Contacts of the helix formed by residues 600 - 618 (chain A) in PDB entry 3KN5
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 ASP 600 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A VAL* 3.9 14.5 - - - +
543A ARG* 4.9 0.9 - - + +
598A GLY 2.8 12.8 + - - +
599A TYR* 1.3 71.9 - - - +
601A GLU* 1.3 66.1 + - - +
602A SER* 3.0 27.1 + - - -
603A CYS* 3.2 29.5 + - - +
604A ASP 4.3 0.7 + - - -
726A LYS* 3.0 29.5 - - - +
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Residues in contact with GLU 601 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A HIS* 3.4 51.3 + - + +
541A VAL* 3.8 13.9 - - + -
572A LYS* 5.1 5.4 + - - -
599A TYR* 3.2 38.0 + - + -
600A ASP* 1.3 73.0 + - - +
602A SER* 1.3 61.2 + - - +
603A CYS 3.2 1.0 + - - -
604A ASP 3.6 5.4 + - - -
605A LEU* 3.6 14.0 + - + +
678A MET* 6.1 1.0 - - - +
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Residues in contact with SER 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A ASP* 3.0 19.4 + - - -
601A GLU* 1.3 77.9 - - - +
603A CYS* 1.3 58.8 + - - +
605A LEU* 3.3 13.8 + - - +
606A TRP* 2.9 30.3 + - - +
675A ARG* 3.7 36.9 - - - +
722A PHE* 5.0 0.8 - - - -
726A LYS* 3.5 21.0 + - - -
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Residues in contact with CYS 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ARG* 4.5 24.7 - - + -
598A GLY 5.5 0.4 - - - -
600A ASP* 3.2 31.9 + - - +
602A SER* 1.3 81.5 + - - +
604A ASP* 1.3 62.5 + - - +
606A TRP* 3.3 5.4 + - - +
607A SER* 3.0 25.2 + - - -
722A PHE* 4.0 22.3 - - + -
723A ASN* 6.3 0.9 - - - -
726A LYS* 3.9 21.1 - - - -
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Residues in contact with ASP 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A VAL* 3.9 7.7 - - + +
535A MET* 5.2 1.1 - - - +
536A HIS* 2.6 38.2 + - + +
541A VAL* 3.4 6.4 - - - +
542A HIS* 3.0 20.6 + - - -
543A ARG* 2.8 28.4 + - - -
545A LEU* 3.2 28.0 - - + +
601A GLU 3.6 1.4 + - - -
602A SER 3.4 0.4 - - - -
603A CYS* 1.3 75.5 - - - +
605A LEU* 1.3 62.2 + - - +
607A SER* 3.3 5.2 + - - -
608A LEU* 3.1 28.6 + - - +
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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
----------------------------------------------------------
536A HIS* 5.2 2.2 - - + -
601A GLU* 3.6 17.2 + - + +
602A SER* 3.3 10.9 + - - +
603A CYS 3.2 0.4 - - - -
604A ASP* 1.3 76.0 - - - +
606A TRP* 1.3 64.9 + - - +
608A LEU* 3.4 7.3 + - + +
609A GLY 3.4 14.2 + - - -
667A LEU* 3.4 28.0 - - + +
675A ARG* 3.8 17.3 - - - +
676A LEU 3.8 20.4 - - - +
677A LYS* 4.1 9.2 - - + -
678A MET* 3.9 29.4 - - + +
681A LEU* 3.7 30.5 - - + -
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Residues in contact with TRP 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A SER 2.9 13.8 + - - +
603A CYS 3.3 7.4 + - - +
605A LEU* 1.3 75.8 - - - +
607A SER* 1.3 65.0 + - - +
609A GLY* 3.0 17.2 + - - -
610A VAL* 3.1 39.4 + - + +
622A PHE* 3.5 26.2 - + - -
641A ILE* 4.1 8.0 - - + +
667A LEU 3.6 21.1 - - - +
668A LEU* 3.3 30.6 + - + +
669A THR 4.7 1.6 - - - -
670A VAL* 4.3 12.7 - - + +
718A THR* 3.8 24.7 - - + -
