Contacts of the helix formed by residues 283 - 307 (chain A) in PDB entry 2OT3
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 VAL 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP 5.6 0.4 - - - +
212A GLU* 3.3 22.9 - - + +
213A LYS* 4.1 35.4 - - + +
216A MET* 4.6 1.1 - - + -
217A THR* 3.6 29.2 - - - +
281A LYS 3.6 0.2 - - - -
282A ARG* 1.3 82.6 - - + +
284A PRO* 1.4 72.3 - - + +
285A ARG* 3.9 11.4 - - + +
286A ASP* 2.9 32.7 + - - +
287A LYS* 3.0 13.5 + - - +
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Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 3.7 13.9 - - - +
216A MET* 3.7 22.0 - - + -
282A ARG 3.9 0.4 - - - -
283A VAL* 1.4 80.7 - - + +
285A ARG* 1.3 55.9 + - - +
287A LYS* 3.1 11.0 + - + +
288A LEU* 2.8 35.6 + - - +
337A TYR* 3.7 25.4 - - + +
338A ILE* 4.6 7.8 - - + +
341A PHE 3.9 21.3 - - - +
342A CYS* 3.7 28.3 - - + +
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Residues in contact with ARG 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 2.9 52.0 + - - +
212A GLU* 3.1 23.6 + - - +
283A VAL* 3.2 6.7 - - + -
284A PRO* 1.3 75.1 - - - +
286A ASP* 1.3 64.2 + - - +
288A LEU* 3.6 13.1 + - - +
289A ALA* 3.1 24.5 + - + +
346A ARG* 2.6 58.8 - - - +
352A ASP* 4.8 1.9 - - - +
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Residues in contact with ASP 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A LYS* 6.0 2.1 - - - +
281A LYS* 3.7 25.7 - - + +
282A ARG 5.5 0.3 + - - -
283A VAL* 2.9 29.7 + - - +
285A ARG* 1.3 83.2 - - - +
287A LYS* 1.3 66.2 + - - +
289A ALA* 3.3 9.5 + - - +
290A CYS* 3.2 26.2 + - - -
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Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 4.5 3.2 - - - -
224A PHE* 4.1 12.0 - - - -
278A MET* 3.1 30.5 + - + +
279A ASP 3.7 9.9 + - - -
281A LYS* 2.5 34.9 + - + +
282A ARG* 4.1 2.7 - - - +
283A VAL 3.0 11.7 + - - +
284A PRO* 3.5 5.8 - - + +
286A ASP* 1.3 76.5 - - - +
288A LEU* 1.3 62.8 + - - +
290A CYS* 3.2 14.9 + - - +
291A ILE* 3.2 16.9 + - - +
334A ASN* 2.7 27.7 + - - +
337A TYR* 3.5 41.1 - - + -
338A ILE* 3.9 16.2 - - + -
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PRO 2.8 21.7 + - - +
285A ARG* 3.7 6.1 - - - +
287A LYS* 1.3 72.4 - - - +
289A ALA* 1.3 56.2 + - - +
291A ILE* 3.1 11.4 + - + +
292A THR* 2.9 32.9 + - - -
338A ILE* 3.9 14.8 - - + -
342A CYS* 3.5 31.6 - - - -
346A ARG* 3.8 19.7 - - + -
347A LEU* 3.7 17.3 - - + -
352A ASP* 3.9 19.2 - - + +
356A PHE* 3.6 34.3 - - + -
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG* 3.1 16.0 + - + +
286A ASP* 3.5 14.8 - - - +
287A LYS 3.2 0.4 - - - -
288A LEU* 1.3 75.1 - - - +
290A CYS* 1.3 58.3 + - - +
292A THR* 3.8 6.3 - - - +
293A LYS* 2.9 41.7 + - + +
352A ASP* 4.8 4.0 + - - +
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Residues in contact with CYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASP* 3.3 22.7 - - - +
275A ILE* 5.2 0.4 - - - -
277A GLU* 3.9 9.9 - - - -
278A MET* 3.8 23.1 - - + -
281A LYS* 3.7 30.5 - - - -
286A ASP 3.2 18.5 + - - -
287A LYS 3.2 9.9 + - - +
289A ALA* 1.3 74.4 - - - +
291A ILE* 1.3 65.3 + - - +
293A LYS* 3.4 16.3 + - - +
294A CYS* 2.9 25.0 + - - +
