Contacts of the helix formed by residues 593 - 611 (chain D) in PDB entry 1O23
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 ARG 593 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590D PHE* 3.4 20.9 - - + -
591D ARG 3.3 6.2 - - - +
592D ASN* 1.3 83.7 - - - +
594D GLN* 1.3 66.1 + - - +
595D GLU 3.3 2.9 - - - -
596D HIS* 2.8 44.3 + - + -
597D LEU 3.0 17.5 + - - -
655D VAL* 3.8 16.7 - - + +
656D ASP* 3.4 14.5 + - - -
749D HIS* 3.3 17.2 + - - +
752D ASP* 3.0 37.5 + - - -
810D UPG 3.1 58.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 594 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557D LEU* 4.5 14.6 - - - +
590D PHE* 3.5 20.2 - - + -
592D ASN* 3.6 2.4 - - - +
593D ARG* 1.3 75.4 - - - +
595D GLU* 1.3 62.1 + - + +
597D LEU* 2.9 32.5 + - - +
598D LYS* 3.0 26.8 + - + +
793D TYR* 3.7 20.9 + - - -
795D LYS* 4.7 4.9 + - - +
812D UDP 3.8 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 595 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593D ARG 3.2 1.4 + - - -
594D GLN* 1.3 80.8 - - + +
596D HIS* 1.3 71.4 + - + +
598D LYS* 3.3 43.9 + - - +
599D TYR* 3.5 27.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 596 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593D ARG* 2.8 53.4 + - - +
595D GLU* 1.3 84.0 - - + +
597D LEU* 1.3 57.7 + - - +
599D TYR* 3.0 6.9 + - - +
600D TRP 2.9 24.4 + - - -
655D VAL* 3.6 25.3 - - + +
656D ASP* 3.7 9.6 - - + -
747D ILE* 3.5 40.7 - - + +
748D ARG 4.6 1.6 - - - -
749D HIS* 3.6 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 597 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588D ILE* 4.3 10.8 - - + -
590D PHE* 4.0 15.5 - - + -
593D ARG 3.0 11.1 + - - +
594D GLN* 2.9 35.5 + - - +
596D HIS* 1.3 76.7 - - - +
598D LYS* 1.3 55.9 + - - +
600D TRP* 3.2 7.3 + - + -
601D LEU* 2.9 51.2 + - + +
619D VAL* 4.1 21.5 - - + -
655D VAL* 4.1 15.0 - - + +
793D TYR* 3.9 34.3 - - + -
795D LYS* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 598 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554D PRO* 6.1 1.6 - - - +
555D VAL* 3.3 40.2 + - + +
557D LEU* 3.8 39.7 - - + +
594D GLN* 3.0 24.6 + - + +
595D GLU* 3.3 44.8 + - - +
596D HIS 3.2 0.4 - - - -
597D LEU* 1.3 75.4 - - - +
599D TYR* 1.3 58.8 + - + +
601D LEU* 4.0 1.5 - - + +
602D TYR* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 599 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D GLU 4.2 3.6 - - - -
551D PHE* 3.4 56.7 + + + -
552D ASN 3.7 2.1 + - - -
553D ILE* 2.7 36.4 + - + -
554D PRO* 3.8 4.5 - - + +
555D VAL* 3.5 18.6 - - + -
595D GLU* 3.5 27.9 + - + -
596D HIS* 3.0 7.9 + - - +
598D LYS* 1.3 78.8 - - + +
600D TRP* 1.3 63.0 + - - +
602D TYR* 3.4 3.9 + + - -
603D TYR* 3.1 40.9 + + - -
658D ILE* 4.7 1.6 - - + -
747D ILE* 3.9 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 600 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D ILE* 3.8 28.5 - - + -
588D ILE* 3.9 19.5 - - + -
596D HIS 2.9 6.3 + - - +
597D LEU* 3.2 13.7 + - + +
599D TYR* 1.3 78.1 - - - +
601D LEU* 1.3 70.6 + - + +
604D LEU* 2.7 79.1 + - + +
605D HIS* 5.3 1.6 - - - -
608D LEU* 4.1 0.7 - - + -
617D ILE* 3.7 43.5 - - + -
653D SER* 3.5 19.6 + - - -
654D ASP 4.0 6.7 + - - -
655D VAL* 3.6 24.9 - - - +
657D LEU 3.5 20.3 + - - -
658D ILE* 4.5 5.8 - - + +
666D TYR* 5.0 4.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 601 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557D LEU* 4.0 25.6 - - + -
560D VAL* 4.2 3.5 - - - +
597D LEU* 2.9 34.5 + - + +
598D LYS 4.0 1.8 - - - +
600D TRP* 1.3 94.0 - - + +
602D TYR* 1.3 70.8 + - - +
603D TYR 3.0 0.7 + - - -
604D LEU 4.6 0.2 - - - +
605D HIS* 3.4 54.1 + - + +
617D ILE* 4.3 2.0 - - + -
792D LEU* 3.8 17.0 - - + +
793D TYR* 3.5 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 602 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D ILE* 5.7 8.2 - - + +
555D VAL* 3.9 26.0 - - + -
560D VAL* 3.8 30.4 - - + +
563D GLN* 4.4 20.5 + - - -
564D ASN* 5.4 0.2 + - - -
598D LYS 2.8 23.8 + - - +
