Contacts of the helix formed by residues 604 - 616 (chain D) in PDB entry 1K0Y
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 THR 604 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602D HIS* 4.8 13.7 - - + -
603D LEU* 1.4 76.2 - - - +
605D PRO* 1.4 76.9 - - - +
606D GLU* 3.5 11.0 + - - +
607D GLU* 3.0 37.4 + - - +
608D LYS* 2.9 19.6 + - - +
732D LYS* 5.3 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 605 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D LEU 4.6 0.9 - - - +
604D THR* 1.4 87.7 - - - +
606D GLU* 1.4 57.9 + - - +
608D LYS* 3.2 7.0 + - + +
609D SER* 2.9 32.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 606 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604D THR* 3.5 12.1 - - - +
605D PRO* 1.4 78.6 - - - +
607D GLU* 1.4 75.8 + - - +
609D SER* 3.3 7.5 + - - -
610D ALA* 2.9 30.0 + - - +
725D PRO* 4.9 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 607 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D LEU* 3.8 13.4 - - + +
604D THR* 3.0 38.1 + - - +
606D GLU* 1.4 90.0 - - - +
608D LYS* 1.4 62.5 + - - +
610D ALA* 3.3 4.1 + - - +
611D VAL* 3.1 28.4 + - - +
725D PRO 5.2 2.5 - - - +
728D ALA* 4.7 5.9 - - - +
729D ALA* 3.8 27.5 + - + +
732D LYS* 3.0 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 608 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D LEU* 3.9 18.8 - - + +
604D THR 2.9 11.6 + - - +
605D PRO* 3.7 10.5 - - + +
607D GLU* 1.4 76.1 - - - +
609D SER* 1.4 56.7 - - - +
611D VAL* 3.4 2.9 + - - +
612D THR* 3.0 47.0 + - - +
675D LEU 5.5 2.8 + - - -
678D LEU* 4.0 29.3 - - + +
679D ASP* 6.0 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 609 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605D PRO 2.9 20.4 + - - -
606D GLU* 3.6 8.4 - - - -
607D GLU 3.3 0.2 - - - -
608D LYS* 1.4 77.3 - - - +
610D ALA* 1.4 54.8 + - - +
612D THR* 4.0 4.6 - - - -
613D ALA* 2.9 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 610 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D GLU 2.9 17.7 + - - +
607D GLU* 3.3 8.9 + - - +
609D SER* 1.4 73.5 - - - +
611D VAL* 1.4 63.3 + - - +
613D ALA* 4.2 2.7 - - - +
614D LEU* 3.2 25.6 + - - +
725D PRO 5.4 1.1 - - - +
726D VAL* 4.0 34.6 - - + +
729D ALA* 4.8 3.1 - - + -
730D TYR* 4.3 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 611 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D LEU* 4.1 5.6 - - + -
607D GLU 3.1 16.9 + - - +
608D LYS* 3.8 6.1 - - - +
610D ALA* 1.4 74.1 - - - +
612D THR* 1.4 61.1 + - - +
615D TRP* 3.0 15.9 + - - +
675D LEU* 4.2 26.9 - - + -
678D LEU* 4.8 8.3 - - + -
729D ALA* 3.7 21.5 - - + -
730D TYR* 2.7 48.0 + - + +
733D VAL* 3.9 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 612 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608D LYS* 3.0 34.0 + - - +
609D SER* 4.1 4.3 - - - -
611D VAL* 1.4 76.1 - - - +
613D ALA* 1.4 65.7 + - - +
615D TRP* 3.4 6.9 + - - +
616D GLY* 3.2 19.1 + - - -
675D LEU* 5.5 3.0 + - - -
678D LEU* 5.6 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 613 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609D SER 2.9 19.8 + - - +
610D ALA* 4.2 4.0 - - - +
612D THR* 1.4 76.9 - - - +
614D LEU* 1.4 63.4 + - - +
616D GLY* 3.4 11.8 + - - -
617D LYS* 4.0 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 614 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610D ALA 3.2 17.5 + - - +
613D ALA* 1.4 78.1 - - - +
615D TRP* 1.4 58.9 + - - +
617D LYS* 3.0 27.8 + - + +
618D VAL* 3.5 6.9 + - + +
714D LEU* 4.3 8.7 - - + -
718D PHE* 3.9 42.4 - - + -
721D GLU* 3.9 30.1 - - + +
722D PHE* 3.9 24.9 - - + -
726D VAL* 4.6 5.2 - - + -
730D TYR* 3.8 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 615 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611D VAL 3.0 17.3 + - - +
612D THR* 3.9 5.6 - - - +
613D ALA 3.4 0.2 - - - -
614D LEU* 1.4 76.4 - - - +
616D GLY* 1.4 61.7 + - - +
618D VAL* 3.0 45.8 + - + +
620D VAL* 4.4 7.2 - - + +
668D LEU* 3.8 28.7 - - + -
671D PHE* 3.6 33.9 - + - -
672D SER* 3.2 34.2 + - - -
675D LEU* 3.4 28.2 - - + +
710D LEU* 4.7 4.7 - - + -
714D LEU* 4.5 12.8 - - + -
730D TYR* 3.5 24.6 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 616 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612D THR 3.2 14.5 + - - -
613D ALA 3.4 4.9 + - - -
614D LEU 3.2 1.4 - - - -
615D TRP* 1.4 75.8 - - - +
617D LYS* 1.4 60.0 + - - +
618D VAL 3.5 2.2 - - - +
----------------------------------------------------------
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