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A ILE* 4.1 16.8 - - + -
278A MET* 3.6 22.0 - - - -
287A LYS 3.5 10.5 - - - +
288A LEU* 3.1 13.1 + - + +
290A CYS* 1.3 76.0 - - - +
292A THR* 1.3 57.8 + - - +
294A CYS* 3.3 3.9 + - + +
295A SER* 2.9 34.1 + - - +
319A LEU* 5.9 4.3 - - + -
338A ILE* 4.0 10.3 - - + -
352A ASP 5.9 0.2 - - - +
355A TYR* 3.5 33.9 - - + +
356A PHE* 3.8 23.1 - - + +
359A LEU* 3.6 30.5 - - + -
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LEU 2.9 13.7 + - - -
289A ALA* 3.8 6.3 - - - -
290A CYS 3.3 0.2 - - - -
291A ILE* 1.3 73.9 - - - +
293A LYS* 1.3 64.7 + - + +
295A SER* 3.2 3.9 + - - -
296A LYS* 3.0 52.9 + - + +
351A GLU* 3.9 6.1 - - - +
352A ASP* 2.8 32.3 + - - +
355A TYR* 3.5 26.9 - - + +
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Residues in contact with LYS 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ASP* 3.2 30.3 + - - +
277A GLU* 5.7 3.0 - - - +
281A LYS* 5.6 5.5 - - - +
289A ALA* 2.9 31.0 + - + +
290A CYS* 3.7 21.2 - - - +
292A THR* 1.3 73.2 - - + +
294A CYS* 1.3 66.5 + - - +
296A LYS* 3.3 7.2 + - - +
297A HIS* 3.0 28.9 + - + +
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Residues in contact with CYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ALA* 3.4 21.8 - - - +
274A ASP* 3.3 20.6 + - + -
275A ILE* 4.0 14.8 - - + +
290A CYS 2.9 17.9 + - - +
291A ILE* 3.4 9.0 - - - +
293A LYS* 1.3 76.5 - - - +
295A SER* 1.3 58.8 + - - +
297A HIS 3.3 1.7 + - - -
298A ILE* 2.9 48.1 + - - +
319A LEU* 4.1 11.7 - - - -
322A ILE* 4.0 12.1 - - - -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ILE* 2.9 17.5 + - - +
292A THR 3.2 8.0 + - - -
294A CYS* 1.3 78.7 - - - +
296A LYS* 1.3 58.3 + - - +
298A ILE* 3.3 5.9 + - - +
299A PHE* 2.8 34.2 + - - -
315A PHE* 3.3 34.5 - - - -
319A LEU* 5.2 3.5 - - - +
355A TYR* 3.5 30.6 + - - +
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Residues in contact with LYS 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 3.0 33.3 + - + +
293A LYS* 3.3 6.5 + - - +
295A SER* 1.3 73.9 - - - +
297A HIS* 1.3 66.8 + - + +
299A PHE* 3.4 18.0 + - + +
300A ASN* 2.9 32.7 + - - +
351A GLU* 2.8 41.4 + - - -
355A TYR* 4.7 5.4 - - - +
52B LEU* 4.5 12.9 - - + +
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Residues in contact with HIS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A MET* 3.6 44.2 - - + +
270A LYS* 3.7 34.9 - - + +
271A ALA* 3.9 5.2 - - + -
274A ASP* 2.5 38.2 + - - -
293A LYS* 3.0 22.2 + - - +
294A CYS 3.7 3.8 - - - +
296A LYS* 1.3 76.2 - - - +
298A ILE* 1.3 63.7 + - - +
300A ASN* 3.3 5.6 + - - +
301A ALA* 3.0 18.9 + - - +
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A MET 6.1 0.2 - - - -
271A ALA* 4.0 6.3 - - + +
294A CYS* 2.9 24.4 + - - +
295A SER* 3.4 6.5 - - - +
297A HIS* 1.3 75.7 - - - +
299A PHE* 1.3 63.8 + - - +
301A ALA* 3.1 10.0 + - - +
302A ILE* 2.9 34.5 + - + +
315A PHE* 3.7 20.2 - - + -
318A THR* 3.5 23.3 - - + -
319A LEU* 3.7 36.1 - - + -
322A ILE* 3.7 33.0 - - + -
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A SER 2.8 29.7 + - - +
296A LYS* 3.7 14.4 - - + +
297A HIS 3.3 0.4 - - - -
298A ILE* 1.3 73.5 - - - +
