Contacts of the helix formed by residues 585 - 605 (chain A) in PDB entry 1K4S
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 585 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574A ASN* 3.1 24.9 - - + +
577A LEU* 3.4 8.5 - - - -
578A GLN* 5.2 1.1 - - - +
583A GLY* 3.9 8.5 + - - +
584A LEU* 1.3 88.2 - - - +
586A ALA* 1.3 67.4 + - - +
587A LYS* 4.0 2.3 + - - +
588A VAL* 2.8 35.2 + - - +
589A PHE* 4.1 4.5 + - - -
117D C 3.1 38.6 + - - +
118D 5IU 4.5 8.5 - - - +
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Residues in contact with ALA 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU* 6.3 0.4 - - - -
482A ILE* 4.3 15.0 - - + +
487A LEU 5.9 0.7 - - - -
489A ALA* 3.8 24.9 - - + +
573A LEU* 4.1 18.2 - - + -
574A ASN* 3.0 11.1 + - - +
577A LEU* 3.4 6.8 - - - +
585A THR* 1.3 70.0 - - - +
587A LYS* 1.3 65.9 + - - +
589A PHE* 3.2 25.0 + - - +
590A ARG* 4.1 2.9 + - - +
117D C 3.8 13.7 - - - +
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Residues in contact with LYS 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A LYS* 3.7 33.5 - - - +
489A ALA* 5.4 1.5 - - - +
585A THR* 4.2 3.4 - - - +
586A ALA* 1.3 70.3 - - - +
588A VAL* 1.3 70.2 + - + +
589A PHE 2.7 2.6 + - - -
590A ARG* 2.9 22.7 + - - +
591A THR* 3.4 18.0 + - - +
723A PTR 6.4 0.7 - - + -
9B 5IU 3.6 17.8 + - - +
10B 5IU 2.3 38.3 + - - +
116D 5IU 3.8 16.5 + - - +
117D C 2.6 25.9 + - - +
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Residues in contact with VAL 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A THR* 4.5 13.9 - - + -
447A ALA* 4.0 29.0 - - + +
450A LEU* 4.7 9.6 - - + -
581A MET* 5.2 0.2 - - + -
583A GLY 3.9 10.3 - - - +
584A LEU* 4.3 17.0 - - + -
585A THR* 2.8 41.3 - - - +
587A LYS* 1.3 76.6 - - + +
589A PHE* 1.3 50.9 + - + +
591A THR* 3.1 12.0 - - - -
592A TYR* 2.7 31.9 + - - +
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Residues in contact with PHE 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A LEU* 3.3 44.0 - - + -
454A VAL* 4.7 9.9 - - + -
457A ILE* 4.8 7.9 - - + -
479A LEU* 3.3 38.1 - - + -
482A ILE* 4.3 20.6 - - + +
483A ASP* 4.5 17.7 - - - -
486A ALA* 6.3 0.2 - - - -
577A LEU* 3.8 20.2 - - + -
584A LEU* 4.7 3.1 - - + -
585A THR 4.4 5.4 - - - -
586A ALA* 3.2 16.3 + - - +
587A LYS 2.7 4.8 + - - -
588A VAL* 1.3 73.1 - - + +
590A ARG* 1.3 58.7 + - - +
592A TYR* 2.6 23.4 + + - +
593A ASN* 2.8 32.4 + - - +
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Residues in contact with ARG 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A ILE* 5.4 0.4 - - + -
486A ALA* 3.1 40.8 + - + +
487A LEU 4.0 9.9 - - - +
488A ARG* 2.8 50.9 - - - +
586A ALA 4.1 4.0 + - - +
587A LYS* 2.9 16.3 + - - +
589A PHE* 1.3 75.2 - - + +
591A THR* 1.3 64.2 + - - +
592A TYR 3.0 0.2 + - - -
593A ASN* 4.5 2.5 - - - +
594A ALA* 3.1 25.9 + - - +
630A CYS* 3.9 23.8 + - - +
632A HIS* 3.1 30.9 + - - -
723A PTR 3.0 43.4 + - + -
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Residues in contact with THR 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A LYS* 4.2 25.4 - - + +
