Contacts of the strand formed by residues 451 - 457 (chain D) in PDB entry 2CKJ
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 GLU 451 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D ARG* 3.6 12.6 + - - -
439D ARG* 2.2 43.5 + - - +
440D VAL* 3.5 8.0 - - - +
441D LEU* 3.1 47.7 + - + +
449D VAL* 4.8 2.6 - - - +
450D GLN* 1.3 90.2 - - - +
452D LEU* 1.3 61.3 + - - +
474D LEU* 5.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 452 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D ARG* 3.6 12.3 - - - +
440D VAL* 3.3 27.8 - - + -
449D VAL* 4.7 11.7 - - + -
450D GLN 4.4 0.2 + - - -
451D GLU* 1.3 75.3 - - - +
453D ALA* 1.4 61.1 + - - +
454D LEU* 4.5 22.0 - - + -
470D THR* 2.8 67.5 - - + +
473D GLN* 4.5 15.5 - - + -
474D LEU* 4.8 8.5 - - + +
478D TRP* 4.4 14.4 - - + -
482D LEU* 6.0 1.8 - - + -
486D VAL* 6.0 3.8 - - + -
516D PHE* 5.3 4.3 - - + -
519D PHE* 4.8 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 453 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366D MET 5.8 0.2 - - - +
367D ALA* 4.7 15.4 - - - +
437D GLY 4.3 0.6 - - - +
438D MET* 3.8 1.7 - - - -
439D ARG* 3.0 48.2 + - + +
452D LEU* 1.4 75.0 - - - +
454D LEU* 1.3 69.8 + - - +
455D CYS* 4.1 10.1 - - - -
465D SER* 4.7 11.0 - - - +
466D ALA* 4.8 0.2 - - - -
470D THR* 3.9 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 454 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437D GLY 4.2 1.6 - - - -
438D MET* 3.9 30.7 - - + -
452D LEU* 4.5 13.9 - - + -
453D ALA* 1.3 86.8 - - - +
455D CYS* 1.3 60.6 + - - +
456D TYR* 3.9 21.3 - - + +
465D SER* 3.8 0.2 - - - -
466D ALA* 2.9 40.5 + - + +
469D THR* 6.2 1.1 - - + -
470D THR* 4.3 7.6 - - - +
486D VAL* 4.4 13.5 - - + -
490D LEU* 4.4 17.5 - - + -
516D PHE* 3.8 25.8 - - + -
519D PHE* 4.3 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 455 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D PRO* 3.6 25.7 - - + +
366D MET* 3.5 24.9 - - - -
367D ALA* 3.3 31.4 - - - -
436D SER* 3.2 7.2 + - - -
437D GLY 3.1 33.1 + - - +
453D ALA* 4.8 4.5 - - - -
454D LEU* 1.3 76.3 - - - +
456D TYR* 1.3 62.3 + - - +
457D GLY 4.4 0.2 - - - -
463D THR* 5.0 0.7 - - + -
464D ILE 3.1 7.2 - - - +
465D SER* 4.5 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 456 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D PRO* 4.4 2.7 - - - -
434D VAL* 4.1 13.0 - - + -
435D THR 3.6 1.3 - - - -
436D SER* 4.0 21.5 - - - -
438D MET* 3.5 18.3 - - + +
454D LEU* 3.9 30.8 - - + +
455D CYS* 1.3 73.0 - - - +
457D GLY* 1.3 61.9 + - - +
458D GLY 3.8 0.9 + - - -
459D MET* 4.1 15.8 + - + -
462D ARG 4.0 1.7 - - - +
463D THR* 5.1 0.4 - - - +
464D ILE* 2.5 44.2 + - + +
465D SER 6.1 0.2 - - - -
466D ALA* 5.7 2.0 - - - -
490D LEU* 4.2 18.2 - - + +
494D LEU* 4.5 16.6 - - + -
512D THR* 2.6 57.7 + - + -
515D PHE* 4.8 2.0 - + - -
516D PHE* 4.5 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 457 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D PRO 3.6 15.5 - - - -
358D ILE* 5.1 0.4 - - - -
363D PRO* 3.6 16.7 - - - +
434D VAL* 3.7 7.4 - - - +
435D THR* 2.7 43.2 + - - +
456D TYR* 1.3 75.5 - - - +
458D GLY* 1.3 61.2 + - - -
459D MET* 3.6 1.6 + - - +
463D THR* 4.8 4.7 - - - -
----------------------------------------------------------
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