Contacts of the helix formed by residues 486 - 498 (chain B) in PDB entry 2WFD
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 LYS 486 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B TYR* 5.3 9.3 + - - +
475B GLY 3.9 8.3 - - - +
476B ILE* 4.4 11.4 - - + +
484B GLY 4.3 0.6 + - - -
485B GLN* 1.3 71.3 + - - +
487B VAL* 1.3 66.3 + - - +
488B GLN* 4.3 24.1 - - + +
489B ASP* 3.0 33.2 + - - +
490B VAL* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ARG* 3.3 24.2 - - - +
297B GLU* 3.6 18.8 - - + +
432B ILE* 3.5 29.6 - - + -
471B GLY 3.5 11.9 - - - +
472B PHE* 3.6 23.3 + - + +
475B GLY 3.5 20.1 + - - +
476B ILE 4.1 0.9 - - - +
477B MSE 4.4 13.2 - - + -
485B GLN 3.3 4.4 + - - -
486B LYS* 1.3 68.9 - - - +
488B GLN* 1.3 64.2 + - - +
490B VAL* 3.1 2.2 + - - +
491B LYS* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A MSE 5.6 2.9 - - + -
472B PHE* 3.6 39.7 + - + +
473B TYR* 3.8 43.5 + - - +
486B LYS* 4.3 22.4 - - + +
487B VAL* 1.3 82.5 - - - +
489B ASP* 1.3 72.0 + - - +
490B VAL 3.2 0.2 + - - -
491B LYS* 3.7 10.2 + - - +
492B LYS* 4.8 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B GLN* 5.9 1.8 - - - +
486B LYS* 3.0 35.7 + - + +
488B GLN* 1.3 91.7 - - - +
490B VAL* 1.3 62.9 + - + +
492B LYS* 4.9 3.3 + - - +
493B THR* 4.2 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLU* 4.6 0.9 - - + -
477B MSE 4.1 15.9 - - + -
482B PHE* 4.4 12.3 - - + -
485B GLN* 3.5 42.2 - - + +
486B LYS 3.0 12.6 + - - +
487B VAL 3.9 2.7 - - - +
489B ASP* 1.3 80.1 - - + +
491B LYS* 1.3 68.9 + - - +
492B LYS 3.3 2.2 - - - -
493B THR* 2.8 31.6 + - - +
494B ILE* 3.1 34.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A PRO 5.2 5.9 + - - -
263A GLU* 4.7 21.2 + - - +
508A MSE 5.4 2.4 - - - +
263B GLU* 5.8 4.5 - - - -
294B LEU 4.0 20.5 + - - +
296B PRO* 3.8 13.8 - - + +
297B GLU* 3.8 30.1 - - - +
472B PHE* 4.1 26.8 - - + -
487B VAL 2.9 16.5 + - - +
488B GLN 3.7 6.9 + - - +
490B VAL* 1.3 78.7 - - - +
492B LYS* 1.3 77.6 + - + +
494B ILE* 3.1 6.3 + - - +
495B GLN* 3.0 27.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 492 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLU* 3.4 25.6 + - - -
492A LYS* 3.0 38.4 - - - +
495A GLN* 5.1 4.0 + - - -
263B GLU* 6.1 0.9 - - - -
488B GLN 4.8 5.1 + - - +
489B ASP 4.9 2.4 + - - +
490B VAL 3.0 2.0 + - - -
491B LYS* 1.3 95.7 - - + +
493B THR* 1.3 62.6 + - + +
495B GLN* 3.5 16.0 - - - +
496B LYS* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 493 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B PHE* 5.2 7.0 - - - -
489B ASP 4.2 12.8 - - - +
490B VAL* 2.8 26.4 + - - +
492B LYS* 1.3 80.8 - - + +
494B ILE* 1.3 61.5 + - - +
496B LYS* 3.7 7.0 + - - +
497B LYS* 3.3 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 494 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B PRO 3.4 25.6 - - - +
297B GLU* 3.6 20.6 - - + -
300B PHE* 4.1 9.6 - - + -
366B LEU* 4.0 18.8 - - + -
477B MSE 3.7 15.0 - - + -
482B PHE* 4.3 17.7 - - + -
490B VAL* 3.1 33.2 + - + -
491B LYS 3.1 7.9 + - - +
493B THR* 1.3 79.1 + - - +
495B GLN* 1.3 67.2 + - - +
496B LYS 3.2 0.2 - - - -
497B LYS* 3.3 14.8 + - + +
498B MSE 3.4 16.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 495 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LYS* 5.3 4.2 + - - -
263B GLU* 3.3 25.8 + - - +
265B THR* 2.3 40.8 + - + +
296B PRO* 4.4 8.7 - - + +
491B LYS* 3.0 18.1 + - + +
492B LYS* 3.5 17.6 - - - +
494B ILE* 1.3 80.1 - - - +
496B LYS* 1.3 63.1 + - + +
498B MSE 3.3 13.1 + - - +
499B ILE* 3.2 35.5 + - + +
506B ILE* 3.6 19.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LYS 3.1 14.9 + - - +
493B THR* 4.2 7.4 - - - +
494B ILE 3.2 0.4 - - - -
495B GLN* 1.3 77.8 - - + +
497B LYS* 1.3 60.6 + - - +
499B ILE* 4.4 11.0 - - + -
500B ASP* 2.8 55.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 497 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B LEU* 5.5 8.3 - - + -
482B PHE* 4.0 28.7 - - + -
493B THR* 3.3 18.2 + - - +
494B ILE* 3.3 11.8 + - + +
495B GLN 3.3 0.8 - - - -
496B LYS* 1.3 78.0 - - - +
498B MSE 1.3 60.3 + - + +
500B ASP* 3.6 3.2 - - - +
501B ALA* 2.8 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 498 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B THR* 4.3 14.1 - - + -
267B LEU* 4.0 29.8 - - + -
296B PRO* 3.5 41.7 - - + +
299B MSE 4.5 1.1 - - + -
365B PRO* 4.5 9.0 - - + -
366B LEU* 3.7 36.6 - - + -
494B ILE* 3.4 13.9 + - + +
495B GLN* 3.3 6.3 + - - +
497B LYS* 1.3 78.6 - - - +
499B ILE* 1.3 56.7 + - - +
501B ALA* 3.6 2.4 + - - -
502B GLY 3.3 2.3 + - - -
503B ASP* 2.6 44.4 + - + +
504B ALA* 3.0 17.8 + - + +
----------------------------------------------------------
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