Contacts of the helix formed by residues 502 - 521 (chain A) in PDB entry 2WOK
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 ASP 502 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A THR* 3.5 8.3 - - + +
501A THR* 1.3 79.8 + - - +
503A PRO* 1.3 71.0 - - - +
504A ALA* 2.6 38.1 + - - +
505A ALA* 3.1 20.0 + - + -
506A ARG* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A PRO* 5.4 5.0 - - + +
501A THR 3.3 9.8 - - - +
502A ASP* 1.3 88.6 - - - +
504A ALA* 1.3 56.0 + - - +
506A ARG* 3.4 26.2 - - + +
507A ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 504 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ASP* 2.6 17.9 + - - +
503A PRO* 1.3 72.6 - - - +
505A ALA* 1.3 62.9 + - - +
507A ALA* 3.3 7.8 + - - +
508A GLU* 3.1 28.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 505 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A THR* 3.7 20.2 - - + -
502A ASP* 3.1 18.2 + - + +
504A ALA* 1.3 73.6 - - - +
506A ARG* 1.3 65.2 + - - +
508A GLU* 3.3 7.6 + - - +
509A LEU* 3.1 30.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 506 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A SER* 4.0 24.9 + - - -
182A ASP* 4.7 8.3 + - - -
460A GLU* 6.0 0.2 + - - -
497A THR* 3.1 42.2 - - - +
500A THR* 2.9 23.0 + - + +
501A THR* 3.2 21.4 + - - +
502A ASP 3.1 11.0 + - - +
503A PRO* 3.4 29.1 - - - +
505A ALA* 1.3 73.8 - - - +
507A ALA* 1.3 65.9 + - - +
509A LEU* 3.3 9.6 + - - +
510A TRP* 2.9 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 507 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A PRO* 4.2 15.7 - - + +
358A ALA* 3.7 26.3 - - - +
460A GLU* 4.9 2.0 - - - -
503A PRO 2.9 16.0 + - - +
504A ALA* 3.3 10.3 + - - +
506A ARG* 1.3 73.7 - - - +
508A GLU* 1.3 64.9 + - - +
510A TRP* 3.2 5.7 + - - +
511A ARG* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 508 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A ALA 3.1 17.1 + - - +
505A ALA* 3.7 9.9 - - - +
506A ARG 3.2 0.2 - - - -
507A ALA* 1.3 77.4 - - - +
509A LEU* 1.3 61.4 + - + +
511A ARG* 2.4 48.7 + - - +
512A ALA* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 509 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 3.8 20.1 - - + +
496A GLU* 3.6 41.1 - - + +
497A THR* 3.6 24.0 - - + +
500A THR* 3.6 25.8 - - + +
505A ALA* 3.1 25.3 + - + +
506A ARG* 3.6 3.6 - - - +
508A GLU* 1.3 74.3 - - - +
510A TRP* 1.3 60.5 + - - +
512A ALA* 3.1 8.9 + - + +
513A VAL* 3.0 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 510 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 3.6 19.0 - + + -
358A ALA* 3.6 15.3 - - + -
460A GLU* 3.5 35.4 + - + +
461A TYR* 3.5 38.7 - + + +
464A LEU* 4.2 10.1 - - + -
465A ALA 4.7 2.5 - - - -
494A ILE* 3.8 36.6 - - + -
497A THR* 3.3 36.8 - - + -
498A LEU* 5.4 0.2 - - + -
506A ARG* 2.9 34.9 + - + +
507A ALA 3.2 6.5 + - - +
509A LEU* 1.3 74.9 - - - +
511A ARG* 1.3 65.0 + - - +
513A VAL* 3.3 22.5 + - + +
514A GLU* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 511 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PHE* 4.9 0.2 - - - -
357A PRO 3.3 17.4 + - - -
358A ALA* 3.1 23.8 + - - +
359A HIS 3.1 20.2 + - - -
360A GLN* 3.1 44.0 + - - +
507A ALA* 2.8 20.8 + - - +
508A GLU* 2.4 51.3 + - - +
510A TRP* 1.3 75.5 - - - +
512A ALA* 1.3 62.8 + - - +
514A GLU* 4.6 0.4 - - - -
515A ARG* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 512 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU* 4.1 19.3 - - + -
508A GLU 3.1 11.1 + - - +
509A LEU* 3.1 13.9 + - - +
511A ARG* 1.3 74.1 - - - +
513A VAL* 1.3 65.0 + - - +
515A ARG* 3.5 8.3 + - - +
