* 3.3 5.3 + - - -
226B SER 5.4 0.4 + - - -
227B LEU* 2.8 50.8 + - + +
228B PHE* 3.6 29.7 - - + -
253B LYS* 2.7 50.9 + - + +
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Residues in contact with THR 195 (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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163B ASN 4.1 8.3 - - - +
164B GLN* 3.5 32.2 - - + +
165B ASP* 2.9 21.7 + - - +
191B GLN* 3.0 31.8 + - - -
192B LEU* 3.7 11.2 - - - -
193B MET 3.2 0.2 - - - -
194B LYS* 1.3 77.0 - - - +
196B ALA* 1.3 59.1 + - - +
197B LEU 3.3 4.7 + - - +
253B LYS* 4.5 1.8 + - - +
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Residues in contact with ALA 196 (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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160B MET* 3.6 25.4 - - + -
163B ASN* 3.4 29.5 + - + +
165B ASP 3.8 0.4 - - - -
166B ALA* 2.8 26.0 + - - +
167B PHE* 3.1 11.9 + - + -
170B ILE* 3.8 7.4 - - + -
192B LEU 3.0 16.5 + - - +
193B MET 3.3 5.6 + - - +
195B THR* 1.3 75.6 - - - +
197B LEU* 1.3 58.8 + - - +
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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