Contacts of the helix formed by residues 486 - 498 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TYR* 5.2 10.0 + - - +
475A GLY 3.9 8.1 - - - +
476A ILE* 4.4 12.3 - - + +
484A GLY 4.4 0.4 + - - -
485A GLN* 1.3 71.1 + - - +
487A VAL* 1.3 67.0 + - - +
488A GLN* 4.2 23.9 - - + +
489A ASP* 3.1 33.7 + - - +
490A VAL* 3.0 23.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ARG* 3.4 23.3 - - - +
297A GLU* 3.6 19.5 - - + +
432A ILE* 3.4 29.6 - - + -
471A GLY 3.6 12.1 - - - +
472A PHE* 3.6 21.9 + - + +
475A GLY 3.6 18.8 + - - +
476A ILE 4.1 0.7 - - - +
477A MSE 4.4 13.5 - - + -
485A GLN 3.4 3.6 + - - -
486A LYS* 1.3 69.2 - - - +
488A GLN* 1.3 65.9 + - - +
490A VAL* 3.1 2.4 + - - +
491A LYS* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PHE* 3.6 40.3 + - + +
473A TYR* 3.8 42.9 + - - +
486A LYS* 4.2 22.7 - - + +
487A VAL* 1.3 83.7 - - - +
489A ASP* 1.3 72.4 + - - +
490A VAL 3.2 0.2 + - - -
491A LYS* 3.7 9.7 + - - +
492A LYS* 4.8 5.0 + - - +
508B MSE 5.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLN* 5.9 1.3 - - - +
486A LYS* 3.1 35.4 + - + +
488A GLN* 1.3 91.3 - - - +
490A VAL* 1.3 62.2 + - + +
492A LYS* 4.9 3.0 + - - +
493A THR* 4.2 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 4.6 0.9 - - + -
477A MSE 4.1 15.7 - - + -
482A PHE* 4.4 12.3 - - + -
485A GLN* 3.4 44.2 - - + +
486A LYS 3.0 13.1 + - - +
487A VAL 3.9 2.2 - - - +
489A ASP* 1.3 79.6 - - + +
491A LYS* 1.3 69.3 + - - +
492A LYS 3.3 2.7 - - - -
493A THR* 2.8 30.9 + - - +
494A ILE* 3.1 36.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLU* 5.8 4.0 - - - -
294A LEU 4.0 19.1 + - - +
296A PRO* 3.9 15.1 - - + +
297A GLU* 3.7 29.6 - - - +
472A PHE* 4.1 26.3 - - + -
487A VAL 2.9 17.0 + - - +
488A GLN 3.7 6.7 + - - +
490A VAL* 1.3 79.1 - - - +
492A LYS* 1.3 77.1 + - + +
494A ILE* 3.2 5.2 + - - +
495A GLN* 3.0 27.9 + - + +
263B GLU* 4.8 23.2 + - - +
508B MSE 5.3 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLU* 6.1 0.4 - - - -
488A GLN 4.8 5.3 + - - +
489A ASP 4.9 2.4 + - - +
490A VAL 3.0 1.0 + - - -
491A LYS* 1.3 95.5 - - + +
493A THR* 1.3 62.0 + - + +
495A GLN* 3.5 15.4 + - - +
496A LYS* 3.1 27.4 + - - +
263B GLU* 3.9 23.1 + - - -
492B LYS* 3.0 38.6 - - - +
495B GLN* 5.3 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A PHE* 5.2 6.9 - - - -
489A ASP 4.2 12.6 - - - +
490A VAL* 2.8 27.8 + - - +
492A LYS* 1.3 80.8 - - + +
494A ILE* 1.3 62.2 + - - +
496A LYS* 3.7 6.9 + - - +
497A LYS* 3.3 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A PRO 3.4 25.4 - - - +
297A GLU* 3.6 20.9 - - + -
300A PHE* 4.1 9.0 - - + -
366A LEU* 4.1 19.3 - - + -
477A MSE 3.6 15.0 - - + -
482A PHE* 4.3 18.6 - - + -
490A VAL* 3.1 33.6 + - + +
491A LYS* 3.2 7.9 + - - +
493A THR* 1.3 77.9 + - - +
495A GLN* 1.3 67.4 + - - +
496A LYS 3.2 1.1 - - - -
497A LYS* 3.3 17.0 + - + +
498A MSE 3.3 15.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLU* 3.4 26.2 + - - +
265A THR* 2.4 38.6 + - + +
296A PRO* 4.4 8.1 - - + +
491A LYS* 3.0 19.5 + - + +
492A LYS* 3.5 18.0 - - - +
494A ILE* 1.3 80.2 - - - +
496A LYS* 1.3 63.1 + - + +
498A MSE 3.3 13.2 + - - +
499A ILE* 3.2 35.5 + - + +
504A ALA* 5.4 0.5 - - - +
506A ILE* 3.6 19.7 - - - +
492B LYS* 5.1 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A LYS 3.1 16.2 + - - +
493A THR* 3.7 7.2 + - - +
494A ILE 3.2 0.6 - - - -
495A GLN* 1.3 76.6 - - + +
497A LYS* 1.3 59.1 + - - +
499A ILE* 4.5 10.8 - - + -
500A ASP* 2.8 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A PHE* 6.6 0.2 - - + -
366A LEU* 5.5 8.3 - - + -
481A GLY* 6.3 0.4 - - - -
482A PHE* 4.0 29.1 - - + -
493A THR* 3.3 18.5 + - - +
494A ILE* 3.3 12.2 + - + +
496A LYS* 1.3 78.4 - - - +
498A MSE 1.3 56.2 + - + +
500A ASP* 3.7 3.3 - - - +
501A ALA* 2.8 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A THR* 4.2 13.7 - - + -
267A LEU* 3.9 30.3 - - + -
296A PRO* 3.4 42.8 - - + +
299A MSE 4.6 1.1 - - + -
365A PRO* 4.6 7.9 - - + -
366A LEU* 3.8 37.5 - - + -
494A ILE 3.3 13.6 + - - +
495A GLN* 3.3 6.1 + - - +
497A LYS* 1.3 78.9 - - - +
499A ILE* 1.3 58.2 + - - +
501A ALA* 3.6 2.0 + - - -
502A GLY 3.3 1.9 + - - -
503A ASP* 2.5 44.1 + - + +
504A ALA* 3.0 19.1 + - + +
----------------------------------------------------------
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