516A ARG* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 513 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LEU* 3.9 20.2 - - + -
468A VAL* 4.7 0.9 - - + -
490A VAL* 4.0 24.0 - - + +
493A LEU* 3.4 33.2 - - + +
494A ILE* 4.2 12.6 - - + +
497A THR* 5.1 0.2 - - + -
509A LEU 3.0 15.5 + - - +
510A TRP* 3.6 28.3 - - + +
512A ALA* 1.3 75.5 - - - +
514A GLU* 1.3 58.6 + - - +
516A ARG* 3.1 6.6 + - - +
517A VAL* 2.9 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 514 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ALA* 3.5 5.0 - - - +
351A LEU* 2.8 44.1 + - + +
352A PHE* 2.9 38.8 + - + +
360A GLN* 2.9 34.6 + - - +
362A LEU* 3.8 12.2 - - + +
464A LEU* 4.4 7.6 - - + +
510A TRP 3.0 17.2 + - - +
513A VAL* 1.3 78.3 - - - +
515A ARG* 1.3 56.5 + - - +
517A VAL* 3.2 6.1 + - - +
518A MET* 3.0 28.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 515 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A GLN* 4.7 8.8 + - - +
361A ASP 4.7 7.9 + - - -
362A LEU* 3.7 34.0 - - + +
364A LEU* 3.6 21.4 - - + +
511A ARG 3.1 17.5 + - - +
512A ALA* 3.8 7.4 - - - +
514A GLU* 1.3 74.7 - - - +
516A ARG* 1.3 58.0 + - - +
518A MET* 3.1 2.9 + - - +
519A GLU* 2.9 51.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 516 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ASP* 4.1 9.0 + - - +
489A GLU* 3.3 40.3 + - - +
490A VAL* 4.0 22.9 - - + +
493A LEU* 4.1 22.7 - - + +
512A ALA* 3.0 18.6 + - - +
513A VAL* 3.4 9.9 - - - +
515A ARG* 1.3 76.0 - - - +
517A VAL* 1.3 63.0 + - - +
519A GLU* 3.3 25.0 + - - +
520A HIS* 3.2 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 517 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A LEU* 3.8 20.4 - - + -
464A LEU* 4.8 1.8 - - + -
468A VAL* 3.7 45.1 - - + -
485A LEU* 4.4 8.7 - - + -
490A VAL* 4.5 5.8 - - + -
513A VAL* 2.9 25.3 + - + +
514A GLU* 3.2 10.3 + - - +
516A ARG* 1.3 76.1 - - - +
518A MET* 1.3 63.9 + - - +
520A HIS* 3.3 18.9 + - - +
521A ALA 3.3 7.4 + - - -
522A VAL* 4.2 10.2 + - + +
523A LEU* 4.2 13.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLN* 3.8 15.3 - - - +
349A THR 4.1 12.6 - - - +
350A ALA* 5.2 1.1 - - - -
351A LEU* 4.3 23.8 - - + -
362A LEU* 3.7 19.1 - - + -
364A LEU* 3.6 25.6 - - + +
365A TYR* 2.8 34.6 + - + -
514A GLU* 3.0 20.5 + - + +
515A ARG 3.7 1.3 - - - +
517A VAL* 1.3 77.9 - - - +
519A GLU* 1.3 58.0 + - - +
521A ALA* 2.9 12.2 + - - +
523A LEU* 3.4 28.5 - - - +
525A PRO* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 519 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A VAL* 3.8 2.4 - - - +
323A ARG* 2.9 31.3 + - - +
364A LEU* 3.5 13.0 - - + +
365A TYR* 3.2 10.0 + - - -
515A ARG* 2.9 37.7 + - + +
516A ARG* 3.3 34.1 + - + +
518A MET* 1.3 76.1 - - - +
520A HIS* 1.3 61.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 520 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A VAL* 3.8 2.6 - - - +
322A ARG* 2.8 47.0 + - - +
485A LEU* 3.9 31.9 - - + +
487A ASP* 2.7 35.4 + - + +
490A VAL* 4.7 0.9 - - + -
516A ARG* 3.2 29.1 + - + +
517A VAL* 3.4 9.2 - - - +
519A GLU* 1.3 75.7 - - + +
521A ALA* 1.3 57.2 + - - +
522A VAL* 3.1 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 521 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A MET* 3.4 13.9 - - - +
319A VAL* 4.6 0.4 - - + -
322A ARG* 3.4 15.3 - - + +
323A ARG* 3.8 22.4 - - + +
326A GLN* 3.1 25.9 + - + +
365A TYR* 3.7 19.7 - - + +
517A VAL 3.3 4.0 + - - -
518A MET* 2.9 14.2 + - - +
519A GLU 4.2 0.2 - - - +
520A HIS* 1.3 78.3 - - - +
522A VAL* 1.3 59.6 + - - +
523A LEU 3.4 2.9 - - - +
----------------------------------------------------------
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