Contacts of the helix formed by residues 333 - 354 (chain A) in PDB entry 2C0O
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 PRO 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A LYS 3.3 9.4 - - - +
332A GLN* 1.4 94.2 - - + +
334A LEU* 1.3 55.4 + - - +
335A PRO* 3.3 11.9 - - + -
336A LYS* 2.8 37.8 + - + +
337A LEU* 3.1 8.5 + - - -
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Residues in contact with LEU 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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332A GLN 3.9 0.6 + - - -
333A PRO* 1.3 71.8 - - - +
335A PRO* 1.4 61.6 - - + +
337A LEU* 3.0 16.2 + - + +
338A ILE* 2.8 54.7 + - + +
430A VAL* 4.6 11.4 - - + -
432A TYR* 5.2 1.2 + - - +
460A ASN* 3.0 40.6 - - + +
462A PRO* 3.3 35.4 - - + -
494A TYR* 3.6 7.4 - - - +
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Residues in contact with PRO 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A PRO* 3.5 13.9 - - + -
334A LEU* 1.4 95.0 - - + +
336A LYS* 1.3 56.3 + - - +
338A ILE* 3.7 3.1 + - - +
339A ASP* 3.2 23.4 + - - +
494A TYR* 3.5 37.4 - - + +
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Residues in contact with LYS 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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139A ALA* 6.3 1.0 - - - +
140A PRO* 5.9 5.5 - - - +
332A GLN* 3.2 26.2 + - + +
333A PRO* 2.8 25.2 + - + +
335A PRO* 1.3 72.5 - - - +
337A LEU* 1.3 68.0 + - - +
339A ASP* 3.2 19.8 + - + +
340A PHE* 3.1 46.8 + - + -
371A SER 5.6 0.6 + - - -
372A LEU* 4.2 26.3 - - - +
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Residues in contact with LEU 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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324A LEU* 3.9 26.7 - - + -
332A GLN* 3.9 26.0 - - + +
333A PRO 3.1 13.1 + - - +
334A LEU* 3.0 23.0 + - + +
336A LYS* 1.3 78.0 - - - +
338A ILE* 1.3 60.7 + - + +
340A PHE* 3.3 14.6 + - + +
341A SER* 3.2 17.9 + - - -
429A ILE* 3.5 37.1 - - + +
430A VAL* 4.2 13.7 - - + +
432A TYR* 3.8 28.5 - - + +
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Residues in contact with ILE 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 LEU* 2.8 40.7 + - + +
335A PRO* 4.0 5.2 - - + +
337A LEU* 1.3 68.8 - - + +
339A ASP* 1.3 56.5 + - - +
341A SER* 2.8 10.3 - - - +
342A ALA* 2.7 32.1 + - - +
426A LEU* 5.9 0.2 - - + -
462A PRO* 4.9 1.3 - - + -
465A LEU* 4.3 26.7 - - + -
490A LEU* 3.9 31.1 - - + +
493A PHE* 4.0 28.7 - - + -
494A TYR* 3.3 30.3 - - + +
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Residues in contact with ASP 339 (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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131A LYS* 4.4 12.0 + - - -
135A ARG* 2.8 48.5 + - - +
335A PRO 3.2 15.0 + - - +
336A LYS* 3.2 27.6 + - + +
338A ILE* 1.3 78.0 - - - +
340A PHE* 1.3 63.1 + - + +
342A ALA* 2.9 9.1 + - - +
343A GLN* 2.9 40.0 + - - +
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Residues in contact with PHE 340 (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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320A LEU* 4.5 12.6 - - + -
323A PHE* 4.2 28.5 - + - -
324A LEU* 4.5 4.3 - - + -
332A GLN* 4.3 5.4 - - + -
336A LYS* 3.1 44.8 + - + -
337A LEU* 3.5 30.7 - - + +
338A ILE 3.2 0.2 - - - -
339A ASP* 1.3 75.7 - - - +
341A SER* 1.3 63.8 + - - +
343A GLN* 3.0 19.3 + - - +
344A ILE* 3.0 21.3 + - + +
368A VAL* 5.9 2.0 - - + -
