Contacts of the helix formed by residues 290 - 311 (chain A) in PDB entry 1OMW
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 290 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A HIS* 5.4 0.8 - - - -
288A VAL 4.0 1.2 + - - -
289A PHE* 1.3 73.9 - - - +
291A GLU* 1.3 51.9 + - - +
292A ALA* 3.1 22.7 + - - +
293A ASP* 2.6 41.7 + - - +
294A MET* 2.9 15.2 + - - +
385A LEU* 4.1 0.4 - - - -
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE 3.6 2.4 + - - -
290A SER* 1.3 70.6 + - - +
292A ALA* 1.3 60.3 + - - +
294A MET* 4.1 1.5 - - - +
295A ARG* 3.3 30.4 + - - +
385A LEU* 3.7 18.4 - - + +
416A SER 5.1 1.0 - - - +
417A PHE* 4.3 1.6 - - - -
418A SER* 2.6 49.4 + - - -
420A GLU* 5.2 0.9 - - - +
421A LEU* 3.6 20.3 - - + +
452A PHE* 3.9 22.4 - - + -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A SER* 3.1 13.0 + - - +
291A GLU* 1.3 78.1 - - - +
293A ASP* 1.3 65.9 - - - +
295A ARG* 3.5 27.6 - - - +
296A PHE* 3.7 7.8 + - - +
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Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A HIS* 4.8 7.8 + - - -
289A PHE* 4.0 22.3 - - + -
290A SER* 2.6 32.4 + - - +
292A ALA* 1.3 76.7 - - - +
294A MET* 1.3 63.2 + - - +
295A ARG 3.1 0.9 - - - -
296A PHE* 3.3 11.3 + - - +
297A TYR* 3.3 20.3 + - - -
469A PRO* 3.5 32.5 - - + +
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Residues in contact with MET 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A PHE* 4.5 4.6 - - + +
290A SER 2.9 12.1 + - - +
291A GLU 4.6 1.3 - - - +
293A ASP* 1.3 73.0 - - - +
295A ARG* 1.3 66.6 + - - +
296A PHE 2.9 0.5 + - - -
297A TYR* 3.0 10.5 + - - -
298A ALA* 2.8 38.3 + - + +
381A LEU* 3.3 58.6 - - + +
384A LEU* 4.4 16.8 - - + -
385A LEU* 4.2 18.8 - - + -
421A LEU* 4.4 12.6 - - + -
424A LEU* 4.7 4.5 - - + -
452A PHE* 3.3 44.2 - - + -
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Residues in contact with ARG 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A GLU* 3.3 31.0 + - - +
292A ALA* 3.5 18.1 - - - +
293A ASP 3.1 0.2 - - - -
294A MET* 1.3 82.7 - - - +
296A PHE* 1.3 60.8 + - - +
298A ALA* 4.0 0.9 - - - +
299A ALA* 3.3 20.6 + - - +
420A GLU* 6.0 0.8 - - - +
452A PHE* 2.9 77.0 + - + -
453A PHE* 3.8 13.7 - - + -
455A SER* 3.5 18.9 + - - -
456A LEU* 4.1 21.3 - - + +
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A ALA 3.7 6.8 + - - +
293A ASP 3.3 8.5 + - - +
294A MET 2.9 1.8 + - - -
295A ARG* 1.3 78.1 - - - +
297A TYR* 1.3 81.0 + + - +
299A ALA* 3.3 6.7 + - + +
300A GLU* 3.3 57.7 + - + +
329A GLY 3.8 12.8 - - - -
330A HIS* 3.8 3.6 - + - -
456A LEU* 6.2 0.4 - - - -
466A TYR* 3.6 40.8 - - + -
467A PRO 4.0 8.5 - - - +
468A PRO* 3.6 22.4 - - + -
469A PRO* 3.4 27.8 - - + -
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Residues in contact with TYR 297 (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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279A LEU* 3.5 39.4 - - + +
282A HIS* 6.0 0.2 - - - +
289A PHE* 4.0 18.9 - + - -
293A ASP 3.3 24.1 + - - -
294A MET* 3.0 4.5 + - - +
296A PHE* 1.3 91.5 - + - +
298A ALA* 1.3 64.9 + - - +
300A GLU* 3.0 6.7 + - - +
301A ILE* 2.8 31.1 + - + +
325A LEU* 4.2 6.4 - - + +
329A GLY 4.4 4.4 + - - -
331A VAL* 3.7 34.1 - - + -
380A MET* 5.2 1.6 - - + -
381A LEU* 5.2 0.2 - - - -
384A LEU* 4.2 17.7 - - + -
469A PRO* 3.6 15.8 - - + +
470A LEU* 3.6 27.2 + - - +
