Contacts of the helix formed by residues 723 - 743 (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 723 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ARG* 3.7 2.2 + - - +
720D LYS 3.3 19.5 - - - +
721D GLU* 2.9 8.7 + - - +
722D PHE* 1.3 73.1 - - - +
724D PRO* 1.3 79.0 - - + +
725D PRO* 3.5 10.2 - - - +
726D VAL* 3.0 27.5 + - - +
727D GLN 2.9 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 724 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C GLU* 4.6 9.9 - - + -
430C GLU* 4.3 21.5 - - + +
431C ARG* 3.8 48.5 - - + +
434C LEU* 3.6 20.4 - - + +
435C SER* 4.7 0.9 + - - -
450C HIS* 6.5 0.2 - - + -
723D THR* 1.3 87.9 - - + +
725D PRO* 1.4 70.5 - - + +
727D GLN* 3.3 2.5 + - + +
728D ALA* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 725 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C GLU* 5.3 2.5 - - - +
434C LEU* 4.0 15.7 - - + -
606D GLU* 4.9 14.1 - - - +
607D GLU* 5.2 3.5 - - - +
610D ALA* 5.4 1.5 - - - +
723D THR* 3.5 13.0 - - - +
724D PRO* 1.4 97.4 - - + +
726D VAL* 1.4 61.5 + - + +
728D ALA* 3.4 6.5 + - + +
729D ALA* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 726 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610D ALA* 4.0 32.8 - - + +
614D LEU* 4.6 7.9 - - + -
721D GLU 4.2 9.6 - - - +
722D PHE* 3.8 23.1 - - + -
723D THR* 3.0 26.7 + - - +
725D PRO* 1.4 74.1 - - + +
727D GLN* 1.4 67.2 + - - +
729D ALA* 3.2 3.6 + - - +
730D TYR* 3.0 39.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 727 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C ARG* 3.0 38.6 + - - +
435C SER* 3.5 17.3 + - - +
503C HIS* 4.1 0.8 + - - -
504C CYS* 3.9 20.4 - - - -
507C VAL* 3.5 20.0 - - - +
711D VAL* 4.0 9.2 - - + -
722D PHE* 3.6 22.4 - - + -
723D THR 2.9 11.5 + - - +
724D PRO 3.7 6.3 - - - +
726D VAL* 1.4 77.0 - - - +
728D ALA* 1.4 50.8 + - - +
730D TYR* 3.0 3.1 + - - +
731D GLN* 2.8 57.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 728 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C LEU* 3.7 34.1 - - + +
435C SER* 3.5 14.6 + - - +
607D GLU* 4.7 7.6 - - - +
724D PRO 3.0 14.0 + - - +
725D PRO* 3.5 11.2 - - + +
726D VAL 3.3 0.2 - - - -
727D GLN* 1.4 74.3 - - - +
729D ALA* 1.4 63.1 + - - +
731D GLN* 3.3 3.3 + - - +
732D LYS* 3.2 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 729 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603D LEU* 4.9 1.8 - - + +
607D GLU* 3.8 38.1 + - + +
610D ALA* 4.8 3.1 - - + -
611D VAL* 3.7 22.0 - - + -
725D PRO 3.1 13.4 + - - +
726D VAL* 3.2 9.8 + - - +
728D ALA* 1.4 74.4 - - - +
730D TYR* 1.4 63.8 + - - +
732D LYS* 3.1 8.7 + - - +
733D VAL* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 730 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611D VAL* 2.7 54.9 + - + +
614D LEU* 3.8 22.2 - - + +
615D TRP* 3.5 35.7 + + - +
671D PHE* 5.3 4.5 - + - -
675D LEU* 5.1 2.9 - - + -
710D LEU* 5.8 0.9 - - + -
711D VAL* 4.4 8.5 - - + -
714D LEU* 3.9 20.4 - - + -
722D PHE* 4.0 15.5 - + + -
726D VAL* 3.0 32.1 + - + +
727D GLN 3.6 8.3 - - - +
729D ALA* 1.4 73.5 - - - +
731D GLN* 1.4 58.2 + - - +
733D VAL* 3.2 10.4 + - + +
734D VAL* 2.9 42.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 731 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C SER* 3.6 30.5 - - - +
436C PHE* 3.9 21.2 - - + -
503C HIS* 2.7 25.1 + - - -
708D ASN* 3.4 21.2 + - - -
711D VAL* 3.4 14.1 - - + +
727D GLN* 2.8 39.3 + - + +
728D ALA 3.3 6.0 + - - +
730D TYR* 1.4 72.9 - - - +
732D LYS* 1.4 62.1 + - - +
734D VAL* 3.3 12.9 - - - +
735D ALA* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 732 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C LEU 5.9 2.9 - - - -
435C SER 5.8 3.1 - - - +
437C PRO* 6.4 2.0 - - - -
601D VAL* 4.3 10.4 - - + +
602D HIS 4.4 16.0 + - - +
603D LEU* 4.4 12.3 - - + -
604D THR* 5.3 4.4 - - - +
607D GLU* 3.0 40.0 + - - +
728D ALA* 3.2 14.0 + - - +
729D ALA 3.1 8.6 + - - +
731D GLN* 1.4 78.2 - - + +
733D VAL* 1.4 56.3 + - - +
735D ALA* 3.4 6.0 + - - +
736D GLY* 2.9 26.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 733 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D VAL* 5.0 5.8 - - - -
