Contacts of the helix formed by residues 596 - 634 (chain O) in PDB entry 5KHU
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 596 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595O SER* 3.7 29.2 - - - +
597O PRO* 3.8 28.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 597 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596O SER* 3.8 25.6 - - - -
598O THR* 3.7 30.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 598 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597O PRO* 3.7 29.2 - - - -
599O ILE* 3.8 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 599 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598O THR* 3.8 26.5 - - - +
600O ALA* 3.8 28.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 600 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599O ILE* 3.8 29.6 - - - +
601O LEU* 3.8 27.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 601 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600O ALA* 3.8 29.6 - - - +
602O PRO* 3.8 25.8 - - - -
604O LEU* 4.3 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 602 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601O LEU* 3.8 25.1 - - - -
603O MET* 3.7 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 603 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602O PRO* 3.7 30.5 - - - -
604O LEU* 3.8 25.8 - - - +
606O GLN* 4.2 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 604 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601O LEU* 4.3 19.1 - - - +
603O MET* 3.8 26.0 - - - +
605O LEU* 3.7 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 605 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604O LEU* 3.7 29.6 - - - +
606O GLN* 3.8 27.6 - - - +
608O LEU* 4.2 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 606 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603O MET* 4.2 19.7 - - - +
605O LEU* 3.8 25.1 - - - +
607O ALA* 3.7 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 607 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606O GLN* 3.7 29.8 - - - +
608O LEU* 3.8 26.7 - - - +
610O LEU* 4.5 17.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605O LEU* 4.2 20.6 - - - +
607O ALA* 3.8 28.0 - - - +
609O ALA* 3.8 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 609 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608O LEU* 3.8 29.8 - - - +
610O LEU* 3.8 24.9 - - - +
612O LYS* 4.2 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 610 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607O ALA* 4.5 16.8 - - - +
609O ALA* 3.8 23.8 - - - +
611O SER* 3.7 29.8 - - - +
613O GLU* 4.6 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 611 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610O LEU* 3.7 30.1 - - - +
612O LYS* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 612 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609O ALA* 4.2 17.0 - - - +
611O SER* 3.8 24.2 - - - +
613O GLU* 3.8 29.4 - - - +
615O ARG* 4.3 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 613 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610O LEU* 4.6 16.6 - - - +
612O LYS* 3.8 26.2 - - - +
614O TYR* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 614 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613O GLU* 3.8 28.9 - - - +
615O ARG* 3.8 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 615 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612O LYS* 4.3 20.4 - - - +
614O TYR* 3.8 28.5 - - - +
616O LEU* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 616 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615O ARG* 3.8 28.9 - - - +
617O GLN* 3.8 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 617 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616O LEU* 3.8 30.3 - - - +
618O TYR* 3.8 25.6 - - - +
620O ALA* 4.3 19.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 618 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617O GLN* 3.8 24.9 - - - +
619O LEU* 3.8 29.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618O TYR* 3.8 29.8 - - - +
620O ALA* 3.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 620 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617O GLN* 4.3 17.5 - - - +
619O LEU* 3.8 25.6 - - - +
621O SER* 3.8 29.4 - - - +
623O THR* 4.4 16.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 621 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620O ALA* 3.8 28.5 - - - +
622O GLU* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 622 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621O SER* 3.8 25.1 - - - +
623O THR* 3.8 29.2 - - - +
625O LEU* 4.5 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 623 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620O ALA* 4.4 16.8 - - - +
622O GLU* 3.8 29.2 - - - +
624O VAL* 3.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 624 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623O THR* 3.8 24.9 - - - +
625O LEU* 3.8 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 625 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622O GLU* 4.5 18.4 - - - +
624O VAL* 3.8 29.8 - - - +
626O ASN* 3.8 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 626 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625O LEU* 3.8 26.5 - - - +
627O LEU* 3.7 29.4 - - - +
629O PHE* 4.2 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 627 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626O ASN* 3.7 29.8 - - - +
628O ALA* 3.8 25.8 - - - +
630O ALA* 4.7 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 628 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627O LEU* 3.8 29.6 - - - +
629O PHE* 3.8 26.0 - - - +
631O GLN* 4.3 19.5 - - - +
640O ALA* 4.6 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 629 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626O ASN* 4.2 18.2 - - - +
628O ALA* 3.8 23.8 - - - +
630O ALA* 3.7 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 630 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627O LEU* 4.7 14.6 - - - +
629O PHE* 3.7 29.6 - - - +
631O GLN* 3.8 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 631 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628O ALA* 4.3 16.6 - - - +
630O ALA* 3.8 24.0 - - - +
632O LEU* 3.8 29.4 - - - +
634O LEU* 4.3 18.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 632 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631O GLN* 3.8 29.6 - - - +
633O ILE* 3.8 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 633 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632O LEU* 3.8 24.5 - - - +
634O LEU* 3.8 29.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 634 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631O GLN* 4.3 20.4 - - - +
633O ILE* 3.8 29.6 - - - +
635O GLY* 3.8 24.2 - - - +
----------------------------------------------------------
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