Contacts of the helix formed by residues 324 - 339 (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 SER 324 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196C TYR* 4.0 0.6 + - - -
272C ASN* 3.3 12.1 - - - +
322C LYS 3.7 4.2 + - - -
323C VAL* 1.3 76.6 - - - +
325C ALA* 1.3 54.3 + - - +
326C LYS* 3.6 6.2 + - - +
327C ASP* 3.1 32.6 + - - +
328C GLY* 2.6 34.5 + - - -
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Residues in contact with ALA 325 (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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196C TYR* 4.1 8.7 - - - -
239C VAL* 4.0 13.0 - - + -
271C VAL 5.1 1.1 - - - +
272C ASN* 3.0 37.7 + - - +
274C LEU* 4.3 17.7 - - + -
282C LEU* 4.5 2.0 - - + -
323C VAL 3.8 0.4 + - - -
324C SER* 1.3 69.4 - - - +
326C LYS* 1.3 58.0 + - - +
329C VAL* 2.6 41.4 + - - +
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Residues in contact with LYS 326 (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* 3.6 33.0 - - + +
324C SER* 3.3 6.1 + - - +
325C ALA* 1.3 81.2 - - - +
327C ASP* 1.3 68.4 + - - +
329C VAL* 3.2 1.6 + - - +
330C GLN* 2.8 49.6 + - - +
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Residues in contact with ASP 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323C VAL* 4.4 9.9 - - + -
324C SER* 3.1 22.8 + - - +
326C LYS* 1.3 89.6 - - - +
328C GLY* 1.3 64.0 - - - +
329C VAL 3.2 0.2 + - - -
330C GLN* 3.3 13.1 + - - +
331C LYS* 3.2 29.5 + - + +
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Residues in contact with GLY 328 (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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196C TYR* 3.1 32.5 - - - -
241C HIS* 4.1 6.0 - - - -
323C VAL* 3.7 13.6 - - - +
324C SER 2.6 16.3 + - - -
327C ASP* 1.3 75.3 - - - +
329C VAL* 1.3 57.2 + - - +
331C LYS* 3.3 5.8 + - - +
332C MET 2.8 24.8 + - - -
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Residues in contact with VAL 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C TYR* 4.5 7.2 - - + +
209C VAL* 4.3 16.4 - - + -
213C CYS* 4.4 4.6 - - - -
239C VAL* 5.2 2.5 - - + -
274C LEU* 4.5 9.0 - - + -
279C LEU* 4.0 21.8 - - + -
282C LEU* 3.7 23.8 - - + -
283C LEU* 3.6 27.8 - - + -
325C ALA* 2.6 28.8 + - - +
327C ASP 3.1 0.2 - - - -
328C GLY* 1.3 73.7 - - - +
330C GLN* 1.3 56.7 + - + +
332C MET* 3.2 6.1 + - - +
333C TYR* 2.8 26.0 + - - +
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Residues in contact with GLN 330 (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* 5.3 5.8 - - + +
286C TYR* 3.4 52.4 - - + +
326C LYS* 2.8 39.7 + - - +
327C ASP* 3.8 12.4 + - - +
329C VAL* 1.3 72.1 - - + +
331C LYS* 1.3 61.1 + - + +
333C TYR* 3.1 4.5 + - - +
334C ASP* 2.8 37.0 + - - +
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Residues in contact with LYS 331 (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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241C HIS* 3.3 18.7 + - - +
243C GLU* 2.6 42.6 + - - -
323C VAL* 5.3 4.4 - - + +
327C ASP* 3.2 20.1 + - + +
328C GLY* 3.5 10.8 - - - +
330C GLN* 1.3 81.2 - - + +
332C MET* 1.4 51.6 + - - +
334C ASP* 3.1 13.0 + - - +
335C TRP* 2.8 35.2 + - - +
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Residues in contact with MET 332 (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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196C TYR* 3.9 18.4 - - + -
