Contacts of the helix formed by residues 208 - 221 (chain B) in PDB entry 2OB1
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 208 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177B ASN* 5.0 1.0 - - - +
206B TYR 5.4 1.3 + - - -
207B MET* 1.3 74.3 - - - +
209B ASN* 1.3 67.6 - - - +
210B ASN* 3.2 2.2 - - + +
211B GLU* 3.1 33.2 + - + +
212B SER* 3.1 12.6 + - - -
258B GLU* 3.1 28.0 + - + -
260B PRO* 3.6 20.7 - - + +
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Residues in contact with ASN 209 (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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208B HIS* 1.3 74.9 - - - +
210B ASN* 1.3 65.4 + - - +
212B SER* 3.4 8.4 + - - -
213B GLN* 2.8 42.3 + - - +
260B PRO* 5.1 0.2 - - - +
261B THR* 3.6 16.9 - - + +
264B THR* 5.7 3.4 - - + -
265B TYR* 2.6 42.2 + - - -
274B ARG* 4.6 1.4 - - - +
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Residues in contact with ASN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B HIS* 3.2 2.4 - - + +
209B ASN* 1.3 86.2 + - - +
211B GLU* 1.3 75.7 + - - +
213B GLN* 3.9 3.8 - - - +
214B LEU* 2.9 33.1 + - - +
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Residues in contact with GLU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU 4.9 0.7 - - - +
177B ASN* 3.3 51.8 - - + +
179B ILE* 4.7 3.8 - - - +
207B MET* 3.5 7.5 - - + +
208B HIS* 3.1 28.6 + - + +
210B ASN* 1.3 88.2 - - - +
212B SER* 1.3 60.1 + - - +
214B LEU* 4.1 5.4 - - - +
215B LEU* 2.9 30.3 + - - +
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Residues in contact with SER 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 4.0 17.7 - - - -
207B MET* 3.6 19.8 + - - +
208B HIS 3.1 15.4 + - - -
209B ASN* 3.2 14.0 + - - -
211B GLU* 1.3 80.0 - - - +
213B GLN* 1.3 55.4 + - - -
215B LEU* 3.3 3.8 + - - +
216B ILE* 2.9 35.8 + - - +
261B THR* 5.0 0.2 - - - +
274B ARG* 3.2 28.7 + - - -
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Residues in contact with GLN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASN* 2.8 31.3 + - - +
210B ASN* 4.0 4.3 - - - +
212B SER* 1.3 74.3 + - - +
214B LEU* 1.3 57.0 + - - +
216B ILE* 3.4 7.6 + - - +
217B ASN* 2.9 62.8 + - - +
265B TYR* 4.2 8.0 + - - -
274B ARG* 2.8 50.1 + - - +
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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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179B ILE* 3.7 27.6 - - + -
210B ASN 2.9 19.0 + - - +
211B GLU* 4.1 5.6 - - - +
213B GLN* 1.3 76.7 - - - +
215B LEU* 1.3 57.8 + - - +
217B ASN* 4.4 10.1 - - + +
218B THR* 2.7 51.5 + - - +
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Residues in contact with LEU 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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104B LEU* 4.3 9.6 - - + -
176B LEU* 3.8 23.1 - - + +
179B ILE* 3.4 23.5 - - + +
182B THR* 3.9 13.0 - - + -
203B LEU* 4.2 12.6 - - + -
204B LEU* 4.1 19.1 - - + -
207B MET* 3.9 21.8 - - + -
211B GLU 2.9 18.3 + - - +
212B SER 3.5 4.9 - - - +
214B LEU* 1.3 73.6 - - - +
216B ILE* 1.3 66.0 + - - +
219B ILE* 2.9 53.4 + - + +
228B TRP* 4.1 2.2 - - + -
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Residues in contact with ILE 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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204B LEU* 4.2 8.1 - - + -
212B SER 2.9 25.7 + - - +
213B GLN* 3.7 9.4 - - - +
215B LEU* 1.3 73.1 - - - +
217B ASN* 1.3 65.3 + - - +
220B MET* 3.0 35.8 + - + +
228B TRP* 3.5 16.1 - - + -
274B ARG* 3.6 43.5 - - + +
275B TRP* 3.5 57.2 - - + +
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Residues in contact with ASN 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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213B GLN* 2.9 48.7 + - - +
214B LEU* 3.8 11.5 - - + +
216B ILE* 1.3 79.9 - - - +
218B THR* 1.3 64.2 + - - +
220B MET* 4.1 8.6 - - - +
221B SER* 3.0 31.7 + - - +
274B ARG 4.7 0.7 - - - +
277B ALA* 5.3 6.4 - - - +
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Residues in contact with THR 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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179B ILE* 3.7 15.5 - - + +
183B THR* 3.4 33.7 - - + -
214B LEU* 2.7 42.0 + - - +
217B ASN* 1.3 74.5 - - - +
219B ILE* 1.3 65.1 + - + +
221B SER* 3.3 6.1 + - - -
222B LYS* 3.2 32.9 + - + +
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Residues in contact with ILE 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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102B VAL* 5.7 2.2 - - + -
104B LEU* 3.8 29.8 - - + -
179B ILE* 5.2 0.7 - - + -
182B THR* 4.3 4.7 - - + -
183B THR* 6.2 0.2 - - + -
186B LEU* 3.7 25.1 - - + -
198B VAL* 3.7 30.3 - - + -
215B LEU* 2.9 44.4 + - + +
218B THR* 1.3 76.6 - - + +
220B MET* 1.3 67.1 + - - +
222B LYS* 3.0 15.8 + - + +
223B PHE* 3.3 27.1 - - + -
228B TRP* 3.7 7.9 - - + -
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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
----------------------------------------------------------
216B ILE* 3.0 41.2 + - + +
217B ASN* 4.1 7.6 - - - +
219B ILE* 1.3 77.5 - - - +
221B SER* 1.3 59.3 + - - +
222B LYS 3.3 0.7 + - - -
223B PHE 3.2 23.0 + - - +
228B TRP* 3.8 10.3 - - + -
274B ARG 5.0 0.4 - - - +
275B TRP* 4.0 19.3 - - + -
277B ALA* 4.4 12.8 - - + -
278B ALA* 3.9 31.4 - - - +
328B TRP* 3.4 55.0 + - + -
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Residues in contact with SER 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ARG* 3.0 22.4 + - - -
217B ASN* 3.0 20.5 + - - +
218B THR* 3.7 6.5 - - - -
219B ILE 3.2 0.4 - - - -
220B MET* 1.3 75.8 - - - +
222B LYS* 1.3 57.9 + - - +
223B PHE 3.4 1.3 - - - -
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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