Contacts of the helix formed by residues 429 - 438 (chain A) in PDB entry 1BK6
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 CYS 429 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ILE* 6.1 0.7 - - + -
389A VAL* 4.1 20.9 - - + -
392A LEU* 5.8 0.4 - - - -
407A ILE* 4.3 20.9 - - + -
424A LEU* 3.5 34.9 + - + +
425A VAL* 4.3 4.2 + - - -
427A GLN 3.8 0.4 - - - -
428A GLY* 1.3 75.5 - - - +
430A ILE* 1.3 63.0 + - - +
432A PRO* 3.1 6.9 - - - +
433A LEU* 2.9 39.0 + - + +
455A ILE* 4.1 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 430 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A VAL* 3.9 40.2 - - + +
428A GLY* 3.4 1.5 - - - -
429A CYS* 1.3 78.4 - - - +
431A LYS* 1.3 60.8 + - - +
433A LEU* 3.1 8.7 + - - +
434A CYS* 2.9 32.9 + - - -
452A LEU* 4.8 2.5 - - + -
455A ILE* 4.3 22.0 - - + -
473A ASN* 4.3 6.5 - - - +
476A PHE* 3.8 30.1 - - + +
477A ILE* 3.7 36.3 - - + +
480A ALA* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 431 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLY* 4.5 3.0 + - - +
430A ILE* 1.3 77.8 - - - +
432A PRO* 1.3 72.7 - - + +
434A CYS* 3.4 1.0 + - - +
435A ASP* 3.1 51.8 + - - +
479A LYS 5.0 0.6 + - - -
480A ALA* 3.1 50.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 432 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A VAL* 4.2 8.1 - - + +
392A LEU* 3.1 32.9 - - + +
393A GLU* 3.8 36.7 - - + +
428A GLY 3.2 21.1 - - - +
429A CYS* 3.1 13.7 - - - +
431A LYS* 1.3 97.4 - - + +
433A LEU* 1.3 58.6 + - - -
435A ASP* 4.0 6.9 - - + +
436A LEU* 3.3 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 433 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 3.7 22.9 - - + +
404A CYS* 5.0 12.1 - - - +
407A ILE* 4.7 17.9 - - + -
408A SER* 6.4 0.2 - - - -
429A CYS* 2.9 29.1 + - + +
430A ILE* 3.1 5.4 + - - +
432A PRO* 1.3 75.8 - - - +
434A CYS* 1.3 67.3 + - - +
436A LEU* 3.1 19.5 + - + +
437A LEU 3.7 0.3 + - - -
448A THR* 3.4 29.1 - - + +
451A ALA* 4.2 19.3 - - + -
452A LEU* 4.5 10.1 - - + -
455A ILE* 3.9 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ILE* 2.9 26.1 + - - +
431A LYS 3.8 3.8 - - - +
433A LEU* 1.3 74.8 - - - +
435A ASP* 1.3 66.8 + - - +
437A LEU* 3.2 23.8 + - - +
452A LEU* 4.1 16.6 - - - +
477A ILE* 3.8 17.9 - - - -
480A ALA* 4.3 8.5 - - + +
481A GLY 4.8 0.2 - - - -
482A GLY* 3.2 37.2 - - - +
485A LYS* 3.3 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 435 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LYS* 3.1 42.5 + - - +
432A PRO* 4.0 7.6 - - + +
433A LEU 3.3 0.2 - - - -
434A CYS* 1.3 75.5 - - - +
436A LEU* 1.3 64.7 + - - +
438A GLU* 3.3 18.8 + - - +
439A ILE* 4.2 5.9 + - - +
480A ALA 3.7 18.2 - - - +
485A LYS* 4.3 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 4.4 14.4 - - + +
397A TYR* 4.3 17.7 - - + -
400A LYS* 4.3 24.7 - - + +
404A CYS* 3.8 19.7 - - + -
432A PRO 3.3 12.8 + - - +
433A LEU* 3.1 15.2 + - + +
435A ASP* 1.3 76.7 - - - +
437A LEU* 1.3 64.6 + - - +
438A GLU 3.1 0.9 + - - -
439A ILE* 3.1 19.4 + - + +
440A ALA* 2.9 33.1 + - + +
444A ILE* 3.7 14.8 - - + -
448A THR* 3.7 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A CYS* 3.2 17.0 + - - +
436A LEU* 1.3 77.5 - - - +
438A GLU* 1.3 60.1 + - - +
439A ILE 3.4 0.9 + - - -
440A ALA* 3.9 9.8 + - - +
445A ILE* 3.9 41.9 - - + +
448A THR* 3.6 32.3 - - + -
449A LEU* 4.0 11.4 - - + -
452A LEU* 4.1 12.8 - - + -
482A GLY 4.8 0.4 - - - +
485A LYS* 4.2 19.7 - - + +
486A ILE* 4.0 30.1 - - + +
489A CYS* 4.6 8.7 - - - -
398B LYS* 5.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A CYS 4.2 0.6 + - - -
435A ASP 3.3 13.5 + - - +
436A LEU 3.0 0.6 - - - -
437A LEU* 1.3 81.2 - - - +
439A ILE* 1.3 65.1 + - + +
485A LYS* 3.3 37.9 - - - +
488A ASN* 5.2 4.7 - - - +
355B GLU* 5.7 5.4 - - - +
356B ASN* 5.8 1.2 + - - -
398B LYS* 3.5 26.0 + - - -
----------------------------------------------------------
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