197C GLY* 3.4 35.4 - - - +
200C GLN* 3.4 31.0 - - + +
202C ALA* 5.5 0.4 - - + -
209C VAL* 4.3 5.6 - - + -
210C GLY* 3.5 17.7 - - - -
213C CYS* 3.8 19.1 - - - -
214C GLN* 6.2 0.4 - - - +
241C HIS* 5.5 1.7 + - + -
328C GLY 2.8 15.0 + - - +
329C VAL* 3.2 9.2 + - - +
331C LYS* 1.4 71.6 - - - +
333C TYR* 1.3 67.0 + - - +
335C TRP* 3.2 25.2 + - + +
336C THR* 2.8 33.0 + - - +
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Residues in contact with TYR 333 (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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213C CYS* 4.1 12.9 - - + -
216C ALA* 4.0 14.4 - - + -
217C VAL* 3.2 29.8 - - + +
220C LYS* 3.4 33.3 - - - +
283C LEU* 4.6 11.2 - - + -
286C TYR* 3.5 31.6 - + + -
287C CYS* 3.6 29.3 - - + +
329C VAL 2.8 13.7 + - - +
330C GLN 3.1 7.8 + - - +
332C MET* 1.3 75.8 - - - +
334C ASP* 1.3 68.6 + - - +
336C THR* 3.0 4.9 + - - -
337C SER* 2.8 36.5 + - - -
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Residues in contact with ASP 334 (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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286C TYR* 2.4 36.9 + - - -
330C GLN* 2.8 18.0 + - - +
331C LYS* 3.1 15.2 + - - +
333C TYR* 1.3 76.4 - - - +
335C TRP* 1.3 62.5 + - - +
337C SER* 3.4 6.6 + - - -
338C SER* 3.1 21.1 + - - -
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Residues in contact with TRP 335 (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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197C GLY 4.0 5.4 - - - -
198C GLY* 3.6 20.8 - - - +
199C ARG* 3.0 43.0 - - - +
200C GLN 2.8 37.5 - - - -
201C PHE* 4.4 13.2 - + - -
331C LYS 2.8 19.6 + - - +
332C MET* 3.7 19.1 - - + +
334C ASP* 1.3 75.6 - - - +
336C THR* 1.3 67.8 + - - +
338C SER* 2.9 34.7 + - - -
339C ILE* 3.5 29.4 + - + +
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Residues in contact with THR 336 (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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210C GLY 4.4 1.7 + - - -
213C CYS* 3.6 15.1 - - - +
214C GLN* 3.7 34.6 + - + +
217C VAL* 3.5 25.4 - - + +
332C MET* 2.8 36.7 + - - +
333C TYR 3.5 3.8 - - - -
335C TRP* 1.3 75.6 - - - +
337C SER* 1.3 69.2 + - - +
339C ILE* 3.0 24.9 + - + +
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Residues in contact with SER 337 (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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217C VAL* 3.9 19.0 - - - +
221C ASN* 5.7 0.9 + - - -
333C TYR* 2.8 34.2 + - - -
334C ASP* 3.5 10.8 - - - -
336C THR* 1.3 76.4 - - - +
338C SER* 1.3 59.9 + - - +
339C ILE 2.9 16.5 + - - +
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Residues in contact with SER 338 (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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334C ASP 3.1 10.1 + - - -
335C TRP* 2.9 33.1 + - - -
337C SER* 1.3 77.9 - - - +
339C ILE* 1.3 60.6 + - - +
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Residues in contact with ILE 339 (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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200C GLN 4.9 0.9 - - - +
201C PHE* 4.2 23.6 - - + -
214C GLN* 5.7 7.6 - - + +
335C TRP* 3.5 42.1 + - + +
336C THR* 3.0 22.1 + - + +
337C SER 2.9 11.9 + - - +
338C SER* 1.3 82.9 - - - +
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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