Contacts of the helix formed by residues 491 - 503 (chain A) in PDB entry 5KJH
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 SER 491 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LYS* 5.0 2.3 + - - +
480A ALA* 4.1 1.1 - - - -
481A SER* 3.9 11.5 + - - -
484A PRO* 6.4 1.6 - - - -
490A PHE* 1.3 77.3 - - - +
492A ARG* 1.3 66.4 + - - +
493A GLU* 3.7 19.5 + - - +
494A THR* 2.9 31.3 + - - -
495A LEU* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A ALA* 3.7 21.7 - - + +
491A SER* 1.3 71.7 - - - +
493A GLU* 1.3 77.6 + - - +
495A LEU* 3.3 6.2 + - + +
496A GLN* 2.8 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 493 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LYS* 4.2 20.3 + - + +
491A SER* 3.2 17.9 + - - +
492A ARG* 1.3 107.5 + - - +
494A THR* 1.4 58.4 + - - +
496A GLN* 3.9 5.5 - - - +
497A ALA* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 494 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PRO* 3.8 15.4 - - + +
415A LYS* 3.1 31.4 + - - +
490A PHE* 3.8 16.5 - - + +
491A SER* 2.9 26.1 + - - -
493A GLU* 1.4 79.2 - - - +
495A LEU* 1.3 62.0 + - - +
497A ALA* 3.4 2.4 + - - +
498A TRP* 3.1 60.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TYR* 4.6 1.9 + - - -
367A MET* 4.6 15.0 - - + +
370A LEU* 4.8 2.7 - - + -
478A VAL* 4.2 24.0 - - + +
479A SER 3.9 10.3 - - - +
480A ALA* 3.8 37.0 - - + +
490A PHE* 3.9 27.6 - - + +
491A SER 3.1 12.8 + - - +
492A ARG* 3.7 7.2 - - + +
494A THR* 1.3 75.0 - - - +
496A GLN* 1.4 57.0 + - - +
498A TRP* 3.5 20.0 + - + +
499A ALA* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A ARG* 2.8 33.8 + - + +
493A GLU* 3.9 6.5 - - - +
494A THR 3.3 0.2 - - - -
495A LEU* 1.4 69.3 - - - +
497A ALA* 1.4 59.2 + - - +
499A ALA* 3.2 11.5 + - - +
500A ASP* 2.9 55.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A LYS* 4.3 26.7 - - + +
493A GLU 3.0 18.6 + - - +
494A THR* 3.6 4.9 - - - +
496A GLN* 1.4 75.1 - - - +
498A TRP* 1.4 65.6 + - + +
500A ASP* 3.4 22.2 + - - +
501A MET* 3.5 13.8 + - - +
512A LYS* 5.4 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TYR* 3.8 18.4 - + + -
366A PHE* 3.8 23.6 - + - -
367A MET* 5.0 0.9 - - - -
408A LYS* 3.7 12.8 - - + -
412A LEU* 3.6 38.5 - - + +
413A VAL 2.8 24.6 + - - +
414A PRO* 3.7 21.5 - - + +
490A PHE* 3.7 38.8 - + - -
494A THR* 3.1 32.4 + - + +
495A LEU* 3.7 17.0 - - + +
497A ALA* 1.4 76.7 - - + +
499A ALA* 1.4 53.9 + - - +
501A MET* 3.2 2.2 + - - -
502A TYR* 2.8 48.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TYR* 3.6 16.7 + - - +
495A LEU 2.9 18.1 + - - +
496A GLN* 3.6 15.7 - - - +
498A TRP* 1.4 71.6 - - - +
500A ASP* 1.3 64.9 + - - +
503A ASP* 2.9 42.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A GLN* 2.9 42.5 + - - +
497A ALA* 3.4 13.5 - - - +
499A ALA* 1.3 75.6 - - - +
501A MET* 1.3 58.5 + - - +
503A ASP 5.5 0.3 - - - +
510A LEU 3.6 7.3 - - - +
511A ILE* 3.5 8.3 - - - +
512A LYS* 2.9 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A PHE* 3.3 0.9 - - - -
497A ALA 3.5 9.8 + - - +
498A TRP* 3.2 7.7 + - - +
500A ASP* 1.3 79.6 - - - +
502A TYR* 1.3 89.3 + - + +
511A ILE* 3.2 14.8 - - - +
512A LYS* 3.7 43.7 - - + +
513A ALA 3.4 19.7 - - - +
514A HIS* 2.9 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ARG* 2.8 56.1 + - + -
360A PHE* 3.5 22.4 - + + +
363A TYR* 3.3 36.5 - + + -
411A TRP* 3.7 10.7 + + - -
412A LEU* 3.5 32.1 - - + -
498A TRP* 2.8 33.0 + + - +
501A MET* 1.3 104.2 - - + +
503A ASP* 1.3 64.4 + - - +
504A LEU* 3.5 4.7 + - - +
514A HIS* 3.5 24.8 - + - -
222B ASN* 5.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A TYR* 3.8 16.5 + - + +
499A ALA* 2.9 35.9 + - + +
500A ASP 5.5 0.5 - - - +
502A TYR* 1.3 76.6 - - - +
504A LEU* 1.3 63.5 + - - +
505A SER* 2.7 40.6 + - - -
506A ASN* 4.2 4.7 + - - +
511A ILE* 4.5 9.9 - - - +
218B SER* 5.3 2.1 + - - -
----------------------------------------------------------
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