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A MET* 2.8 45.8 + - + +
295A ARG 4.0 2.0 - - - +
297A TYR* 1.3 72.0 - - - +
299A ALA* 1.3 62.4 + - - +
301A ILE* 3.4 5.1 + - - +
302A ILE* 2.9 32.6 + - + +
377A LEU* 5.1 0.2 - - - -
381A LEU* 3.8 22.8 - - + +
453A PHE* 4.0 14.1 - - + -
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Residues in contact with ALA 299 (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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295A ARG 3.3 9.0 + - - +
296A PHE* 3.3 10.0 + - + +
298A ALA* 1.3 78.6 - - - +
300A GLU* 1.3 64.4 + - + +
303A LEU* 3.5 12.6 + - - +
453A PHE* 4.4 1.1 - - + -
456A LEU* 3.7 28.3 - - + -
458A TRP* 3.6 21.1 - - + -
461A VAL* 3.5 29.3 - - + +
466A TYR* 6.0 0.9 - - + -
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PHE* 3.7 37.7 - - + +
296A PHE* 3.3 32.2 + - + +
297A TYR 3.0 7.0 + - - +
299A ALA* 1.3 76.9 - - + +
301A ILE* 1.3 66.4 + - - +
302A ILE 2.9 1.9 + - - -
303A LEU* 3.1 13.7 + - - +
304A GLY 3.2 6.9 + - - -
330A HIS* 2.7 33.5 + - - +
331A VAL* 3.0 44.6 + - + +
461A VAL* 4.4 13.0 - - + +
464A GLN* 4.3 2.1 - - - +
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Residues in contact with ILE 301 (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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253A PHE* 5.4 1.1 - - + +
297A TYR* 2.8 25.8 + - + +
298A ALA* 3.6 5.8 - - - +
300A GLU* 1.3 75.9 - - - +
302A ILE* 1.3 51.5 + - - +
303A LEU 3.2 0.2 - - - -
304A GLY* 3.0 4.3 + - - +
305A LEU* 2.6 35.5 + - + +
318A LEU* 3.8 19.5 - - + -
323A ILE* 3.3 47.3 - - + -
331A VAL* 4.3 7.2 - - + -
332A ARG* 5.1 0.7 - - - -
333A ILE* 3.7 21.6 - - + +
377A LEU* 3.6 26.5 - - + -
380A MET* 4.9 4.7 - - + -
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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
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298A ALA* 2.9 31.4 + - + +
299A ALA 4.0 4.3 - - - +
300A GLU 2.9 2.0 + - - -
301A ILE* 1.3 73.3 - - - +
303A LEU* 1.3 62.4 + - + +
305A LEU* 3.4 8.1 + - - +
306A GLU* 3.0 24.6 + - - +
374A TRP* 4.3 17.4 - - + -
377A LEU* 3.6 32.3 - - + -
381A LEU* 5.4 0.2 - - + -
444A ALA* 4.7 6.3 - - + +
447A VAL* 4.2 9.2 - - + -
448A LYS* 4.4 14.4 - - + -
453A PHE* 3.6 29.8 - - + -
458A TRP* 4.2 19.1 - - + -
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Residues in contact with LEU 303 (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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251A CYS* 4.9 1.6 - - - -
253A PHE* 3.7 19.3 - - + -
299A ALA 3.5 8.5 + - - +
300A GLU 3.1 7.5 + - - +
302A ILE* 1.3 77.1 - - - +
304A GLY* 1.3 62.2 + - - +
306A GLU* 3.3 26.2 - - - +
307A HIS* 3.3 20.3 + - - +
448A LYS* 3.8 13.2 - - - +
458A TRP* 4.1 17.3 - - + +
461A VAL* 3.5 31.2 - - + -
462A PHE* 3.7 38.5 - - + +
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Residues in contact with GLY 304 (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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251A CYS* 4.9 0.7 - - - -
253A PHE* 3.8 19.6 - - - +
254A ILE* 3.9 7.8 - - - +
300A GLU 3.2 6.5 + - - -
301A ILE 3.0 8.3 + - - -
303A LEU* 1.3 73.8 - - - +
305A LEU* 1.3 65.7 + - - +
307A HIS* 3.5 6.2 - - - +
308A MET* 3.4 23.4 + - - +
333A ILE* 3.6 17.9 - - - +
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Residues in contact with LEU 305 (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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301A ILE* 2.6 23.3 + - + +
