Contacts of the helix formed by residues 324 - 339 (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 SER 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A TYR* 3.8 1.1 + - - -
272A ASN* 3.4 11.0 - - - +
322A LYS 3.6 4.6 + - - -
323A VAL* 1.3 79.4 - - - +
325A ALA* 1.3 55.4 + - - +
326A LYS* 3.4 6.6 + - - +
327A ASP* 2.9 38.8 + - - +
328A GLY* 2.7 30.8 + - - -
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Residues in contact with ALA 325 (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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196A TYR* 4.1 7.6 - - - -
239A VAL* 4.0 23.3 - - + -
271A VAL 5.2 0.9 - - - +
272A ASN* 3.0 27.5 + - - +
273A SER 5.3 0.2 - - - +
274A LEU* 4.0 21.3 - - + -
282A LEU* 4.5 2.0 - - + -
324A SER* 1.3 72.2 - - - +
326A LYS* 1.3 58.3 + - - +
329A VAL* 2.9 36.4 + - - +
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Residues in contact with LYS 326 (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* 3.9 31.1 - - + +
324A SER* 3.2 5.9 + - - +
325A ALA* 1.3 81.5 - - - +
327A ASP* 1.3 76.6 + - - +
329A VAL* 4.0 0.9 - - - +
330A GLN* 3.1 56.2 + - + +
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Residues in contact with ASP 327 (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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323A VAL* 4.4 5.6 - - + -
324A SER* 2.9 30.6 + - - +
326A LYS* 1.3 92.7 - - - +
328A GLY* 1.3 62.2 + - - +
330A GLN* 3.4 10.4 + - - +
331A LYS* 3.0 35.4 + - - +
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Residues in contact with GLY 328 (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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196A TYR* 3.1 27.4 - - - -
241A HIS* 3.9 5.9 - - - -
323A VAL* 3.7 13.0 - - - +
324A SER 2.7 15.9 + - - -
327A ASP* 1.3 72.2 - - - +
329A VAL* 1.3 59.9 + - - +
331A LYS* 3.1 6.2 + - - +
332A MET* 2.8 29.3 + - - +
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Residues in contact with VAL 329 (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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196A TYR* 3.7 7.2 + - + -
209A VAL* 4.1 15.0 - - + -
213A CYS* 4.4 5.2 - - - -
239A VAL* 5.2 0.9 - - + -
274A LEU* 4.3 9.4 - - + -
279A LEU* 3.8 29.2 - - + -
282A LEU* 4.2 17.3 - - + -
283A LEU* 3.8 26.9 - - + -
325A ALA* 2.9 22.3 + - - +
326A LYS 4.1 2.0 - - - +
328A GLY* 1.3 76.7 - - - +
330A GLN* 1.3 58.2 + - + +
332A MET* 3.2 6.6 + - - +
333A TYR* 2.8 28.4 + - - +
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Residues in contact with GLN 330 (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* 5.4 3.2 - - + +
286A TYR* 3.5 54.5 - - + +
326A LYS* 3.1 50.4 + - + +
327A ASP* 3.7 10.2 + - - +
329A VAL* 1.3 77.6 - - + +
331A LYS* 1.3 64.0 + - - +
333A TYR* 3.3 3.5 + - - +
334A ASP* 3.1 30.0 + - - +
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Residues in contact with LYS 331 (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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241A HIS* 4.2 15.9 - - + +
243A GLU* 4.1 30.3 + - - +
323A VAL* 3.9 30.6 - - - +
327A ASP* 3.0 23.3 + - - +
328A GLY 3.3 8.3 - - - +
330A GLN* 1.3 77.4 - - - +
332A MET* 1.3 58.3 + - - +
334A ASP* 3.2 12.0 + - - +
335A TRP* 2.9 28.9 + - - +
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Residues in contact with MET 332 (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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196A TYR* 4.0 15.3 - - + -
