Contacts of the helix formed by residues 276 - 288 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C TRP* 4.0 22.0 - - + -
212C PHE* 3.9 22.2 - - + -
229C ILE* 4.1 17.3 - - + -
233C GLY* 2.9 20.0 + - - +
235C GLN* 3.5 35.0 + - + +
237C ARG* 6.4 0.7 - - + -
275C SER* 1.3 73.2 - - - +
277C LEU* 1.3 58.6 + - - +
279C LEU* 2.9 7.7 + - - +
280C PHE* 2.8 43.7 + - + -
1401C CDP 3.7 38.6 - - + +
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Residues in contact with LEU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C GLU 3.9 15.9 - - - +
142C THR* 4.0 13.7 - - + +
232C ASN 3.9 15.5 - - - +
233C GLY* 3.1 14.6 + - - +
234C LYS* 3.7 29.6 - - + -
275C SER* 3.8 5.2 - - - +
276C LEU* 1.3 76.4 - - - +
278C GLU* 1.3 61.6 + - - +
280C PHE* 3.2 14.2 + - + +
281C LYS* 3.1 33.0 + - - -
293C PHE* 4.4 22.9 - - + -
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Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C THR* 3.1 33.4 + - + -
143C ARG* 2.9 43.9 + - - +
274C LEU* 3.5 16.5 - - + +
275C SER* 2.8 33.1 + - - +
277C LEU* 1.3 75.8 - - - +
279C LEU* 1.3 63.3 + - - +
281C LYS* 3.3 19.3 + - + +
282C LEU* 3.3 17.7 + - + +
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C TRP* 3.4 34.5 - - + -
209C VAL* 4.3 17.0 - - + +
212C PHE* 3.9 26.2 - - + -
213C CYS* 5.5 0.2 - - - -
274C LEU* 4.1 16.5 - - + +
275C SER 2.9 14.2 + - - +
276C LEU 2.9 7.1 + - - +
278C GLU* 1.3 79.7 - - - +
280C PHE* 1.3 65.4 + - + +
282C LEU* 3.5 3.4 + - + +
283C LEU* 3.2 29.2 + - + +
329C VAL* 4.0 36.3 - - + -
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Residues in contact with PHE 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C PHE* 3.7 35.0 - + + -
227C PHE* 3.9 18.2 - + - -
229C ILE* 3.9 16.8 - - + -
276C LEU* 2.8 33.2 + - + -
277C LEU* 3.2 14.1 + - + +
279C LEU* 1.3 81.9 - - + +
281C LYS* 1.3 68.8 + - - +
283C LEU* 3.1 2.6 + - - +
284C GLU* 2.8 36.7 + - - +
291C MET* 4.0 27.8 - - + +
293C PHE* 3.7 39.7 - + - -
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Residues in contact with LYS 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C THR* 5.0 16.4 - - + -
277C LEU* 3.1 25.3 + - - +
278C GLU* 3.4 12.8 - - + +
280C PHE* 1.3 77.7 - - - +
282C LEU* 1.3 68.3 + - + +
284C GLU* 3.0 25.4 + - - +
285C ASP* 2.8 39.0 + - - +
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C LEU* 5.1 14.4 - - + -
278C GLU* 3.3 10.0 + - + +
279C LEU* 3.6 11.0 - - - +
281C LYS* 1.3 81.6 - - + +
283C LEU* 1.4 55.8 + - - +
285C ASP* 3.4 7.2 + - - +
286C TYR* 3.1 28.7 + - - +
325C ALA* 4.2 1.8 - - + +
326C LYS* 3.6 51.6 - - + +
329C VAL* 3.7 30.5 - - + -
330C GLN* 5.3 5.0 - - + +
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Residues in contact with LEU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C PHE* 3.5 30.7 - - + +
213C CYS* 4.2 13.7 - - - -
216C ALA* 3.9 7.6 - - + -
279C LEU* 3.3 28.9 - - + +
280C PHE* 3.1 2.3 + - - +
282C LEU* 1.4 72.3 - - - +
284C GLU* 1.3 68.4 + - - +
286C TYR* 4.4 3.6 - - + +
287C CYS* 2.8 32.3 + - - -
289C ILE* 4.5 0.7 - - - -
291C MET* 3.5 28.9 - - + -
329C VAL* 3.6 24.9 - - + -
333C TYR* 4.6 19.5 - - + -
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Residues in contact with GLU 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280C PHE* 2.8 23.7 + - - +
281C LYS* 3.4 25.7 + - - +
283C LEU* 1.3 78.1 - - - +
285C ASP* 1.3 56.9 + - - +
288C ASN* 2.6 35.2 + - - -
289C ILE* 3.1 30.7 + - - +
290C ASP* 3.4 10.4 - - - +
291C MET* 2.5 50.8 + - + +
292C ARG* 4.0 6.4 + - - -
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Residues in contact with ASP 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281C LYS* 2.8 34.4 + - - +
282C LEU* 3.5 8.3 - - - +
284C GLU* 1.3 74.2 - - - +
286C TYR* 1.3 58.0 + - - +
288C ASN* 4.1 8.1 - - - +
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C LEU 3.1 16.1 + - - +
283C LEU* 3.2 6.9 + - + +
285C ASP* 1.3 78.1 - - - +
287C CYS* 1.3 64.8 + - - +
288C ASN* 3.3 11.8 + - - +
330C GLN* 3.4 53.8 - - + +
333C TYR* 3.5 34.1 - + + -
334C ASP* 2.4 40.8 + - - -
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Residues in contact with CYS 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C ALA* 4.5 4.3 - - - -
220C LYS* 2.3 55.3 + - + +
283C LEU* 2.8 24.5 + - - -
286C TYR* 1.3 82.0 - - - +
288C ASN* 1.3 66.6 + - - +
289C ILE* 3.2 11.5 + - + +
333C TYR* 3.6 41.5 - - + +
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Residues in contact with ASN 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C LYS* 3.4 16.6 + - - +
284C GLU 2.6 15.3 + - - -
285C ASP* 4.1 7.0 - - - +
286C TYR 3.3 11.4 + - - +
287C CYS* 1.3 82.3 + - - +
289C ILE* 1.4 56.5 + - - +
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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