300A ASN* 1.3 57.8 + - - +
302A ILE* 3.3 5.5 + - + +
303A LYS* 2.9 30.8 + - - +
310A ALA* 3.8 13.3 - - + +
315A PHE* 3.3 35.0 - + + -
355A TYR* 3.2 42.6 - + - -
52B LEU* 3.9 20.2 - - + +
53B GLN* 3.4 38.8 - - + -
55B SER* 3.8 17.3 - - - -
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Residues in contact with ASN 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A MET* 3.7 30.2 - - + +
296A LYS* 2.9 25.4 + - - +
297A HIS* 3.6 9.8 + - - +
298A ILE 3.3 0.2 - - - -
299A PHE* 1.3 76.6 - - - +
301A ALA* 1.3 62.6 + - - +
303A LYS* 3.3 2.0 + - - +
304A ILE* 2.9 36.4 + - + +
52B LEU* 3.7 25.7 - - - +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 4.2 12.3 - - + -
264A VAL* 3.8 22.6 - - + +
267A MET* 3.8 19.8 - - + +
268A VAL* 4.4 10.3 - - + -
297A HIS 3.0 12.9 + - - +
298A ILE* 3.1 12.1 + - - +
300A ASN* 1.3 75.2 - - - +
302A ILE* 1.3 61.3 + - - +
305A THR* 2.9 30.2 + - - -
318A THR* 5.7 0.7 - - + -
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Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO* 3.7 23.8 - - + +
257A VAL* 3.8 18.4 - - + -
298A ILE* 2.9 32.3 + - + +
299A PHE* 3.8 5.6 - - - +
301A ALA* 1.3 76.9 - - - +
303A LYS* 1.3 57.9 + - - +
305A THR* 3.3 0.9 + - - -
306A LYS* 2.9 36.7 + - + +
308A GLU 4.4 5.2 - - - +
310A ALA* 3.7 34.8 - - + -
314A ASP* 3.6 17.9 - - + +
315A PHE* 4.0 3.1 - - + -
318A THR* 3.6 18.2 - - - +
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Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A PHE 2.9 21.0 + - - +
300A ASN* 3.9 3.4 - - - +
302A ILE* 1.3 72.6 - - - +
304A ILE* 1.3 60.4 + - + +
307A ASN* 2.8 53.0 + - - +
308A GLU* 3.5 26.9 - - - +
309A PRO* 3.8 5.6 - - + -
310A ALA 5.7 0.2 - - - +
50B THR* 3.8 20.6 + - - +
51B THR 2.7 29.2 + - - +
52B LEU* 4.0 22.8 - - + +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ILE* 4.0 22.0 - - + +
263A GLU* 3.5 46.4 - - + +
264A VAL* 3.5 19.7 - - + -
267A MET* 4.2 14.4 - - + -
300A ASN* 2.9 34.4 + - + +
301A ALA* 4.5 1.6 - - - +
303A LYS* 1.3 78.6 - - + +
305A THR* 1.3 62.5 + - - +
307A ASN* 3.7 15.6 + - - +
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Residues in contact with THR 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO 3.5 21.3 - - - +
257A VAL* 3.3 3.0 - - - -
258A ASN* 2.8 43.0 + - + +
261A ILE* 4.4 9.9 - - + +
264A VAL* 3.4 9.4 - - - +
301A ALA 2.9 18.8 + - - -
302A ILE 3.7 0.2 - - - -
304A ILE* 1.3 79.0 - - - +
306A LYS* 1.3 71.5 + - - +
307A ASN* 4.1 4.5 - - - +
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Residues in contact with LYS 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A PRO* 3.6 42.5 - - + +
302A ILE* 2.9 20.4 + - + +
305A THR* 1.3 89.9 - - - +
307A ASN* 1.3 71.7 + - - +
308A GLU* 3.2 23.7 + - + +
314A ASP* 5.8 2.2 - - - +
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Residues in contact with ASN 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LYS* 2.8 37.1 + - - +
304A ILE* 3.7 15.4 + - - +
305A THR 4.1 4.0 - - - +
306A LYS* 1.3 81.4 - - - +
308A GLU* 1.3 69.2 + - - +
309A PRO* 4.9 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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