Contacts of the helix formed by residues 333 - 354 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B LYS 3.3 9.8 - - - +
332B GLN* 1.3 87.5 - - + +
334B LEU* 1.3 68.9 + - + +
335B PRO* 3.7 15.9 - - + -
336B LYS* 2.8 31.7 + - + +
337B LEU* 3.2 6.6 + - - -
432B TYR* 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A GLU* 5.4 3.1 - - - +
332B GLN 3.8 1.2 + - - -
333B PRO* 1.3 68.9 - - - +
335B PRO* 1.4 65.3 - - + +
337B LEU* 2.9 19.1 + - + +
338B ILE* 2.9 37.1 + - + +
430B VAL* 4.0 21.5 - - + -
432B TYR* 4.9 1.6 + - - -
460B ASN* 3.1 31.9 - - + +
462B PRO* 3.6 33.4 - - + -
465B LEU* 4.5 0.7 - - + -
494B TYR* 3.9 8.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B PRO* 3.3 19.1 - - + -
334B LEU* 1.4 92.1 - - + +
336B LYS* 1.3 55.5 + - - +
338B ILE* 3.9 3.3 + - + +
339B ASP* 3.2 24.8 + - - +
494B TYR* 3.5 37.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 5.9 1.4 - - - +
332B GLN* 3.5 33.2 - - + +
333B PRO* 2.8 27.8 + - + +
335B PRO* 1.3 72.5 - - - +
337B LEU* 1.3 68.5 + - - +
339B ASP* 3.1 24.7 + - - +
340B PHE* 2.9 41.1 + - + -
372B LEU* 4.7 18.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 3.7 30.5 - - + -
332B GLN* 3.8 21.5 - - + +
333B PRO 3.7 7.6 - - - +
334B LEU* 2.9 26.5 + - + +
336B LYS* 1.3 76.7 - - - +
338B ILE* 1.3 63.6 + - - +
340B PHE* 3.1 13.9 + - + +
341B SER* 3.1 22.8 + - - -
429B ILE* 3.9 26.6 - - + +
430B VAL* 4.5 9.9 - - + +
432B TYR* 3.7 32.5 - - + +
460B ASN* 5.5 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 2.9 32.1 + - + +
335B PRO* 4.0 6.1 - - + +
337B LEU* 1.3 71.9 - - - +
339B ASP* 1.3 53.6 + - - +
341B SER* 2.9 11.9 + - - +
342B ALA* 2.8 31.7 + - - +
430B VAL* 6.2 0.2 - - + -
462B PRO* 4.9 0.9 - - + -
465B LEU* 4.3 27.1 - - + -
490B LEU* 3.7 29.3 - - + +
493B PHE* 3.8 34.1 - - + -
494B TYR* 3.0 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS* 4.5 9.9 - - - +
135B ARG* 2.6 51.9 + - - +
335B PRO 3.2 13.8 + - - +
336B LYS* 3.1 34.0 + - - +
338B ILE* 1.3 80.3 - - - +
340B PHE* 1.3 63.3 + - - +
342B ALA* 3.2 7.2 + - - +
343B GLN* 3.1 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B LEU* 4.6 12.6 - - + -
323B PHE* 4.3 13.0 - + - -
324B LEU* 4.4 9.6 - - + -
332B GLN* 4.2 22.9 - - + -
336B LYS* 2.9 38.7 + - + -
337B LEU* 3.4 32.1 - - + +
339B ASP* 1.3 72.3 - - - +
341B SER* 1.3 68.2 + - - +
343B GLN* 3.0 25.8 + - - +
344B ILE* 3.0 19.3 + - + +
368B VAL* 5.9 1.8 - - + -
372B LEU* 4.2 24.5 - - + -
374B CYS* 3.8 25.5 - - - -
429B ILE* 4.7 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU 3.1 11.2 + - - -
338B ILE* 2.9 18.2 + - - +
340B PHE* 1.3 77.2 - - - +
342B ALA* 1.3 55.2 + - - +
344B ILE* 3.2 6.8 + - - +
345B ALA* 2.9 30.5 + - - +
422B PHE* 3.6 5.7 - - - -
426B LEU* 3.5 31.4 - - - +
429B ILE* 3.7 20.8 - - - +
465B LEU* 5.8 0.3 - - - +
490B LEU* 3.7 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS* 5.4 0.9 - - - -
135B ARG* 4.0 8.1 - - - +
338B ILE 2.8 11.6 + - - +
339B ASP* 3.3 14.8 - - - +
340B PHE 3.1 0.2 - - - -
341B SER* 1.3 76.5 - - - +
343B GLN* 1.3 56.0 + - - +
345B ALA* 3.3 4.7 + - - +
346B GLU* 2.8 28.5 + - - +
487B GLN* 3.9 5.4 - - - +
490B LEU* 4.0 22.2 - - + +
491B ASP* 3.3 28.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 343 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ARG* 3.5 24.4 - - - +
295B LYS* 3.1 41.7 + - + +
339B ASP* 3.1 34.9 + - - +
340B PHE* 3.0 17.0 + - - +
342B ALA* 1.3 74.2 - - - +
344B ILE* 1.3 60.1 + - - +
346B GLU* 3.2 10.6 + - - +
347B GLY 3.0 22.5 + - - -
372B LEU 4.1 12.5 + - - -
373B VAL* 3.5 6.5 - - - +
374B CYS* 2.9 32.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 344 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LYS* 5.8 0.4 - - - -
320B LEU* 3.9 28.9 - - + -
340B PHE 3.0 14.2 + - - +
341B SER* 3.5 6.5 - - - +
343B GLN* 1.3 74.1 - - - +
345B ALA* 1.3 59.8 + - - +
347B GLY* 3.2 2.4 + - - -
348B MET* 2.8 34.3 + - + +
361B LEU* 4.6 2.2 - - + -