197A GLY* 3.3 38.8 - - - +
200A GLN* 3.3 37.5 - - + +
209A VAL* 4.7 1.3 - - + -
210A GLY* 3.4 20.9 - - - -
213A CYS* 3.7 18.4 - - - -
241A HIS* 5.3 1.1 + - - +
328A GLY 2.8 16.4 + - - +
329A VAL* 3.5 6.5 - - - +
331A LYS* 1.3 75.5 - - - +
333A TYR* 1.3 65.8 + - - +
335A TRP* 3.3 14.4 + - + +
336A THR* 2.8 35.2 + - - +
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Residues in contact with TYR 333 (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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213A CYS* 3.8 13.4 - - + -
216A ALA* 3.9 6.1 - - + -
217A VAL* 3.0 42.8 - - + +
220A LYS* 3.7 29.6 - - - +
221A ASN* 5.5 0.7 + - - -
283A LEU* 4.3 12.1 - - + -
286A TYR* 3.9 24.5 - + + -
287A CYS* 3.6 28.2 - - + -
329A VAL 2.8 13.9 + - - +
330A GLN 3.6 7.0 - - - +
332A MET* 1.3 77.6 - - - +
334A ASP* 1.3 58.6 + - - +
336A THR* 3.1 4.4 + - - -
337A SER* 2.7 53.6 + - - -
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Residues in contact with ASP 334 (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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286A TYR* 3.0 30.8 + - - -
330A GLN 3.1 12.9 + - - +
331A LYS* 3.3 13.6 - - - +
333A TYR* 1.3 79.7 - - - +
335A TRP* 1.3 62.7 + - - +
337A SER* 3.2 10.7 + - - -
338A SER* 3.1 20.8 + - - -
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Residues in contact with TRP 335 (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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197A GLY 4.2 4.3 - - - -
198A GLY* 3.7 20.3 - - - +
199A ARG* 3.0 46.7 - - - +
200A GLN 2.8 35.9 - - - -
201A PHE* 4.1 16.8 - + - -
331A LYS 2.9 13.9 + - - +
332A MET* 3.7 16.2 - - + +
333A TYR 3.2 0.2 - - - -
334A ASP* 1.3 77.0 - - - +
336A THR* 1.3 80.5 + - - +
338A SER* 2.8 34.0 + - - -
339A ILE* 3.4 30.3 + - + +
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Residues in contact with THR 336 (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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210A GLY 4.7 1.7 + - - +
213A CYS* 3.7 10.9 - - - +
214A GLN* 3.3 41.9 - - + +
217A VAL* 3.6 19.2 - - + +
332A MET* 2.8 24.4 + - - +
333A TYR* 3.4 6.7 - - - -
335A TRP* 1.3 83.0 - - + +
337A SER* 1.3 63.8 + - - +
338A SER 3.1 0.9 + - - -
339A ILE* 3.2 31.5 + - + +
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Residues in contact with SER 337 (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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217A VAL* 3.9 25.6 - - - +
221A ASN* 6.0 0.9 - - - -
333A TYR* 2.7 39.0 + - - -
334A ASP* 3.2 13.7 + - - -
335A TRP 3.2 0.2 - - - -
336A THR* 1.3 75.6 - - - +
338A SER* 1.3 60.2 + - - +
339A ILE 3.5 4.9 + - - +
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Residues in contact with SER 338 (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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334A ASP 3.1 12.1 + - - -
335A TRP* 2.8 30.3 + - - -
337A SER* 1.3 74.4 - - - +
339A ILE* 1.3 69.4 + - - +
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A GLN 5.2 0.2 - - - +
201A PHE* 4.6 18.8 - - + -
214A GLN* 5.5 4.5 - - - +
335A TRP* 3.6 45.5 - - + +
336A THR* 3.2 28.5 + - + +
337A SER 4.3 4.7 - - - +
338A SER* 1.3 90.9 + - - +
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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