603D LEU* 4.2 13.2 - - + -
611D VAL* 3.9 24.2 - - + -
671D PHE* 4.2 14.1 - - + -
675D LEU* 3.5 28.3 - - + -
678D LEU* 4.1 20.9 - - + -
681D LEU* 4.6 1.5 - - + +
729D ALA 3.1 13.9 + - - +
730D TYR* 3.2 12.1 + - + +
732D LYS* 1.4 74.7 - - - +
734D VAL* 1.4 58.5 + - + +
736D GLY* 3.1 2.4 + - - -
737D VAL* 2.9 31.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 734 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671D PHE* 4.1 23.6 - - + -
703D PHE 5.2 1.9 - - - +
704D ARG* 6.0 0.2 - - - -
707D GLY* 3.8 38.7 - - - +
708D ASN* 5.0 1.6 - - - +
710D LEU* 4.3 8.3 - - + -
711D VAL* 4.4 7.4 - - + -
730D TYR* 2.9 31.0 + - + +
731D GLN* 3.3 26.9 - - - +
733D VAL* 1.4 72.6 - - + +
735D ALA* 1.4 55.7 + - + +
737D VAL* 3.5 6.7 + - - +
738D ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 735 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731D GLN 3.1 19.0 + - - +
732D LYS* 3.8 5.8 - - - +
734D VAL* 1.4 76.2 - - + +
736D GLY* 1.4 58.3 + - - +
738D ALA* 3.5 6.0 + - - +
739D ASN* 3.0 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 736 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D VAL* 3.7 28.3 - - - -
681D LEU* 3.6 10.9 - - - +
732D LYS 2.9 11.3 + - - -
733D VAL 3.1 3.6 + - - -
735D ALA* 1.4 73.5 - - - +
737D VAL* 1.4 56.9 + - - +
739D ASN* 3.4 7.8 + - - +
740D ALA* 2.9 29.5 + - - +
1300D SO4 4.9 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 737 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671D PHE* 3.9 38.1 - - + +
674D GLY* 5.6 0.9 - - - -
675D LEU* 5.7 1.6 - - + -
681D LEU* 4.2 20.9 - - + -
685D PHE* 4.3 19.1 - - + -
733D VAL* 2.9 25.6 + - + +
734D VAL* 3.9 4.0 - - - +
736D GLY* 1.4 71.2 - - - +
738D ALA* 1.4 66.4 + - - +
740D ALA* 3.2 7.1 + - - +
741D LEU* 3.0 40.3 + - + +
748D HEM 4.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 738 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700D PRO 5.4 0.4 - - - +
703D PHE* 3.9 40.4 - - + +
704D ARG* 4.3 15.9 - - + +
734D VAL 2.9 18.5 + - - +
735D ALA* 3.7 7.6 - - - +
736D GLY 3.4 0.2 - - - -
737D VAL* 1.4 77.2 - - - +
739D ASN* 1.4 62.7 + - - +
741D LEU* 3.4 3.4 + - - +
742D ALA* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 739 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682D LYS* 4.0 17.0 + - - +
704D ARG* 4.8 11.4 + - - -
735D ALA* 3.0 27.4 + - - +
736D GLY* 3.7 6.5 - - - +
738D ALA* 1.4 76.1 - - - +
740D ALA* 1.4 63.6 + - - +
742D ALA* 3.3 6.7 + - - +
743D HIS* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 740 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681D LEU* 3.5 40.2 - - + +
682D LYS* 3.8 17.8 - - + +
685D PHE* 4.1 15.4 - - + +
686D ALA* 5.5 0.5 - - - -
689D SER* 3.9 8.1 - - - -
736D GLY 2.9 17.6 + - - +
737D VAL 3.6 5.4 - - - +
739D ASN* 1.4 74.4 - - - +
741D LEU* 1.4 60.5 + - - +
743D HIS* 3.3 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 741 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685D PHE* 4.2 15.7 - - + -
688D LEU* 3.9 20.4 - - + +
689D SER* 2.8 44.9 + - - +
692D HIS* 4.3 12.8 - - + +
703D PHE* 3.8 26.9 - - + -
737D VAL* 3.0 24.8 + - + +
738D ALA 3.9 0.2 - - - +
739D ASN 3.3 0.4 - - - -
740D ALA* 1.4 76.9 - - - +
742D ALA* 1.4 53.0 + - - +
743D HIS 3.4 0.2 - - - -
745D TYR* 3.2 13.7 - - - -
748D HEM 3.4 45.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 742 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 5.9 1.3 - - + +
700D PRO* 3.7 27.1 - - + -
703D PHE* 4.8 0.2 - - + -
738D ALA 3.2 16.5 + - - +
739D ASN* 3.3 7.4 + - - +
741D LEU* 1.4 75.3 - - - +
743D HIS* 1.4 64.0 + - - +
744D LYS 3.3 2.0 - - - -
745D TYR* 3.1 29.7 + - - +
801D CNO 5.1 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 743 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682D LYS* 4.0 41.4 + - + +
686D ALA* 6.2 1.0 - - - +
689D SER* 4.7 0.2 - - - +
739D ASN 3.1 12.4 + - - +
740D ALA* 3.3 20.3 + - - +
742D ALA* 1.4 77.9 - - - +
744D LYS* 1.4 83.8 + - + +
745D TYR 3.3 5.0 + - - +
----------------------------------------------------------
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