Contacts of the helix formed by residues 596 - 613 (chain B) in PDB entry 1KEK
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 596 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B HIS* 4.2 12.1 + - - -
595B GLY* 1.3 72.0 - - - -
597B LYS* 1.3 59.2 + - - +
598B ILE 3.3 0.9 - - - -
599B VAL* 3.2 27.0 + - - +
600B LYS* 2.8 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B LYS* 5.1 13.2 - - - +
595B GLY* 3.4 0.8 - - - -
596B GLU* 1.3 78.3 - - - +
598B ILE* 1.3 64.7 + - + +
600B LYS* 3.3 7.2 + - - +
601B MET* 2.9 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B LEU* 5.7 4.9 - - + -
591B TYR* 3.9 25.6 - - + -
592B GLY 5.6 0.2 - - - +
593B LYS* 4.2 21.8 - - + -
594B LYS* 3.7 26.0 - - + +
595B GLY 4.4 4.0 + - - +
596B GLU 3.3 0.4 - - - -
597B LYS* 1.3 84.2 - - + +
599B VAL* 1.3 63.7 + - + +
601B MET* 3.5 17.9 + - - +
602B ASN* 2.8 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B ILE* 3.7 17.1 - - + +
588B HIS* 3.6 39.7 - - + +
591B TYR* 3.7 12.1 - - + -
592B GLY* 3.5 33.2 - - - +
595B GLY 4.2 3.1 + - - +
596B GLU* 3.2 28.7 + - - +
598B ILE* 1.3 78.4 - - - +
600B LYS* 1.3 56.8 + - - +
602B ASN* 3.3 3.8 + - - +
603B THR* 3.0 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B GLU* 2.8 26.3 + - - +
597B LYS* 3.6 6.7 - - - +
599B VAL* 1.3 75.8 - - - +
601B MET* 1.3 60.9 + - + +
603B THR* 3.3 20.5 + - - +
604B ASP* 2.8 55.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B VAL* 3.4 22.5 - - - +
554B GLY* 3.1 41.5 - - - +
555B LEU* 3.8 19.1 - - + -
597B LYS* 2.9 47.2 + - + +
598B ILE* 3.7 17.3 - - - +
600B LYS* 1.3 75.9 - - + +
602B ASN* 1.3 57.4 - - - +
604B ASP* 3.4 7.3 + - - +
605B ALA* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B LEU* 3.8 21.8 - - - +
560B ASN* 5.2 2.2 + - - -
561B MET* 3.6 34.2 - - + +
587B ILE* 3.7 24.2 - - + -
591B TYR* 4.0 22.4 + - - -
598B ILE* 2.8 33.4 + - - +
601B MET* 1.3 73.8 - - - +
603B THR* 1.3 59.6 + - - +
605B ALA* 3.2 7.1 - - - +
606B VAL* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B LYS* 4.4 19.4 + - + +
587B ILE* 4.1 18.4 - - - +
588B HIS* 4.6 9.8 - - + -
599B VAL* 3.0 23.1 + - - +
600B LYS* 3.5 28.3 - - - +
602B ASN* 1.3 74.7 - - - +
604B ASP* 1.3 59.6 + - - +
606B VAL* 3.1 5.3 + - - +
607B ASP* 2.9 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B VAL* 3.8 22.3 - - + +
600B LYS* 2.8 46.0 + - - +
601B MET* 3.6 8.0 - - - +
602B ASN 3.3 0.2 - - - -
603B THR* 1.3 74.6 - - - +
605B ALA* 1.3 60.4 + - - +
607B ASP* 3.9 9.5 - - - +
608B GLN* 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ILE* 4.5 6.2 - - - +
553B VAL* 4.0 12.5 - - + +
555B LEU* 3.8 20.6 - - + -
561B MET* 4.0 13.7 - - + -
562B ILE* 4.3 12.2 - - + +