719A PHE* 4.7 13.2 - + - -
722A PHE* 3.5 62.6 - + + -
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Residues in contact with SER 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ARG 5.6 2.1 - - - -
544A ASP 5.5 0.9 + - - -
545A LEU* 3.5 36.1 + - - +
603A CYS 3.0 16.1 + - - -
604A ASP* 3.3 8.7 + - - -
606A TRP* 1.3 82.7 - - - +
608A LEU* 1.3 59.9 + - - +
610A VAL* 3.1 3.9 + - - +
611A ILE* 2.8 34.5 + - - +
719A PHE* 3.6 18.4 - - - -
722A PHE* 5.8 0.9 - - - -
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Residues in contact with LEU 608 (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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525A MET* 4.1 14.6 - - - +
528A LEU* 4.1 22.9 - - + -
529A VAL* 4.5 11.2 - - + +
532A VAL* 4.1 35.4 - - + -
545A LEU* 4.8 5.2 - - + -
604A ASP 3.1 20.0 + - - +
605A LEU* 3.6 15.3 - - + +
606A TRP 3.3 0.2 - - - -
607A SER* 1.3 75.5 - - - +
609A GLY* 1.3 57.5 + - - +
611A ILE* 3.4 15.1 + - + +
612A LEU* 2.9 30.8 + - - +
667A LEU* 4.2 9.6 - - + -
678A MET* 4.9 0.7 - - + -
681A LEU* 4.1 24.9 - - + -
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Residues in contact with GLY 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605A LEU 3.4 4.0 + - - -
606A TRP 3.0 9.6 + - - -
608A LEU* 1.3 77.3 - - - +
610A VAL* 1.3 59.5 + - - +
612A LEU* 3.2 3.8 + - - +
613A TYR* 2.9 30.5 + - - +
664A ILE* 4.5 4.7 - - - +
667A LEU* 3.7 26.4 - - - +
668A LEU* 3.9 13.0 - - - +
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Residues in contact with VAL 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A PRO* 6.1 1.1 - - + -
606A TRP* 3.1 49.4 + - + +
607A SER* 3.1 7.7 + - - +
609A GLY* 1.3 74.3 - - - +
611A ILE* 1.3 63.1 + - - +
613A TYR* 3.4 1.9 + - - +
614A THR* 3.1 25.9 + - - +
620A VAL* 5.8 0.2 - - + -
621A PRO* 3.7 28.3 - - + -
668A LEU* 3.7 10.5 - - + +
715A VAL* 5.0 7.4 - - + -
718A THR* 5.0 5.6 - - + -
719A PHE* 3.5 26.9 - - + -
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Residues in contact with ILE 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU* 4.4 15.5 - - + -
507A PHE* 4.1 8.9 - - + -
525A MET* 3.8 18.6 - - + -
528A LEU* 4.3 10.5 - - + -
545A LEU* 3.2 34.8 - - + +
547A PRO* 4.6 17.0 - - + -
550A LEU* 4.1 19.5 - - + -
607A SER 2.8 23.9 + - - +
608A LEU* 3.6 15.3 - - + +
610A VAL* 1.3 78.2 - - - +
612A LEU* 1.3 57.5 + - - +
614A THR* 4.0 0.5 - - - -
615A MET* 2.9 32.9 + - + +
719A PHE* 5.0 2.0 - - + -
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Residues in contact with LEU 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A MET* 4.0 17.9 - - + -
608A LEU 2.9 17.7 + - - +
609A GLY* 3.2 3.3 + - - +
611A ILE* 1.3 73.8 - - - +
613A TYR* 1.3 66.6 + - - +
615A MET* 3.3 17.8 + - + -
616A LEU* 3.1 45.4 + - + +
660A ALA 4.9 1.1 - - - +
663A LEU* 3.8 32.8 - - + -
664A ILE* 3.7 23.8 - - + +
667A LEU* 5.0 4.9 - - + -
686A TRP* 3.8 24.7 - - + -
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Residues in contact with TYR 613 (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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609A GLY 2.9 17.0 + - - +
