Contacts of the helix formed by residues 276 - 288 (chain B) in PDB entry 1ORR
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 LEU 276 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208B TRP* 3.9 20.9 - - + -
212B PHE* 4.2 14.1 - - + -
229B ILE* 4.0 21.3 - - + -
233B GLY* 3.1 15.4 + - - +
235B GLN* 4.0 31.9 - - + +
237B ARG* 6.3 1.1 - - + -
275B SER* 1.3 73.7 - - - +
277B LEU* 1.3 58.1 + - - +
279B LEU* 3.1 9.5 + - - +
280B PHE* 2.8 42.9 + - + -
1301B CDP 3.6 44.4 - - + +
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Residues in contact with LEU 277 (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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141B GLU 4.2 15.3 - - - +
142B THR* 4.1 13.0 - - + +
232B ASN 3.8 20.2 - - - +
233B GLY* 3.2 14.3 + - - +
234B LYS* 3.9 22.4 - - + -
275B SER* 3.2 5.8 - - - +
276B LEU* 1.3 78.3 - - - +
278B GLU* 1.3 62.5 + - - +
280B PHE* 3.2 13.6 + - + +
281B LYS* 3.1 22.2 + - - +
293B PHE* 3.9 28.3 - - + -
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Residues in contact with GLU 278 (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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142B THR* 2.7 36.1 + - + +
143B ARG* 2.7 47.4 + - - +
273B SER 4.0 0.7 - - - +
274B LEU* 3.6 15.6 - - + +
275B SER* 3.1 29.0 + - - +
277B LEU* 1.3 72.1 - - - +
279B LEU* 1.3 66.9 + - - +
281B LYS* 3.2 8.7 + - - +
282B LEU* 3.0 25.1 + - - +
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Residues in contact with LEU 279 (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 TRP* 3.3 32.3 - - + -
209B VAL* 4.3 14.8 - - + +
212B PHE* 3.9 24.5 - - + -
213B CYS* 5.3 0.7 - - - -
274B LEU* 3.9 27.0 - - + +
275B SER 2.9 13.2 + - - +
276B LEU* 3.3 9.6 - - - +
278B GLU* 1.3 74.5 - - - +
280B PHE* 1.3 68.4 + - + +
282B LEU* 3.1 6.5 + - + +
283B LEU* 3.1 30.8 + - + +
329B VAL* 3.9 30.3 - - + -
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Residues in contact with PHE 280 (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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212B PHE* 3.7 33.4 - + + -
227B PHE* 3.8 8.5 - + - -
229B ILE* 3.6 27.6 - - + -
276B LEU* 2.8 34.2 + - + -
277B LEU* 3.6 12.8 - - + +
279B LEU* 1.3 84.0 - - + +
281B LYS* 1.3 57.7 + - - +
283B LEU* 3.2 2.3 + - - +
284B GLU* 2.9 38.4 + - - +
291B MET* 3.8 34.2 - - + +
293B PHE* 3.6 42.4 - + - -
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Residues in contact with LYS 281 (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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277B LEU 3.1 12.7 + - - +
278B GLU* 3.4 11.7 - - - +
279B LEU 3.1 0.2 - - - -
280B PHE* 1.3 74.2 - - - +
282B LEU* 1.3 66.3 + - + +
284B GLU* 3.2 16.3 + - + +
285B ASP* 3.0 57.3 + - - +
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Residues in contact with LEU 282 (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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274B LEU* 3.9 26.2 - - + -
278B GLU 3.0 15.3 + - - +
279B LEU* 3.5 7.0 - - - +
281B LYS* 1.3 77.5 - - + +
283B LEU* 1.3 63.7 + - - +
285B ASP* 3.4 7.1 + - - +
286B TYR* 3.0 24.6 + - - +
325B ALA* 4.4 1.1 - - + +
326B LYS* 4.0 48.2 - - + +
329B VAL* 4.3 26.7 - - + -
330B GLN* 5.5 2.6 - - + +
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Residues in contact with LEU 283 (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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212B PHE 3.6 29.2 - - - +
213B CYS* 4.0 13.9 - - - -
216B ALA* 4.1 7.9 - - + -
279B LEU* 3.1 35.7 + - + +
280B PHE 3.7 5.2 - - - +
282B LEU* 1.3 78.3 - - - +
284B GLU* 1.3 68.5 + - - +
286B TYR* 3.3 6.0 + - + +
287B CYS* 3.0 30.7 + - - +
289B ILE* 4.7 0.9 - - - -
291B MET* 3.9 22.4 - - + -
329B VAL* 3.9 20.0 - - + -
333B TYR* 4.1 25.6 - - + -
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Residues in contact with GLU 284 (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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280B PHE* 2.9 24.8 + - - +
281B LYS* 3.2 21.2 + - + +
283B LEU* 1.3 74.9 - - - +
285B ASP* 1.3 59.0 + - - +
288B ASN* 2.6 35.7 + - - -
289B ILE* 3.2 29.5 + - + +
290B ASP* 3.7 3.2 - - - +
291B MET* 2.6 46.6 + - + +
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Residues in contact with ASP 285 (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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281B LYS* 3.0 51.9 + - - +
282B LEU* 3.8 7.4 - - - +
284B GLU* 1.3 80.1 - - - +
286B TYR* 1.3 66.0 + - - +
287B CYS 3.3 0.5 + - - -
288B ASN* 3.6 6.8 + - - +
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Residues in contact with TYR 286 (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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282B LEU 3.0 17.3 + - - +
283B LEU* 3.8 8.1 - - + +
285B ASP* 1.3 77.6 - - - +
287B CYS* 1.3 59.5 + - - +
330B GLN* 3.5 60.4 - - + +
333B TYR* 3.7 32.5 - + + -
334B ASP* 2.7 37.1 + - - -
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Residues in contact with CYS 287 (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 ALA* 4.3 3.6 - - - -
220B LYS* 2.7 35.6 + - - +
283B LEU* 3.0 18.9 + - - +
286B TYR* 1.3 81.9 - - - +
288B ASN* 1.3 63.9 + - - +
289B ILE* 3.8 28.0 - - + -
333B TYR* 3.1 50.3 - - - -
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Residues in contact with ASN 288 (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 LYS* 4.5 7.1 + - - +
284B GLU 2.6 18.3 + - - -
285B ASP 3.6 7.0 + - - +
287B CYS* 1.3 77.6 - - - +
289B ILE* 1.3 60.0 + - - +
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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