565B THR* 4.9 0.4 - - - -
601B MET 3.0 14.1 + - - +
602B ASN 3.2 10.5 - - - +
604B ASP* 1.3 75.6 - - - +
606B VAL* 1.3 65.5 + - - +
608B GLN* 3.9 0.5 - - - +
609B ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561B MET* 3.9 8.7 - - + -
565B THR* 3.5 22.8 - - + +
580B VAL* 4.7 7.9 - - + -
583B LEU* 3.5 27.1 - - + -
584B LYS* 3.9 22.9 - - + -
587B ILE* 3.5 21.1 - - + -
602B ASN 2.9 18.7 + - - +
603B THR 3.1 6.7 + - - +
605B ALA* 1.3 76.0 - - - +
607B ASP* 1.3 58.3 + - - +
609B ALA* 3.7 1.2 - - - +
610B VAL* 2.9 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B VAL* 5.5 1.4 - - - +
584B LYS* 2.8 31.7 + - - -
603B THR* 2.9 30.5 + - - +
604B ASP* 4.0 8.6 - - - +
606B VAL* 1.3 77.5 - - - +
608B GLN* 1.3 56.2 + - - +
610B VAL* 3.4 7.6 + - - +
611B THR* 3.0 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B ILE* 3.5 34.6 - - + +
552B ASP* 3.6 29.9 + - - +
553B VAL* 3.8 16.0 - - + +
604B ASP 2.9 18.8 + - - +
605B ALA 4.0 1.8 - - - +
607B ASP* 1.3 72.5 - - - +
609B ALA* 1.3 59.9 + - - +
611B THR* 3.2 7.0 + - - -
612B SER* 2.9 37.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ILE* 4.2 8.0 - - - +
549B ILE* 4.5 3.7 - - - +
562B ILE* 4.1 22.9 - - + -
565B THR* 3.8 22.7 - - + +
605B ALA 2.9 18.7 + - - +
606B VAL 3.7 3.1 - - - +
608B GLN* 1.3 74.4 - - - +
610B VAL* 1.3 60.3 + - - +
612B SER 3.2 0.7 + - - -
613B LEU* 2.8 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B THR* 3.5 18.2 - - + -
569B LYS* 2.7 47.2 + - + +
576B PHE* 4.1 25.8 - - + -
580B VAL* 4.6 16.6 - - + -
606B VAL* 2.9 29.9 + - + +
607B ASP* 3.8 6.7 - - - +
609B ALA* 1.3 76.4 - - - +
611B THR* 1.3 65.2 + - - +
613B LEU* 3.6 1.4 + - - -
614B GLN* 3.9 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ASP* 3.0 16.1 + - - +
608B GLN* 3.4 11.7 - - - +
609B ALA 3.1 0.2 - - - -
610B VAL* 1.3 79.7 - - - +
612B SER* 1.3 59.9 + - - +
614B GLN* 2.9 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B ASN 4.9 7.3 - - - +
544B ILE* 4.3 6.9 - - - +
549B ILE* 4.1 22.1 - - - +
608B GLN* 2.9 21.6 + - - +
609B ALA 3.9 2.5 - - - -
611B THR* 1.3 77.6 - - - +
613B LEU* 1.3 60.8 + - - +
614B GLN* 2.8 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B VAL* 4.9 1.6 - - + -
542B TYR* 3.9 19.9 - - + -
543B ASN 5.4 1.1 - - - +
544B ILE* 3.3 32.3 - - + -
562B ILE 4.8 0.4 - - - +
565B THR* 4.2 5.4 - - + -
566B ALA* 3.8 32.5 - - + +
569B LYS* 2.9 34.8 + - + +
570B LEU* 3.8 25.6 - - + -
609B ALA* 2.8 43.4 + - + +
610B VAL* 3.6 3.1 + - - +
611B THR 3.4 2.0 - - - -
612B SER* 1.3 69.3 - - - +
614B GLN* 1.3 64.9 + - - +
----------------------------------------------------------
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