Contacts of the helix formed by residues 276 - 288 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A TRP* 3.0 43.3 - - + -
212A PHE* 3.7 21.8 - - + -
229A ILE* 4.1 14.6 - - + -
233A GLY* 3.0 25.9 + - - +
235A GLN* 3.4 11.3 + - - +
275A SER* 1.3 71.6 - - - +
277A LEU* 1.3 63.7 + - - +
279A LEU* 3.0 2.0 + - - +
280A PHE* 2.9 39.6 + - + -
1201A CDP 3.7 39.9 - - + +
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU 4.3 5.6 - - - +
142A THR* 4.0 25.1 - - + +
229A ILE* 4.7 0.7 - - + -
232A ASN 3.8 22.4 - - - +
233A GLY* 3.1 14.4 + - - +
234A LYS* 3.9 22.9 - - + -
275A SER 3.2 0.2 - - - -
276A LEU* 1.3 79.0 - - - +
278A GLU* 1.3 62.2 + - - +
280A PHE* 3.3 10.0 + - + +
281A LYS* 3.2 19.6 + - - +
293A PHE* 3.9 29.4 - - + -
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A THR* 2.7 35.6 + - + +
143A ARG* 2.7 48.7 + - - +
273A SER 4.1 0.7 - - - +
274A LEU* 3.6 14.9 - - + +
275A SER* 3.0 25.5 + - - +
277A LEU* 1.3 74.9 - - - +
279A LEU* 1.3 65.7 + - - +
281A LYS* 3.3 8.2 + - - +
282A LEU* 3.1 24.1 + - - +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TRP* 3.6 28.7 - - + -
209A VAL* 4.3 16.8 - - + +
212A PHE* 3.7 31.0 - - + -
213A CYS* 5.4 0.4 - - - -
274A LEU* 4.3 16.5 - - + +
275A SER 2.9 13.3 + - - +
276A LEU 3.0 7.6 + - - +
278A GLU* 1.3 75.6 - - - +
280A PHE* 1.3 66.8 + - + +
282A LEU* 3.1 9.1 + - + +
283A LEU* 3.0 29.3 + - + +
329A VAL* 3.8 40.4 - - + -
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PHE* 3.6 35.2 - + + -
227A PHE* 3.8 11.2 - + - -
229A ILE* 3.7 26.9 - - + -
276A LEU* 2.9 34.3 + - + -
277A LEU* 3.7 11.7 - - + +
279A LEU* 1.3 82.3 - - + +
281A LYS* 1.3 52.2 + - - +
283A LEU* 3.1 5.9 + - + +
284A GLU* 2.7 44.2 + - - +
291A MET* 3.8 30.9 - - + +
293A PHE* 3.6 40.6 - + - -
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A LEU 3.2 10.9 + - - +
278A GLU* 3.6 10.1 - - - +
279A LEU 3.2 0.6 - - - -
280A PHE* 1.3 74.4 - - - +
282A LEU* 1.3 68.2 + - + +
284A GLU* 3.9 16.8 + - + +
285A ASP* 2.9 64.6 + - - +
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU* 4.2 30.3 - - + -
278A GLU 3.1 13.7 + - - +
279A LEU* 3.1 10.2 + - + +
281A LYS* 1.3 77.3 - - + +
283A LEU* 1.3 59.2 + - - +
285A ASP* 3.4 9.9 + - + +
286A TYR* 3.0 29.6 + - - +
325A ALA* 4.2 8.3 - - + +
326A LYS* 3.9 33.4 - - + +
329A VAL* 4.2 30.5 - - + -
330A GLN* 5.4 3.2 - - + +
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PHE* 3.8 30.3 - - + +
213A CYS* 4.1 14.1 - - - +
216A ALA* 4.2 7.9 - - + -
279A LEU* 3.0 33.4 + - + +
280A PHE* 3.6 6.1 - - - +
282A LEU* 1.3 76.0 - - - +
284A GLU* 1.3 66.9 + - - +
286A TYR* 4.5 4.5 - - + -
287A CYS* 2.8 33.6 + - - +
289A ILE* 4.7 0.9 - - - -
291A MET* 4.0 17.9 - - + -
329A VAL* 3.8 25.4 - - + -
333A TYR* 4.3 23.3 - - + -
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A PHE* 2.7 26.9 + - - +
281A LYS* 3.7 22.1 - - + +
283A LEU* 1.3 72.3 - - - +
285A ASP* 1.3 61.7 + - - +
288A ASN* 2.9 28.8 + - - +
289A ILE* 3.2 27.2 + - - +
290A ASP* 3.7 9.3 - - - +
291A MET* 2.8 44.0 + - + +
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Residues in contact with ASP 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A LYS* 2.9 65.1 + - - +
282A LEU* 3.7 11.1 - - + +
284A GLU* 1.3 81.3 - - - +
286A TYR* 1.3 62.5 + - - +
288A ASN* 3.4 17.0 - - - +
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Residues in contact with TYR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A LEU 3.0 15.5 + - - +
283A LEU* 3.9 5.4 - - + +
285A ASP* 1.3 80.9 - - - +
287A CYS* 1.3 63.0 + - - +
288A ASN* 4.9 1.3 - - - +
330A GLN* 3.5 62.7 + - + +
333A TYR* 3.9 23.3 - + + -
334A ASP* 3.0 34.9 + - - -
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Residues in contact with CYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ALA* 4.5 6.3 - - - -
220A LYS* 2.9 32.6 + - + +
283A LEU* 2.8 22.5 + - - +
286A TYR* 1.3 86.1 - - - +
288A ASN* 1.3 65.8 + - - +
289A ILE* 3.5 21.6 - - + +
333A TYR* 3.6 52.3 - - + +
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Residues in contact with ASN 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LYS* 4.4 9.4 + - - +
284A GLU 2.9 10.2 + - - +
285A ASP* 3.4 15.0 - - - +
286A TYR 5.4 1.1 - - - -
287A CYS* 1.3 81.6 - - - +
289A ILE* 1.3 62.4 + - - +
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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