Contacts of the helix formed by residues 213 - 222 (chain B) in PDB entry 1OPL
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 213 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B LEU* 4.1 7.7 - - - +
211B PHE* 3.8 5.5 - - - +
212B ASN* 1.3 86.6 - - + +
214B LEU* 1.3 65.4 + - - +
215B ALA* 3.6 7.8 + - - +
216B GLU* 2.9 40.9 + - - +
217B LEU* 3.2 17.3 + - - +
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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
----------------------------------------------------------
141B LEU* 4.0 26.7 - - + +
146B TRP* 3.8 20.2 - - + -
147B TYR* 3.9 25.1 - - + -
170B VAL* 4.0 7.9 - - + -
180B ARG* 4.2 10.5 - - - +
195B ILE* 3.8 26.5 - - + -
203B LEU* 3.7 24.3 - - + +
213B THR* 1.3 73.6 - - - +
215B ALA* 1.3 65.0 + - - +
217B LEU* 3.1 9.2 + - + +
218B VAL* 3.0 34.6 + - + +
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Residues in contact with ALA 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LEU* 5.4 1.4 - - + +
144B HIS* 3.9 31.4 + - + +
146B TRP* 3.9 14.5 - - + -
213B THR* 3.3 7.9 + - - +
214B LEU* 1.3 80.3 - - - +
216B GLU* 1.3 58.1 + - + +
218B VAL* 3.3 1.0 + - - +
219B HIS* 2.9 47.1 + - + -
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Residues in contact with GLU 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B PHE* 3.8 21.5 - - + -
212B ASN* 3.4 15.2 + - - +
213B THR* 2.9 48.9 + - - +
214B LEU 3.2 0.2 - - - -
215B ALA* 1.3 76.8 - - + +
217B LEU* 1.3 58.5 + - - +
219B HIS* 3.4 9.8 + - - +
220B HIS* 2.9 29.1 + - - +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 5.1 4.7 - - + -
195B ILE* 3.8 39.5 - - + -
203B LEU* 4.0 12.3 - - + +
204B TYR* 4.0 21.8 - - - +
205B VAL* 4.2 6.7 - - + +
209B SER 4.3 0.7 - - - +
211B PHE* 3.4 29.6 - - + -
213B THR 3.2 11.7 + - - +
214B LEU* 3.1 13.8 + - + +
216B GLU* 1.3 78.7 - - - +
218B VAL* 1.3 62.1 + - + +
220B HIS* 3.2 1.6 + - - +
221B HIS* 3.1 58.1 + - + +
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Residues in contact with VAL 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B TRP* 3.7 48.9 - - + +
168B PHE* 3.9 19.3 - - + -
170B VAL* 4.0 14.6 - - + -
182B ILE* 5.5 3.8 - - + -
214B LEU* 3.0 24.6 + - + +
215B ALA 3.7 4.0 - - - +
217B LEU* 1.3 76.1 - - + +
219B HIS* 1.3 63.1 + - + +
221B HIS* 3.2 2.9 + - - +
222B SER* 2.8 41.4 + - - +
232B LEU* 4.1 12.9 - - + +
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Residues in contact with HIS 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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144B HIS* 5.5 4.9 + + - -
146B TRP* 4.7 10.9 + - - -
215B ALA* 2.9 38.0 + - + +
216B GLU* 3.7 8.3 - - - +
218B VAL* 1.3 85.2 - - + +
220B HIS* 1.3 65.8 + - - +
222B SER* 3.3 18.9 + - - -
223B THR* 3.6 13.0 + - - +
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Residues in contact with HIS 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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209B SER* 3.8 6.3 + - - -
211B PHE* 3.2 39.1 - + + -
216B GLU 2.9 13.5 + - - +
217B LEU 3.5 3.4 - - - +
218B VAL 3.2 0.2 - - - -
219B HIS* 1.3 76.8 - - - +
221B HIS* 1.3 77.4 + + - +
223B THR* 3.0 28.4 + - - -
224B VAL* 3.3 25.7 + - + +
226B ASP* 2.8 33.5 + - + +
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Residues in contact with HIS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 5.4 1.6 - - + -
205B VAL* 4.3 18.4 + - + +
206B SER* 4.9 3.4 + - - -
209B SER* 5.1 2.2 - - - -
211B PHE* 4.9 0.6 - - - -
217B LEU* 3.1 48.2 + - + +
218B VAL 3.2 0.6 + - - -
220B HIS* 1.3 82.5 - + - +
222B SER* 1.3 60.8 + - - +
223B THR 3.2 0.7 - - - -
224B VAL 3.3 10.6 + - - +
225B ALA* 2.9 18.5 + - - -
226B ASP* 3.3 35.9 + - + -
228B LEU* 3.7 18.0 - - + +
230B THR 4.8 0.2 - - - +
231B THR* 3.5 8.8 - - - -
232B LEU* 3.0 43.0 + - + +
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Residues in contact with SER 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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168B PHE* 4.7 1.9 - - - -
218B VAL* 2.8 32.3 + - - +
219B HIS* 3.4 14.8 - - - -
220B HIS 3.1 0.6 - - - -
221B HIS* 1.3 78.3 - - - +
223B THR* 1.3 62.7 + - - +
231B THR* 4.1 0.9 - - - -
232B LEU* 3.0 24.1 + - - +
233B HIS* 2.9 30.6 + - - -
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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