599D TYR* 3.6 5.2 - + - +
601D LEU* 1.3 73.4 - - - +
603D TYR* 1.3 99.7 + + - +
606D PRO* 3.4 18.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 603 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D LEU 4.1 8.2 + - - -
549D ILE* 3.8 24.9 - - + -
550D GLU* 2.6 44.0 + - - +
551D PHE* 4.1 14.8 - + - -
553D ILE* 6.0 1.2 - - - +
599D TYR* 3.1 30.5 + + - +
600D TRP 4.0 1.1 - - - +
602D TYR* 1.3 108.8 - + - +
604D LEU* 1.3 66.3 + - + +
605D HIS 3.4 0.4 - - - -
606D PRO* 3.2 11.6 - - - +
607D ILE* 3.3 22.8 - - + +
658D ILE* 4.0 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 604 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600D TRP* 2.7 70.5 + - + +
603D TYR* 1.3 76.5 - - + +
605D HIS* 1.3 54.0 + - - +
607D ILE* 3.0 10.9 + - + +
608D LEU* 2.7 57.4 + - + +
657D LEU 4.3 0.4 - - - +
658D ILE* 4.0 12.1 - - + -
659D PRO* 3.9 31.9 - - + -
666D TYR* 3.9 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 605 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560D VAL* 4.9 1.1 - - + -
564D ASN* 4.1 14.6 - - - +
567D VAL* 3.8 21.8 - - + +
571D GLY 4.6 0.7 - - - -
600D TRP* 5.5 1.1 - + - -
601D LEU* 3.4 36.2 + - + +
604D LEU* 1.3 76.6 - - - +
606D PRO* 1.3 72.7 - - + +
608D LEU* 4.1 2.4 - - + +
609D GLN* 3.1 30.0 + - - +
615D TYR* 2.8 31.3 + + - +
617D ILE* 3.7 20.9 - - + -
792D LEU* 2.9 48.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 606 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D GLN* 5.5 6.3 - - + +
564D ASN* 3.8 23.8 - - - +
601D LEU 4.0 0.2 - - - +
602D TYR 3.4 19.5 - - - +
603D TYR* 3.2 12.8 - - - +
605D HIS* 1.3 94.7 - - + +
607D ILE* 1.3 55.8 + - - +
609D GLN* 3.4 5.5 + - + +
610D ARG* 3.0 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 607 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D MET* 3.4 39.7 - - + -
549D ILE* 5.3 0.2 - - + -
603D TYR* 3.3 30.1 - - + +
604D LEU* 3.0 17.8 + - + +
606D PRO* 1.3 75.6 - - - +
608D LEU* 1.3 65.1 + - - +
610D ARG* 3.3 18.1 + - - +
611D GLN* 3.0 41.1 + - - +
658D ILE* 5.2 0.9 - - + -
659D PRO* 4.3 21.8 - - + +
662D ASP* 4.1 16.2 - - + -
666D TYR* 5.8 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 608 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D ILE* 3.6 35.0 - - + -
600D TRP* 4.1 0.9 - - + -
604D LEU* 2.7 47.5 + - + +
605D HIS* 4.1 0.9 - - - +
607D ILE* 1.3 73.2 - - + +
609D GLN* 1.3 62.0 + - - +
611D GLN* 3.3 15.5 + - - +
612D GLN 3.5 7.1 + - - -
613D LEU* 3.5 21.9 + - + +
615D TYR* 3.4 37.7 - - + +
617D ILE* 4.1 5.4 - - + -
666D TYR* 3.8 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 609 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D LEU* 4.4 5.2 - - - +
564D ASN* 3.0 27.7 + - - +
566D LYS* 3.8 23.4 - - - +
567D VAL* 3.5 16.3 - - - +
573D TYR* 3.3 54.4 + - + +
605D HIS 3.1 20.3 + - - +
606D PRO* 3.6 5.3 - - + +
607D ILE 3.1 0.6 - - - -
608D LEU* 1.3 74.2 - - - +
610D ARG* 1.3 60.0 + - - +
611D GLN 3.0 1.8 - - - -
612D GLN* 2.8 24.4 + - - +
615D TYR* 3.7 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 610 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D SER* 2.6 30.0 + - - -
542D LEU* 3.7 41.8 - - + +
543D LEU* 3.7 6.5 - - + +
544D VAL* 3.6 10.7 - - - +
547D MET* 3.5 22.0 - - - -
606D PRO* 3.0 32.8 + - - +
607D ILE* 3.3 25.6 + - - +
609D GLN* 1.3 77.2 - - - +
611D GLN* 1.3 55.2 + - + +
612D GLN* 3.2 4.3 + - - +
662D ASP* 2.8 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 611 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D SER* 4.2 10.2 - - - -
543D LEU* 4.4 5.4 - - + -
582D HIS* 5.2 1.2 - - - -
607D ILE* 3.0 29.6 + - + +
608D LEU* 3.7 12.0 - - - +
609D GLN 3.0 1.2 - - - -
610D ARG* 1.3 76.0 - - - +
612D GLN* 1.3 72.3 + - - +
613D LEU* 3.2 28.9 - - + +
662D ASP* 3.1 28.9 + - + +
664D ASN 3.1 9.3 + - - -
665D THR* 3.0 33.7 - - + +
666D TYR* 3.1 24.3 + - - +
----------------------------------------------------------
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