610A VAL 3.6 4.5 - - - +
612A LEU* 1.3 77.6 - - - +
614A THR* 1.3 59.6 + - - +
616A LEU 3.4 0.2 + - - -
617A SER* 2.9 35.1 + - - -
619A GLN* 3.2 28.5 + - + +
620A VAL 3.6 6.6 + - - -
621A PRO* 3.4 36.0 - - + +
622A PHE 4.9 1.0 + - - -
646A PHE* 4.8 7.0 - - + -
647A SER 2.9 30.4 + - - -
648A PHE* 4.1 15.7 - + - -
653A TRP* 3.6 28.2 + + - -
664A ILE* 3.8 15.4 - - + +
668A LEU* 4.1 17.0 - - + -
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Residues in contact with THR 614 (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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507A PHE* 3.5 33.6 - - + -
610A VAL* 3.1 15.5 + - - +
611A ILE* 5.1 0.2 - - - -
613A TYR* 1.3 75.5 - - - +
615A MET* 1.3 62.3 + - - +
617A SER* 4.1 0.4 - - - -
618A GLY* 2.6 35.1 + - - +
619A GLN 2.9 32.2 + - - +
620A VAL* 4.2 1.4 - - - -
621A PRO* 3.7 9.0 - - - +
700A THR* 4.1 1.9 + - - -
704A LEU* 4.5 7.7 - - + +
711A VAL* 4.6 8.3 - - + -
715A VAL* 4.4 10.2 - - + +
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Residues in contact with MET 615 (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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506A LEU* 4.2 6.3 - - + -
507A PHE* 3.7 22.4 - - + -
510A ILE* 3.9 12.1 - - + -
516A PHE* 3.4 32.3 - - + -
521A ALA* 3.7 22.0 - - + +
524A ILE* 4.0 22.0 - - + -
525A MET* 2.9 37.2 - - + -
611A ILE* 2.9 19.9 + - + +
612A LEU* 3.3 14.8 + - + +
614A THR* 1.3 76.6 - - - +
616A LEU* 1.3 59.4 + - + +
700A THR* 2.9 24.0 + - - +
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Residues in contact with LEU 616 (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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518A GLU* 4.6 5.4 - - + -
521A ALA* 3.6 24.5 - - + -
612A LEU* 3.1 35.9 + - + +
615A MET* 1.3 77.9 - - - +
617A SER* 1.3 59.8 + - - +
652A ALA 4.2 8.1 - - - +
653A TRP* 4.1 13.2 - - + -
656A VAL* 4.2 11.3 - - + +
660A ALA* 3.6 30.5 - - + -
664A ILE* 4.1 13.0 - - + -
686A TRP* 4.3 9.0 - - + -
698A LEU* 3.6 39.4 - - + +
699A MET 4.7 1.6 + - - -
700A THR* 3.8 9.3 - - - +
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Residues in contact with SER 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A TYR* 2.9 18.6 + - - -
616A LEU* 1.3 80.6 - - - +
618A GLY* 1.3 56.1 + - - +
619A GLN* 3.0 27.8 + - - +
652A ALA* 4.0 16.4 - - - +
653A TRP* 3.5 33.6 - - - -
699A MET* 4.4 0.6 - - - -
700A THR* 3.8 11.1 + - - +
703A ILE* 3.2 26.5 - - - +
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Residues in contact with GLY 618 (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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614A THR* 2.6 27.0 + - - -
617A SER* 1.3 73.2 - - - +
619A GLN* 1.3 58.4 + - - +
700A THR* 3.5 13.4 - - - -
703A ILE* 3.2 22.2 - - - +
704A LEU* 3.7 26.2 - - - +
711A VAL* 3.8 9.9 - - - +
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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
------------------------------------------------------------
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