366B ILE* 3.9 28.7 - - + -
374B CYS* 4.1 8.7 - - + -
376B ILE* 3.9 10.4 - - + +
422B PHE* 3.5 23.3 - - + -
425B LEU* 4.0 19.1 - - + -
429B ILE* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B SER 2.9 16.8 + - - +
342B ALA* 3.5 7.0 - - - +
344B ILE* 1.3 77.5 - - - +
346B GLU* 1.3 51.6 + - - +
348B MET* 3.2 6.6 + - - +
349B ALA* 2.6 36.2 + - - +
422B PHE* 3.8 20.4 - - + -
483B PHE* 4.2 7.1 - - + +
486B ILE* 4.4 5.4 - - + -
487B GLN* 4.0 27.1 - - - +
490B LEU* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 346 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B ASP* 4.9 9.7 - - - +
135B ARG* 5.0 8.1 + - - -
293B HIS* 3.8 21.9 + - + +
294B ASP* 5.3 2.1 - - - +
295B LYS* 4.0 24.6 + - - +
342B ALA 2.8 14.5 + - - +
343B GLN* 3.2 12.6 + - - +
345B ALA* 1.3 76.2 - - - +
347B GLY* 1.3 61.6 + - - +
349B ALA* 3.5 3.1 + - - +
350B PHE* 3.4 18.7 + - - +
487B GLN* 3.3 31.0 + - + +
491B ASP* 5.6 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 347 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B HIS* 4.6 7.0 - - - -
295B LYS* 3.7 18.1 - - - +
296B LEU* 4.6 1.8 - - - +
343B GLN 3.0 10.5 + - - -
344B ILE 3.2 0.4 + - - -
346B GLU* 1.3 73.2 - - - +
348B MET* 1.3 66.0 + - - +
350B PHE* 3.2 14.1 + - - +
351B ILE* 3.3 16.6 + - - +
376B ILE* 3.5 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B ILE* 2.8 25.9 + - + +
345B ALA 3.2 1.5 + - - +
347B GLY* 1.3 74.3 - - - +
349B ALA* 1.3 65.5 + - - +
350B PHE 3.1 0.3 + - - -
351B ILE* 3.2 29.0 + - + +
352B GLU* 2.9 22.7 + - - +
358B HIS* 4.4 9.0 - - + -
361B LEU* 3.8 29.6 - - + -
376B ILE* 3.6 7.6 - - + +
415B ILE* 4.0 13.7 - - + -
418B ASP* 4.1 11.4 - - + +
422B PHE* 4.9 0.2 - - + -
483B PHE* 3.5 50.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA 2.6 20.2 + - - +
346B GLU 3.7 7.2 - - - +
348B MET* 1.3 71.1 - - - +
350B PHE* 1.3 56.9 + - - +
352B GLU* 3.1 7.9 - - - +
353B GLN* 2.8 30.0 + - - +
483B PHE* 3.5 13.6 - - + +
484B GLU* 3.9 24.2 - - + +
487B GLN* 4.0 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 350 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU* 3.7 47.8 - - + -
292B GLN 3.9 13.9 - - - -
293B HIS* 3.4 44.6 - + + +
296B LEU* 4.0 12.8 - - + -
346B GLU 3.4 5.2 + - - +
347B GLY 3.2 10.2 + - - +
348B MET 3.1 0.6 - - - -
349B ALA* 1.3 75.6 - - - +
351B ILE* 1.3 71.0 + - + +
353B GLN* 3.1 19.4 + - - +
354B ARG* 3.1 51.6 + - + +
379B PHE* 5.4 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 351 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 3.9 21.5 - - + -
347B GLY 3.3 14.3 + - - +
348B MET* 3.2 35.6 + - + +
350B PHE* 1.3 80.8 - - + +
352B GLU* 1.3 63.1 + - - +
354B ARG* 3.1 10.2 + - - +
356B TYR* 3.1 45.7 + - + +
357B ILE* 3.8 15.7 - - - +
358B HIS* 4.6 6.7 - - + -
376B ILE* 4.2 3.4 - - + -
379B PHE* 3.7 36.6 - - + -
415B ILE* 4.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 352 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B MET 2.9 12.9 + - - +
349B ALA* 3.1 13.3 - - - +
351B ILE* 1.3 77.8 - - - +
353B GLN* 1.3 55.8 + - - +
355B ASN* 2.9 27.0 + - - +
356B TYR 4.8 1.8 - - - +
415B ILE* 3.7 34.9 - - + +
416B LYS* 5.7 1.4 + - - -
419B VAL* 5.0 1.4 - - - +
481B PRO 5.0 0.2 - - - +
482B THR* 3.6 20.1 - - - +
483B PHE* 2.8 35.3 + - + +
484B GLU* 3.3 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 353 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ALA 2.8 18.7 + - - +
350B PHE* 3.1 12.4 + - - +
352B GLU* 1.3 74.3 - - - +
354B ARG* 1.3 69.5 + - - +
355B ASN* 3.2 7.6 + - - -
484B GLU* 5.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B THR 5.2 4.8 + - - -
291B LEU* 3.7 28.5 - - + +
350B PHE* 3.1 41.8 + - + +
351B ILE* 3.5 7.2 - - - +
352B GLU 3.0 1.0 - - - -
353B GLN* 1.3 90.8 + - - +
355B ASN* 1.3 70.9 + - - +
356B TYR* 3.1 31.0 - - + -
----------------------------------------------------------
Back to top of page
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