302A ILE 3.7 5.6 - - - +
303A LEU 3.2 0.2 - - - -
304A GLY* 1.3 73.3 - - - +
306A GLU* 1.3 65.1 + - - +
308A MET* 3.0 14.1 + - - -
309A HIS* 3.1 25.1 + - + +
315A TYR* 4.3 11.4 - - + -
318A LEU* 3.8 29.6 - - + -
333A ILE* 4.0 15.3 - - + -
373A ASP* 3.8 35.7 - - + +
374A TRP* 3.4 39.0 - - + -
377A LEU* 4.3 3.8 - - + -
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Residues in contact with GLU 306 (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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302A ILE 3.0 16.1 + - - +
303A LEU* 3.3 18.1 - - + +
304A GLY 3.3 0.2 - - - -
305A LEU* 1.3 74.7 - - - +
307A HIS* 1.3 57.7 + - - +
309A HIS* 3.2 5.3 + - - +
310A ASN* 2.9 53.0 + - - +
444A ALA* 3.9 22.1 - - + +
445A GLN* 5.3 1.4 + - - +
448A LYS* 2.7 42.6 + - - -
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Residues in contact with HIS 307 (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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246A VAL* 2.9 28.4 + - + -
248A THR 3.4 11.0 + - - -
249A GLY* 3.6 4.9 - - - -
251A CYS* 3.5 29.0 - - + +
254A ILE* 3.3 25.4 - - + -
303A LEU 3.3 10.7 + - - +
304A GLY 3.5 10.8 - - - +
306A GLU* 1.3 80.8 - - - +
308A MET* 1.3 62.6 + - - +
309A HIS 3.3 0.5 + - - -
310A ASN* 3.4 8.0 + - - -
311A ARG* 3.2 56.0 + - - +
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Residues in contact with MET 308 (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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246A VAL* 3.8 21.3 - - + -
254A ILE* 4.1 26.0 - - + -
304A GLY 3.4 8.2 + - - +
305A LEU* 3.0 12.6 + - + +
307A HIS* 1.3 80.4 - - - +
309A HIS* 1.3 56.6 + - + +
311A ARG* 3.2 3.4 - - - -
312A PHE 2.9 8.3 + - - -
313A VAL* 2.7 51.3 + - + +
315A TYR* 3.8 40.2 - - + -
333A ILE* 4.2 17.7 - - + -
336A LEU* 3.6 28.3 - - + -
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Residues in contact with HIS 309 (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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305A LEU* 3.1 25.9 + - + +
306A GLU* 3.8 5.8 - - - +
308A MET* 1.3 74.7 - - + +
310A ASN* 1.3 70.0 + - - +
311A ARG 3.1 1.1 - - - -
312A PHE* 3.7 16.2 + - - +
313A VAL 3.0 28.4 + - - +
314A VAL* 4.2 0.2 - - - -
315A TYR 4.6 0.2 + - - -
342A PHE* 4.8 5.0 - - + -
370A SER* 3.4 44.4 + - - +
373A ASP* 2.8 35.1 + - + -
374A TRP* 3.9 25.0 + + - -
444A ALA* 5.7 2.0 + - + +
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Residues in contact with ASN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLU* 2.9 40.6 + - - +
307A HIS* 3.4 6.1 + - - +
308A MET 3.4 0.2 - - - -
309A HIS* 1.3 83.8 + - - +
311A ARG* 1.3 71.1 + - - +
312A PHE* 3.4 18.6 + - - -
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Residues in contact with ARG 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.3 33.0 - - + +
246A VAL* 4.5 2.5 - - + +
248A THR* 3.5 32.7 + - - -
249A GLY* 4.5 4.9 - - - -
307A HIS* 3.2 57.8 + - - +
308A MET* 3.2 6.9 + - - +
309A HIS 3.1 0.2 - - - -
310A ASN* 1.3 89.6 + - - +
312A PHE* 1.3 74.1 + - - +
313A VAL* 3.3 10.3 + - + +
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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) + - + + + + + -
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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