Contacts of the helix formed by residues 213 - 226 (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 HIS 213 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B LEU* 3.1 38.9 + - + +
28B TRP* 4.3 8.9 - + - -
208B GLU* 3.3 38.7 - - + +
209B CYS* 2.7 39.7 + - + +
212B LEU* 1.3 102.6 - - + +
214B LEU* 1.3 64.5 + - - +
215B ASP* 3.2 4.7 - - - -
216B LEU* 3.1 17.1 + - + +
217B ILE* 3.0 22.6 + - - +
242B PRO* 5.7 1.3 - - + -
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Residues in contact with LEU 214 (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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209B CYS 4.1 1.2 + - - -
210B GLN* 3.8 24.2 - - + +
212B LEU 3.7 2.0 - - - -
213B HIS* 1.3 76.6 - - - +
215B ASP* 1.3 57.5 + - - +
217B ILE* 3.7 8.4 - - + +
218B LYS* 2.9 33.4 + - + +
293B PHE* 3.8 30.1 - - + +
294B ALA* 4.1 20.0 - - + -
297B ALA* 3.8 24.9 - - + -
298B LEU* 4.3 17.9 - - + -
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Residues in contact with ASP 215 (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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213B HIS* 4.9 1.6 - - - -
214B LEU* 1.3 78.8 - - - +
216B LEU* 1.3 57.0 + - - +
218B LYS* 3.4 5.1 + - - +
219B GLU* 3.0 38.9 + - + +
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Residues in contact with LEU 216 (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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177B PRO* 4.7 17.7 - - + -
185B PHE* 5.0 10.8 - - + +
208B GLU* 3.7 33.2 - - + -
213B HIS* 3.1 17.9 + - + +
215B ASP* 1.3 78.6 - - - +
217B ILE* 1.3 57.8 + - + +
219B GLU* 3.3 19.4 + - + +
220B MET* 2.8 58.0 + - + +
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Residues in contact with ILE 217 (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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207B GLY 3.4 20.9 - - - +
208B GLU* 4.0 2.2 - - + +
209B CYS 3.6 7.2 - - - +
210B GLN* 3.6 25.4 - - + +
213B HIS* 3.0 23.8 + - + +
214B LEU* 3.7 7.9 - - + +
215B ASP 3.3 0.2 - - - -
216B LEU* 1.3 76.7 - - + +
218B LYS* 1.3 58.8 + - - +
220B MET* 3.9 6.1 - - - +
221B ARG* 3.0 30.6 + - + +
233B TYR* 3.6 46.7 - - + +
249B MET* 5.0 1.5 - - + +
298B LEU* 3.8 24.0 - - + -
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Residues in contact with LYS 218 (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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214B LEU* 2.9 18.1 + - + +
215B ASP* 3.8 5.2 - - - +
217B ILE* 1.3 77.2 - - - +
219B GLU* 1.3 56.7 + - + +
221B ARG* 3.5 4.2 + - + +
222B GLN* 3.1 60.4 + - + +
297B ALA* 3.4 36.6 + - + +
298B LEU* 3.8 15.0 - - + +
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Residues in contact with GLU 219 (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* 5.4 6.1 - - - +
215B ASP* 3.0 23.9 + - + +
216B LEU* 3.5 23.1 - - + +
218B LYS* 1.3 73.3 - - - +
220B MET* 1.3 67.8 + - + +
222B GLN* 3.3 8.7 + - - +
223B PHE* 3.0 25.1 + - - +
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Residues in contact with MET 220 (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* 4.6 15.7 - - + -
187B GLU* 6.4 1.3 - - - -
190B TYR* 2.8 42.0 - - + +
206B GLN 4.5 11.4 - - - +
207B GLY* 4.6 15.3 - - - +
216B LEU* 2.8 50.7 + - + +
217B ILE* 3.9 5.4 - - - +
219B GLU* 1.3 72.5 - - + +
221B ARG* 1.3 57.3 - - - +
223B PHE* 3.4 5.4 + - - +
224B CYS* 2.8 34.9 + - - -
249B MET* 3.5 24.5 - - + -
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Residues in contact with ARG 221 (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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217B ILE* 3.0 18.4 + - + +
218B LYS* 3.7 5.8 - - - +
219B GLU 3.2 0.2 - - - -
220B MET* 1.3 77.6 - - - +
222B GLN* 1.3 58.0 + - + +
224B CYS* 3.5 1.2 + - - +
225B GLN* 2.8 58.2 + - - +
231B VAL* 4.1 20.3 + - + +
232B ALA* 3.7 9.9 - - - +
233B TYR* 3.5 34.9 - - + +
249B MET* 3.5 12.1 - - + +
260B GLN* 6.1 0.4 - - - +
290B LEU* 6.0 0.4 - - - +
298B LEU* 3.3 46.7 + - - +
299B ASN* 3.4 25.7 + - - +
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Residues in contact with GLN 222 (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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218B LYS* 3.1 57.8 + - + +
219B GLU* 3.8 6.9 - - - +
221B ARG* 1.3 73.2 - - + +
223B PHE* 1.3 67.1 + - - +
225B GLN* 3.3 23.4 + - - +
226B SER* 3.4 12.5 + - - -
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Residues in contact with PHE 223 (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* 3.0 61.7 - - + -
188B SER* 5.2 1.3 - - - -
190B TYR* 4.1 9.2 - + + -
191B GLN* 5.3 3.1 - - + -
219B GLU 3.0 17.5 + - - +
220B MET* 3.7 5.2 - - - +
222B GLN* 1.3 75.6 - - - +
224B CYS* 1.3 67.0 + - - +
226B SER* 3.1 23.0 + - - -
227B LEU* 3.4 37.1 + - + +
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Residues in contact with CYS 224 (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* 3.3 47.8 - - - -
220B MET* 2.8 24.7 + - - +
223B PHE* 1.3 76.9 - - - +
225B GLN* 1.3 58.8 + - - +
227B LEU* 3.0 4.0 + - - +
228B PHE* 2.9 35.5 + - + -
231B VAL* 3.5 14.5 - - + +
249B MET* 3.8 7.0 - - + -
251B CYS* 3.6 24.7 - - - -
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Residues in contact with GLN 225 (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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221B ARG* 2.8 57.1 + - - +
222B GLN* 3.6 19.1 - - - +
223B PHE 3.3 0.4 - - - -
224B CYS* 1.3 75.6 - - - +
226B SER* 1.3 58.9 + - - +
227B LEU 3.2 0.2 - - - -
228B PHE 3.2 15.0 - - - +
231B VAL* 3.8 21.2 + - + +
298B LEU 5.0 2.8 + - - -
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Residues in contact with SER 226 (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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194B LYS* 5.4 0.3 + - - -
222B GLN 3.4 7.3 + - - -
223B PHE* 3.1 17.5 + - - -
225B GLN* 1.3 78.0 - - - +
227B LEU* 1.3 61.3 + - - +
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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