372A LEU* 3.9 26.9 - - + -
374A CYS* 3.7 27.7 - - - +
429A ILE* 4.5 11.0 - - + -
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Residues in contact with SER 341 (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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337A LEU 3.2 5.8 + - - -
338A ILE* 2.8 21.0 - - - -
340A PHE* 1.3 79.4 - - - +
342A ALA* 1.3 54.4 + - - -
344A ILE* 3.3 5.7 + - - +
345A ALA* 2.9 29.8 + - - +
422A PHE* 3.8 6.6 - - - -
426A LEU* 2.7 32.5 - - - +
429A ILE* 3.8 18.0 - - - +
490A LEU* 3.7 17.0 - - - -
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Residues in contact with ALA 342 (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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135A ARG* 3.9 7.0 - - - +
338A ILE 2.7 15.4 + - - +
339A ASP* 2.9 12.5 + - - +
341A SER* 1.3 72.8 - - - +
343A GLN* 1.3 58.8 + - - +
345A ALA* 3.4 5.0 + - - +
346A GLU* 2.8 28.6 + - - +
487A GLN* 4.1 3.9 - - - +
490A LEU* 3.9 24.0 - - + +
491A ASP* 3.2 29.5 - - - +
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Residues in contact with GLN 343 (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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135A ARG* 3.4 22.9 - - - +
295A LYS* 3.0 42.3 + - + +
336A LYS* 6.0 0.2 - - - +
339A ASP* 2.9 42.2 + - - +
340A PHE* 3.0 10.6 + - - +
342A ALA* 1.3 78.2 - - - +
344A ILE* 1.3 56.9 + - - +
346A GLU* 3.2 10.7 + - - +
347A GLY 3.0 22.9 + - - -
372A LEU 4.0 15.0 + - - -
373A VAL* 3.3 5.2 - - - +
374A CYS* 2.8 35.9 + - + -
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Residues in contact with ILE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 4.0 18.6 - - + -
340A PHE 3.0 18.1 + - - +
341A SER* 3.6 4.9 - - - +
343A GLN* 1.3 72.8 - - - +
345A ALA* 1.3 66.8 + - - +
347A GLY* 3.0 4.0 + - - +
348A MET* 2.8 30.6 + - + +
361A LEU* 4.6 2.0 - - + -
366A ILE* 3.7 39.3 - - + -
374A CYS* 4.3 7.0 - - + -
376A ILE* 3.8 10.2 - - + +
422A PHE* 3.6 21.8 - - + -
425A LEU* 4.4 11.4 - - + -
429A ILE* 3.9 25.6 - - + -
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Residues in contact with ALA 345 (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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341A SER 2.9 19.9 + - - +
342A ALA* 3.5 7.9 - - - +
344A ILE* 1.3 73.0 - - - +
346A GLU* 1.3 57.8 + - - +
348A MET* 3.7 5.8 - - - +
349A ALA* 2.8 31.5 + - - +
422A PHE* 3.5 20.5 - - + -
483A PHE* 4.2 5.8 - - + +
486A ILE* 4.0 6.1 - - + -
487A GLN* 3.7 30.4 - - + +
490A LEU* 4.4 0.9 - - + -
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Residues in contact with GLU 346 (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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132A ASP* 5.0 5.8 - - - +
135A ARG* 4.6 11.3 + - - -
293A HIS* 3.6 22.8 + - + +
294A ASP* 5.3 2.8 - - - +
295A LYS* 3.5 29.1 + - - +
342A ALA 2.8 17.7 + - - +
343A GLN* 3.4 10.4 - - - +
344A ILE 3.1 0.4 + - - -
345A ALA* 1.3 71.0 - - - +
347A GLY* 1.3 64.3 + - - +
349A ALA* 3.4 3.5 + - - +
350A PHE* 3.3 18.7 + - - +
487A GLN* 3.6 27.3 + - + +
491A ASP* 5.5 2.4 - - - +
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Residues in contact with GLY 347 (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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293A HIS* 4.6 1.3 - - - -
295A LYS* 3.7 17.6 - - - +
296A LEU* 4.4 5.7 - - - +
343A GLN 3.0 8.1 + - - -
344A ILE 3.0 6.7 + - - -
346A GLU* 1.3 75.5 - - - +