444A TYR* 4.4 10.3 - - + -
447A ALA* 4.3 13.7 - - + -
587A LYS* 3.5 30.9 + - - +
588A VAL* 3.1 14.0 + - - -
590A ARG* 1.3 80.7 - - - +
592A TYR* 1.3 62.5 + - - +
595A SER* 3.2 17.0 + - - -
722A ASN 5.6 0.4 + - - +
723A PTR 3.3 38.4 - - + +
10B 5IU 4.6 0.2 + - - -
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Residues in contact with TYR 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A ALA* 3.9 24.0 - - + -
450A LEU* 3.8 20.9 - - + -
451A LYS* 3.6 47.3 + - + +
454A VAL* 4.5 7.0 - - + +
458A ARG* 4.3 16.0 + - - -
588A VAL 2.7 13.9 + - - +
589A PHE* 2.6 22.6 + + - +
591A THR* 1.3 71.2 - - - +
593A ASN* 1.3 93.9 + - - +
594A ALA 2.8 2.9 + - - -
595A SER* 3.2 3.2 + - - -
596A ILE* 3.0 46.8 + - + +
765A PHE* 4.3 7.9 - + - -
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Residues in contact with ASN 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A ARG* 3.8 20.3 + - - -
483A ASP* 3.9 23.0 + - - +
486A ALA* 5.9 2.8 - - + +
589A PHE* 2.8 36.5 + - - +
590A ARG* 4.5 2.6 - - - +
592A TYR* 1.3 91.1 - - - +
594A ALA* 1.3 56.3 + - - +
596A ILE* 3.1 12.2 - - + +
597A THR* 2.7 46.7 + - + +
629A LEU* 4.8 15.7 - - + -
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Residues in contact with ALA 594 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A ARG 3.1 21.7 + - - +
591A THR* 3.4 5.6 - - - +
592A TYR 2.8 0.4 + - - -
593A ASN* 1.3 82.1 - - - +
595A SER* 1.3 59.9 + - - +
596A ILE 3.0 2.9 + - - -
597A THR* 3.0 14.5 + - - -
598A LEU* 3.2 5.7 + - - +
626A VAL* 3.7 8.4 - - + +
629A LEU* 5.6 3.3 - - - +
719A SER* 6.3 0.2 - - - -
723A PTR 3.7 20.4 - - + +
724A LEU* 3.3 21.5 - - + +
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Residues in contact with SER 595 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444A TYR* 4.8 2.3 - - - -
591A THR* 3.2 13.5 + - - +
592A TYR 3.2 1.4 + - - -
594A ALA* 1.3 78.0 - - - +
596A ILE* 1.3 55.8 + - - +
598A LEU* 3.9 1.0 - - - +
599A GLN* 3.3 11.9 + - - +
723A PTR 4.1 0.4 + - - -
724A LEU* 3.4 15.6 - - - +
725A ASP* 3.2 32.9 + - - -
728A ILE* 3.0 32.3 - - - +
765A PHE* 3.4 24.2 - - - -
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Residues in contact with ILE 596 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A LYS* 5.2 6.1 - - + -
592A TYR* 3.0 39.3 + - + +
593A ASN* 3.0 38.4 - - + +
594A ALA 3.0 1.4 + - - -
595A SER* 1.3 76.5 - - - +
597A THR* 1.3 67.0 + - + +
598A LEU 2.9 1.6 - - - -
599A GLN* 2.6 56.1 + - + +
600A GLN* 3.3 5.0 + - - +
765A PHE* 4.2 16.4 - - + +
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Residues in contact with THR 597 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A ASN* 2.7 35.9 + - + +
594A ALA 3.0 5.9 + - - -
596A ILE* 1.3 76.9 - - + +
598A LEU* 1.3 71.0 + - - +
600A GLN* 3.2 11.1 + - - +
601A GLN* 3.0 29.4 + - - +
625A ALA 5.9 0.7 - - - -
626A VAL* 3.7 19.6 - - - +
629A LEU* 4.8 16.5 - - + +
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Residues in contact with LEU 598 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A ALA 3.2 14.1 + - - +
595A SER* 3.9 7.6 - - - +
