Contacts of the helix formed by residues 471 - 484 (chain A) in PDB entry 1WKB
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 ASN 471 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LYS 5.3 0.6 + - - -
174A GLY 4.7 5.3 + - - -
175A TYR* 3.6 27.5 - - + -
468A ASP* 3.1 32.5 + - - +
469A TYR 3.2 0.6 - - - +
470A GLY* 1.3 74.2 - - - +
472A PRO* 1.3 65.1 - - - +
473A GLU* 2.9 32.8 + - - +
474A TRP* 3.0 16.8 + - + +
475A LYS* 2.9 27.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 472 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A GLY 3.0 10.5 - - - +
471A ASN* 1.3 82.9 - - - +
473A GLU* 1.3 82.9 + - - +
475A LYS* 3.4 13.1 + - + +
476A GLU* 3.1 21.1 + - - +
479A ARG* 4.7 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 473 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 5.1 4.9 - - + +
471A ASN* 2.9 22.6 + - - +
472A PRO* 1.3 90.4 - - - +
474A TRP* 1.3 63.3 + - - +
476A GLU* 3.1 16.8 + - - +
477A LYS* 3.2 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 474 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 4.1 9.2 - - + -
175A TYR* 3.5 52.5 + + + +
467A ILE* 3.4 31.6 - - + -
468A ASP 3.1 31.0 - - - -
469A TYR* 3.8 12.6 - + - -
471A ASN* 3.0 21.1 + - + +
473A GLU* 1.3 75.2 - - - +
475A LYS* 1.3 64.7 + - - +
476A GLU 3.2 0.3 + - - -
477A LYS* 3.2 7.3 + - - +
478A ALA* 3.0 18.9 + - - +
623A PHE* 2.9 50.3 + + + -
624A ASN* 4.1 3.4 - - - -
626A VAL* 3.6 11.8 - - + +
627A ALA* 3.4 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 475 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A TYR 2.7 23.3 + - - +
470A GLY* 3.7 15.0 - - - +
471A ASN 2.9 17.4 + - - +
472A PRO* 3.6 12.1 - - + +
474A TRP* 1.3 75.6 - - - +
476A GLU* 1.3 58.0 + - - +
478A ALA* 3.2 3.3 + - - +
479A ARG* 2.9 53.1 + - - +
500A ILE* 2.9 28.3 + - - +
501A ASP 3.2 17.6 + - - +
503A LEU* 2.6 35.5 + - - +
623A PHE* 3.8 11.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 476 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PRO 3.1 11.7 + - - +
473A GLU* 3.1 12.7 + - - +
474A TRP 3.1 0.6 - - - -
475A LYS* 1.3 74.7 - - - +
477A LYS* 1.3 65.1 + - - +
479A ARG* 3.0 37.4 + - - +
480A LYS* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 477 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LYS* 6.6 0.2 - - - -
175A TYR* 3.4 24.0 + - - -
473A GLU* 3.2 8.4 + - - +
474A TRP* 3.2 17.9 + - - +
476A GLU* 1.3 78.0 - - - +
478A ALA* 1.3 57.1 + - - +
480A LYS* 3.2 13.4 + - + +
481A ALA* 3.0 27.7 + - - +
626A VAL* 3.5 35.0 - - + +
627A ALA* 4.7 2.5 - - - +
634A TRP* 3.6 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A TRP 3.0 12.9 + - - +
475A LYS 3.4 9.2 - - - +
476A GLU 3.1 0.2 - - - -
477A LYS* 1.3 75.3 - - - +
479A ARG* 1.3 60.9 + - - +
481A ALA* 3.3 2.6 + - - +
482A LEU* 2.9 29.3 + - - +
500A ILE* 4.1 10.4 - - + +
622A ILE* 3.7 15.8 - - + +
623A PHE* 3.9 35.7 - - + -
626A VAL* 4.1 7.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 479 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A PRO 4.7 2.0 + - - -
475A LYS* 2.9 47.2 + - - +
476A GLU* 3.0 39.2 + - - +
478A ALA* 1.3 75.7 - - - +
480A LYS* 1.3 62.7 + - - +
482A LEU* 3.4 9.6 + - + +
483A GLU* 3.0 26.4 + - - +
497A GLU* 5.2 5.8 + - + +
500A ILE* 4.0 14.5 - - + +
501A ASP* 2.4 46.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 480 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A GLU* 3.1 13.0 + - - +
477A LYS* 3.4 15.7 - - - +
478A ALA 3.2 0.2 - - - -
479A ARG* 1.3 75.3 - - - +
481A ALA* 1.3 65.6 + - - +
483A GLU* 3.3 23.9 + - - +
484A ARG* 3.3 51.6 - - - +
631A GLU* 4.4 6.3 + - - +
634A TRP* 3.5 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 481 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A LYS 3.0 6.3 + - - -
478A ALA 3.7 5.6 - - - +
480A LYS* 1.3 76.3 - - - +
482A LEU* 1.3 63.6 + - - +
484A ARG* 3.1 16.2 + - - +
485A MET* 3.4 18.4 + - - +
622A ILE* 4.0 9.2 - - + -
626A VAL* 3.4 33.2 - - + -
634A TRP* 3.4 25.7 - - + -
635A PRO* 4.8 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 482 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ALA 2.9 16.5 + - - +
479A ARG* 3.7 6.3 - - - +
481A ALA* 1.3 76.2 - - - +
483A GLU* 1.3 61.1 + - - +
485A MET* 3.1 24.6 + - + +
487A ILE* 3.7 34.1 - - + -
493A ARG* 2.9 27.6 + - + +
496A PHE* 3.8 26.0 - - + -
497A GLU* 3.7 33.4 - - + +
500A ILE* 3.9 17.3 - - + -
622A ILE* 4.3 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 483 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A ARG 3.0 13.1 + - - +
480A LYS* 3.4 21.9 - - - +
482A LEU* 1.3 77.6 - - - +
484A ARG* 1.3 62.5 + - + +
485A MET 3.6 2.3 + - - +
493A ARG* 4.0 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A LYS* 3.3 47.6 - - - +
481A ALA* 3.1 7.5 + - - +
483A GLU* 1.3 79.6 - - + +
485A MET* 1.3 59.5 + - - +
631A GLU* 2.9 45.0 + - - +
634A TRP* 4.0 11.3 - - + -
635A PRO 5.2 1.7 - - - +
636A LYS* 4.4 5.7 - - - +
----------------------------------------------------------
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