Contacts of the helix formed by residues 485 - 510 (chain B) in PDB entry 3OY3
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 485 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU* 3.6 19.5 - - - -
419B LYS* 3.5 9.8 - - - +
422B VAL* 4.9 0.7 - - - -
484B PRO* 1.3 75.3 - - - +
486B PHE* 1.3 59.2 + - - +
487B ALA* 3.4 5.8 + - - +
488B GLU* 3.0 40.0 + - - +
489B ILE* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER* 4.1 5.8 - - - +
351B MET* 3.4 57.0 - - + +
352B GLU* 3.6 12.6 - - - +
355B GLU* 2.9 14.8 + - - +
418B ILE* 3.3 35.4 - - + -
421B ASP* 3.3 28.0 - - + -
422B VAL* 3.6 18.2 - - + -
425B PHE* 3.7 28.0 - + + -
484B PRO 4.3 0.2 + - - -
485B SER* 1.3 69.4 - - - +
487B ALA* 1.3 59.7 + - - +
489B ILE* 3.6 18.5 - - + +
490B HIS* 2.8 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B GLU* 3.8 27.6 - - + +
355B GLU* 3.1 17.2 + - - +
485B SER* 3.1 6.0 - - - +
486B PHE* 1.3 78.3 - - - +
488B GLU* 1.3 62.0 - - + +
490B HIS* 3.9 1.7 - - - +
491B GLN* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B LEU* 6.0 0.2 - - - -
484B PRO* 3.6 18.9 - - + +
485B SER* 3.0 42.1 + - - +
487B ALA* 1.3 78.5 - - + +
489B ILE* 1.3 61.3 + - - +
491B GLN* 3.3 12.4 + - - +
492B ALA* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B SER* 3.7 14.6 - - - -
422B VAL* 3.6 30.3 - - + -
425B PHE* 3.6 26.2 - - + -
471B LEU* 3.8 20.4 - - + -
475B CYS* 3.8 13.5 - - - -
484B PRO* 4.0 15.5 - - + -
485B SER 2.9 19.9 + - - +
486B PHE* 3.8 20.0 - - + +
487B ALA 3.3 0.2 - - - -
488B GLU* 1.3 74.6 - - - +
490B HIS* 1.3 67.2 + - - +
492B ALA* 3.2 7.1 + - - +
493B PHE* 3.0 25.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B THR* 3.9 9.3 + - + +
348B SER* 3.4 27.8 + - - +
349B SER* 3.9 32.0 + - - -
352B GLU* 2.9 26.7 - - - +
486B PHE 2.8 18.2 + - - +
487B ALA 3.9 0.4 - - - +
489B ILE* 1.3 78.2 - - - +
491B GLN* 1.3 57.6 + - - +
493B PHE* 3.3 0.7 + - - +
494B GLU* 2.8 59.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B ALA 3.2 12.6 + - - +
488B GLU* 3.5 13.7 - - - +
489B ILE 3.3 0.2 - - - -
490B HIS* 1.3 79.8 - - - +
492B ALA* 1.3 64.4 + - - +
494B GLU* 3.3 5.8 + - - +
495B THR* 3.1 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B LEU* 3.5 27.8 - - + -
488B GLU 3.1 12.9 + - - +
489B ILE 3.2 8.5 + - - +
491B GLN* 1.3 77.8 - - - +
493B PHE* 1.3 61.2 + - - +
495B THR* 3.3 5.9 + - - -
496B MET* 3.0 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.7 16.8 - - + +
344B ALA* 3.5 26.2 - - + -
345B THR* 3.3 21.4 + - - +
348B SER* 4.1 5.4 - - - +
425B PHE* 4.0 11.7 - + - -
429B LEU* 3.3 28.0 - - + -
468B VAL* 4.3 11.9 - - + -
471B LEU* 3.1 31.9 - - + -
489B ILE* 3.0 31.7 + - + +
490B HIS 4.0 2.5 - - - +
492B ALA* 1.3 73.9 - - - +
494B GLU* 1.3 56.6 + - - +
496B MET* 3.5 27.9 - - + +
497B PHE* 2.7 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B THR* 3.4 16.6 + - - +
490B HIS* 2.8 42.6 + - + +
491B GLN* 3.5 7.9 - - - +
493B PHE* 1.3 75.7 - - - +
495B THR* 1.3 53.5 + - - +
497B PHE* 3.7 9.6 - - - +
498B GLN* 2.7 73.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B GLN* 3.1 17.6 + - - +
492B ALA* 3.5 10.5 - - - -
494B GLU* 1.3 76.1 - - - +
496B MET* 1.3 65.4 + - + +
498B GLN* 3.6 6.7 + - - +
499B GLU* 3.1 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B LEU* 3.3 14.3 - - + +
465B PRO* 6.3 0.2 - - - -
467B LYS* 4.1 28.7 - - - +
468B VAL* 3.6 24.5 - - + -
471B LEU* 5.3 5.6 - - + -
492B ALA* 3.0 17.8 + - + +
493B PHE* 3.1 47.1 + - + +
495B THR* 1.3 77.0 - - + +
497B PHE* 1.3 59.1 + - - +
499B GLU* 3.5 13.0 + - - +
500B SER* 2.9 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B VAL* 4.0 17.3 - - + -
341B LEU* 4.1 10.5 - - + +
342B TYR* 3.6 55.4 - + + -
345B THR* 3.5 18.4 - - + +
493B PHE 2.7 17.1 + - - +
494B GLU* 3.7 18.6 - - - +
496B MET* 1.3 75.8 - - - +
498B GLN* 1.3 64.7 + - - +