597A THR* 1.3 78.6 + - - +
599A GLN* 1.3 57.5 + - - +
600A GLN 2.7 15.7 + - - -
601A GLN* 2.7 27.5 + - + +
602A LEU* 3.4 22.5 + - + +
619A TYR* 5.3 3.8 - - - +
622A ALA* 5.7 1.6 - - + -
623A ASN* 4.1 24.5 - - - +
626A VAL* 4.0 12.8 - - + -
724A LEU* 3.6 27.6 - - + -
725A ASP 5.3 0.2 - - - +
728A ILE* 3.3 34.5 - - + -
729A THR* 5.3 6.1 - - - +
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Residues in contact with GLN 599 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A SER 3.3 8.8 + - - +
596A ILE* 2.6 35.4 + - + +
598A LEU* 1.3 82.5 - - - +
600A GLN* 1.3 55.8 + - - -
602A LEU* 4.5 3.8 + - - +
603A LYS* 3.9 14.4 + - - +
728A ILE* 3.8 28.1 - - + +
763A TYR 4.6 2.2 + - - -
764A GLU* 3.3 14.1 - - - +
765A PHE* 2.6 46.1 + - - +
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Residues in contact with GLN 600 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A ILE 3.3 5.3 + - - +
597A THR* 3.2 10.8 + - - +
598A LEU 2.7 4.8 + - - -
599A GLN* 1.3 76.0 - - - +
601A GLN* 1.3 70.4 + - - +
602A LEU 3.3 0.4 - - - -
603A LYS* 2.7 31.5 + - + +
604A GLU* 2.8 38.2 + - + +
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Residues in contact with GLN 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A THR* 3.0 23.5 + - - +
598A LEU* 2.7 17.7 + - - +
600A GLN* 1.3 91.8 + - - +
602A LEU* 1.3 53.4 + - - +
603A LYS 2.7 1.6 + - - -
604A GLU* 2.6 27.9 + - - +
605A LEU* 2.8 31.2 + - + +
622A ALA* 3.4 40.4 - - + +
625A ALA* 3.6 21.6 - - + +
626A VAL* 4.7 1.6 - - + -
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Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A LEU* 3.4 28.4 + - + +
599A GLN 4.8 3.8 - - - +
600A GLN 3.3 0.6 - - - -
601A GLN* 1.3 75.1 - - - +
603A LYS* 1.3 62.4 + - - +
605A LEU* 5.8 0.2 - - - -
606A THR* 2.7 33.5 + - - +
618A SER 4.8 1.3 - - - +
619A TYR* 3.4 55.9 - - + +
622A ALA* 4.1 13.2 - - + -
623A ASN* 5.8 0.2 - - - +
728A ILE* 5.0 5.8 - - + -
729A THR* 5.1 2.7 - - - -
732A TRP* 3.2 50.0 - - + +
736A TRP* 4.9 1.7 + - - -
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Residues in contact with LYS 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A GLN 3.9 10.7 + - - +
600A GLN* 2.7 22.4 + - + +
602A LEU* 1.3 87.8 + - - +
604A GLU* 1.3 73.4 + - - +
606A THR* 4.6 6.9 - - - +
732A TRP* 6.1 0.2 - - - -
736A TRP* 5.0 11.9 - - - +
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Residues in contact with GLU 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A GLN* 2.8 40.2 + - + +
601A GLN* 2.6 10.7 + - - +
603A LYS* 1.3 89.1 - - - +
605A LEU* 1.3 64.3 + - + +
606A THR 2.7 21.9 + - - +
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Residues in contact with LEU 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A GLN* 2.8 30.0 + - - +
602A LEU* 5.8 0.2 - - - -
604A GLU* 1.3 77.9 - - + +
606A THR* 1.3 59.6 + - - +
607A ALA* 4.0 1.0 + - - +
618A SER* 3.6 14.2 + - - +
621A ARG* 2.8 65.6 + - + +
622A ALA* 4.1 12.3 - - + -
625A ALA* 5.5 2.0 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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