348A MET* 1.3 60.6 + - - +
350A PHE* 3.1 18.9 + - - +
351A ILE* 3.2 16.1 + - - +
376A ILE* 3.6 18.4 - - - -
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Residues in contact with MET 348 (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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344A ILE* 2.8 22.0 + - + +
345A ALA* 3.9 0.7 - - - +
347A GLY* 1.3 75.7 - - - +
349A ALA* 1.3 56.8 + - - +
351A ILE* 3.4 22.8 + - + +
352A GLU* 2.9 30.5 + - - +
358A HIS* 3.9 15.7 - - + -
361A LEU* 3.8 32.3 - - + -
376A ILE* 3.6 10.3 - - + +
415A ILE* 4.1 7.2 - - + -
418A ASP* 3.8 20.9 - - - +
483A PHE* 3.4 49.0 - - + -
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Residues in contact with ALA 349 (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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345A ALA 2.8 18.4 + - - +
346A GLU 3.6 6.5 - - - +
347A GLY 3.2 0.2 - - - -
348A MET* 1.3 77.5 - - - +
350A PHE* 1.3 56.1 + - - +
352A GLU* 3.4 5.2 - - - +
353A GLN* 3.0 28.1 + - - +
483A PHE* 3.6 17.6 - - + +
484A GLU* 4.1 17.1 - - + +
487A GLN* 3.6 17.5 - - - +
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Residues in contact with PHE 350 (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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291A LEU* 3.5 37.0 - - + -
292A GLN 3.8 15.5 - - - -
293A HIS* 3.4 44.0 - + + +
296A LEU* 3.8 15.9 - - + -
346A GLU 3.3 4.0 + - - +
347A GLY 3.1 9.9 + - - +
349A ALA* 1.3 76.7 - - - +
351A ILE* 1.3 72.6 + - + +
353A GLN* 3.1 18.3 + - - +
354A ARG* 3.3 59.4 + - + +
379A PHE* 5.6 0.9 - + - -
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Residues in contact with ILE 351 (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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296A LEU* 4.4 13.0 - - + -
347A GLY 3.2 11.7 + - - +
348A MET* 3.7 30.7 - - + +
350A PHE* 1.3 85.3 - - + +
352A GLU* 1.3 64.6 + - - +
354A ARG* 3.0 14.8 + - - +
356A TYR* 3.2 30.0 + - + +
357A ILE* 3.6 31.2 - - - +
358A HIS* 4.5 6.3 - - + -
376A ILE* 4.6 1.8 - - + -
379A PHE* 3.8 40.4 - - + -
415A ILE* 4.2 6.3 - - + -
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Residues in contact with GLU 352 (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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348A MET 2.9 18.0 + - - +
349A ALA 3.4 5.8 - - - +
351A ILE* 1.3 78.4 - - - +
353A GLN* 1.3 63.6 + - - +
355A ASN* 3.1 18.2 + - - +
356A TYR 4.8 0.4 - - - -
415A ILE* 3.6 37.9 - - + +
416A LYS* 5.1 1.4 + - - -
419A VAL* 4.8 1.7 - - - +
482A THR* 3.4 18.2 - - - +
483A PHE* 2.7 41.9 + - + -
484A GLU* 3.2 17.5 + - - +
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Residues in contact with GLN 353 (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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349A ALA 3.0 16.4 + - - +
350A PHE* 3.1 13.5 + - - +
352A GLU* 1.3 76.8 - - - +
354A ARG* 1.3 72.5 + - - +
355A ASN* 3.2 10.9 + - - +
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Residues in contact with ARG 354 (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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290A THR 5.4 4.6 + - - -
291A LEU* 4.0 21.3 - - + +
292A GLN 5.8 0.2 + - - -
350A PHE* 3.4 45.1 - - + +
351A ILE* 3.0 6.3 + - - +
353A GLN* 1.3 87.6 - - + +
355A ASN* 1.3 74.9 + - - +
356A TYR* 3.1 31.0 + - + -
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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