501B SER* 2.7 59.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494B GLU* 2.7 52.1 + - - +
495B THR* 3.9 7.2 - - - +
497B PHE* 1.3 82.6 - - - +
499B GLU* 1.3 67.2 + - + +
501B SER* 3.3 5.7 + - - -
502B ILE* 3.1 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 499 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B THR* 3.1 34.6 + - + +
496B MET* 3.9 12.9 - - - +
498B GLN* 1.3 79.5 - - + +
500B SER* 1.3 62.4 + - - +
502B ILE* 3.6 8.9 + - - +
503B SER* 3.2 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 500 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B ALA* 4.9 0.7 - - - +
338B VAL* 3.4 28.8 + - - +
341B LEU* 3.3 18.6 - - - +
496B MET 2.9 19.5 + - - -
497B PHE 3.9 2.2 - - - -
499B GLU* 1.3 75.2 - - - +
501B SER* 1.3 65.4 + - - +
503B SER* 3.4 8.1 + - - -
504B ASP* 3.1 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 501 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B VAL* 4.1 9.9 - - - +
497B PHE* 2.7 54.5 + - - -
498B GLN* 3.3 8.7 + - - -
500B SER* 1.3 70.3 + - - +
502B ILE* 1.3 55.8 + - - +
504B ASP* 2.8 5.9 + - - +
505B GLU* 2.7 42.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 502 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR 3.4 20.8 - - - +
265A SER* 3.9 33.0 - - - +
266A LEU* 4.7 12.8 - - + -
498B GLN* 3.1 26.7 + - + +
499B GLU* 3.9 6.7 - - - +
501B SER* 1.3 77.0 - - - +
503B SER* 1.3 65.9 + - - +
505B GLU* 3.4 7.3 + - - +
506B VAL* 3.2 24.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 6.0 2.2 - - - -
499B GLU 3.2 13.3 + - - -
500B SER* 3.7 9.5 - - - -
501B SER 3.2 0.4 - - - -
502B ILE* 1.3 81.5 - - - +
504B ASP* 1.3 57.0 + - - +
506B VAL* 3.6 6.7 + - - +
507B GLU* 3.2 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B SER* 5.2 1.2 + - - -
338B VAL* 4.0 28.6 - - + +
500B SER 3.1 14.4 + - - +
501B SER* 2.8 11.1 + - - +
503B SER* 1.3 76.7 - - - +
505B GLU* 1.3 64.2 + - - +
507B GLU* 3.1 9.5 + - - +
508B LYS* 2.8 50.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A TYR* 3.8 20.8 - - + -
501B SER* 2.7 25.3 + - - +
502B ILE* 3.9 6.5 - - - +
504B ASP* 1.3 76.0 - - - +
506B VAL* 1.3 57.6 + - - +
508B LYS* 3.5 31.5 + - - +
509B GLU* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 506 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TRP* 4.2 16.2 - - + -
264A TYR* 3.8 30.5 - - + +
266A LEU* 4.3 26.2 - - + -
302A LEU* 4.6 10.3 - - + -
502B ILE 3.2 17.4 + - - +
503B SER* 3.8 6.5 - - - +
504B ASP 3.2 0.4 - - - -
505B GLU* 1.3 76.1 - - - +
507B GLU* 1.3 67.2 + - + +
509B GLU* 3.1 8.5 + - - +
510B LEU* 3.1 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 507 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LYS* 5.0 7.1 + - - -
300A GLN* 4.5 6.9 + - - +
503B SER* 3.2 15.4 + - - +
504B ASP* 3.1 14.3 + - - +
506B VAL* 1.3 80.2 - - + +
508B LYS* 1.3 64.9 + - + +
510B LEU* 3.3 33.9 + - - +
511B GLY 4.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 508 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ASP* 2.8 43.9 + - - +
505B GLU* 3.6 30.4 + - - +
507B GLU* 1.3 72.5 - - - +
509B GLU* 1.3 62.8 + - - +
511B GLY* 3.2 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 509 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TRP* 4.3 13.0 - - + -
263A LYS* 5.4 1.8 + - - -
264A TYR* 2.8 42.0 + - + +
505B GLU 2.9 19.3 + - - +
506B VAL* 3.1 8.7 + - - +
508B LYS* 1.3 73.8 - - - +
510B LEU* 1.3 57.5 - - + +
511B GLY* 3.0 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A TRP* 6.0 2.9 - - + -
261A TRP* 4.6 9.0 - - + -
294A LYS* 5.0 7.9 - - - +
300A GLN* 3.6 28.0 - - - +
301A LEU 5.2 2.9 - - - +
302A LEU* 4.1 41.3 - - + +
506B VAL* 3.1 21.5 + - + +
507B GLU* 3.7 25.1 - - - +
508B LYS 3.2 1.2 - - - -
509B GLU* 1.3 78.2 - - + +
511B GLY* 1.3 55.7 + - - +
----------------------------------------------------------
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