Contacts of the helix formed by residues 215 - 227 (chain B) in PDB entry 2OT7
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 215 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B ALA* 6.2 1.1 - - + -
211B VAL* 4.0 10.7 - - + +
212B PRO* 2.8 27.5 + - + +
214B GLU* 1.3 101.0 + - + +
216B GLY* 1.3 63.0 + - - +
217B LYS 3.4 2.7 - - - -
218B ARG* 3.1 55.5 + - - +
219B LEU 3.4 3.8 + - - -
255B ILE* 4.8 0.3 - - - +
256B PRO* 3.7 35.0 - - + +
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Residues in contact with GLY 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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211B VAL* 4.3 7.0 - - - -
212B PRO 3.3 6.8 + - - -
213B PRO 3.2 8.9 + - - -
215B HIS* 1.3 74.5 - - - +
217B LYS* 1.3 63.8 + - - +
219B LEU* 3.3 5.5 + - - +
220B GLU* 3.1 24.3 + - - +
273B TYR* 3.5 20.9 - - - -
275B TYR* 3.7 15.4 - - - -
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Residues in contact with LYS 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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214B GLU 5.6 0.4 - - - -
215B HIS 3.4 0.8 - - - -
216B GLY* 1.3 75.9 - - - +
218B ARG* 1.3 58.8 + - + +
220B GLU* 3.3 21.0 + - - +
221B ARG* 2.9 51.8 + - - +
273B TYR* 3.4 34.1 + - + +
304B VAL* 4.7 17.4 - - - +
343B HIS* 6.3 0.4 - - - +
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Residues in contact with ARG 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 GLU 5.5 0.2 - - - -
215B HIS* 3.1 53.7 + - + +
217B LYS* 1.3 76.0 - - + +
219B LEU* 1.3 65.1 + - - +
221B ARG* 3.3 29.2 + - - +
222B LEU* 3.0 22.7 + - - +
253B TYR 5.0 1.8 + - - -
254B GLY* 2.7 31.3 + - - -
255B ILE* 3.8 18.2 - - + +
256B PRO* 3.8 11.9 - - - +
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Residues in contact with LEU 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 TRP* 3.9 22.9 - - + -
211B VAL* 4.0 9.6 - - + -
215B HIS 3.4 4.4 + - - +
216B GLY* 3.3 13.1 + - - +
218B ARG* 1.3 78.1 - - - +
220B GLU* 1.3 55.2 + - - +
222B LEU* 3.1 9.6 + - + +
223B ALA* 2.8 29.4 + - + +
238B LEU* 5.2 5.8 - - + -
245B ILE* 4.3 15.9 - - + -
250B LEU* 3.6 33.2 - - + -
255B ILE* 4.2 16.0 - - + +
275B TYR* 3.5 39.5 - - + -
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Residues in contact with GLU 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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216B GLY 3.1 16.5 + - - +
217B LYS* 3.5 26.6 + - + +
218B ARG 3.3 0.2 - - - -
219B LEU* 1.3 76.1 - - - +
221B ARG* 1.3 57.6 + - + +
223B ALA* 3.9 6.7 - - - +
224B LYS* 3.0 30.3 + - - +
237B PHE* 5.4 1.0 - - - -
238B LEU* 4.4 7.2 - - + -
273B TYR* 2.8 29.6 + - - -
275B TYR* 2.7 32.9 + - + +
304B VAL* 5.9 2.8 - - - +
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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 LYS* 2.9 39.9 + - - +
218B ARG* 3.3 35.4 - - - +
220B GLU* 1.3 73.9 - - + +
222B LEU* 1.3 60.4 + - - +
224B LYS* 3.5 9.3 + - + +
225B GLY* 3.0 24.8 + - - -
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Residues in contact with LEU 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 ARG 3.0 14.5 + - - +
219B LEU* 3.3 13.2 - - + +
221B ARG* 1.3 73.6 - - - +
223B ALA* 1.3 65.8 + - - +
225B GLY* 3.0 5.0 + - - -
226B PHE* 3.0 58.5 + - + -
245B ILE* 4.7 4.9 - - + -
249B MET 4.7 3.8 - - - +
250B LEU* 3.8 29.4 - - + -
253B TYR* 3.4 35.2 - - + -
255B ILE* 3.9 15.7 - - + -
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Residues in contact with ALA 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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219B LEU* 2.8 18.8 + - + +
220B GLU 3.9 3.8 - - - +
222B LEU* 1.3 73.5 - - - +
224B LYS* 1.3 52.9 - - - +
226B PHE* 3.0 5.4 + - - -
227B PHE* 2.8 41.7 + - + +
237B PHE* 3.9 18.6 - - + -
238B LEU* 3.9 24.0 - - + -
245B ILE* 4.4 19.0 - - + +
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Residues in contact with LYS 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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220B GLU 3.0 19.0 + - - +
221B ARG* 3.8 9.6 - - + +
223B ALA* 1.3 75.3 - - - +
225B GLY* 1.3 62.8 + - - +
227B PHE 4.5 0.2 - - - -
228B PRO* 3.3 25.2 - - + +
231B ALA* 3.6 26.9 - - + -
237B PHE* 4.2 12.2 - - + -
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Residues in contact with GLY 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 3.0 15.5 + - - -
222B LEU* 3.0 5.8 + - - -
224B LYS* 1.3 78.5 - - - +
226B PHE* 1.3 63.7 + - - +
227B PHE 3.6 0.2 + - - -
228B PRO* 3.7 11.4 - - - +
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Residues in contact with PHE 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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81B LEU* 3.3 40.2 - - + +
222B LEU* 3.0 61.3 + - + -
223B ALA* 3.6 4.3 - - - +
225B GLY* 1.3 81.3 - - - +
227B PHE* 1.3 80.1 + - + +
228B PRO* 3.3 7.7 - - - +
245B ILE* 4.5 6.1 - - + -
249B MET* 3.3 23.6 - - + -
253B TYR* 3.5 25.4 - + - -
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Residues in contact with PHE 227 (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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81B LEU* 4.4 18.4 - - + -
82B PHE 4.1 21.8 - - - -
83B THR* 3.9 19.7 - - - -
223B ALA 2.8 23.3 + - - +
224B LYS 3.5 3.3 - - - +
226B PHE* 1.3 90.8 - + + +
228B PRO* 1.3 64.8 - - - +
229B GLY 3.3 2.7 - - - -
230B SER* 3.3 16.0 + - - +
231B ALA* 3.1 21.7 + - - +
237B PHE* 3.9 16.4 - + + -
243B THR* 3.6 34.5 - - + -
245B ILE* 5.0 2.0 - - + -
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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