Contacts of the helix formed by residues 559 - 571 (chain A) in PDB entry 1KEK
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 ILE 559 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A ASP* 4.4 23.1 + - + +
430A THR* 5.2 0.2 - - - +
490A HIS* 3.6 33.7 - - + +
513A ASN* 3.8 7.0 - - - +
546A ALA* 3.5 30.5 - - + -
547A VAL* 3.6 19.5 - - + -
557A GLY 3.3 16.1 + - - +
558A ARG* 1.3 72.5 - - - +
560A ASN* 1.3 66.7 + - - +
561A MET 3.4 2.0 - - - -
562A ILE* 3.2 8.6 + - - +
563A MET* 3.1 43.4 + - + +
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Residues in contact with ASN 560 (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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428A ASP 3.7 18.1 + - - +
429A GLY* 4.0 17.1 - - - +
430A THR* 5.6 1.3 - - - +
433A ALA* 4.5 9.7 - - + +
490A HIS* 6.3 0.4 - - - -
555A LEU* 6.3 1.0 - - - +
558A ARG* 3.7 34.1 + - - +
559A ILE* 1.3 80.1 - - - +
561A MET* 1.3 66.0 + - - +
563A MET* 3.4 4.7 + - - +
564A GLN* 2.9 30.8 + - - +
591A TYR* 4.5 12.1 + - - -
602A ASN* 5.8 0.5 + - - +
1210B GLU* 5.9 2.4 - - - +
1211B ALA* 4.4 9.7 + - - +
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Residues in contact with MET 561 (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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555A LEU* 4.4 10.1 - - + -
558A ARG 4.9 0.6 + - - +
559A ILE 3.4 0.6 - - - -
560A ASN* 1.3 86.6 - - - +
562A ILE* 1.3 55.6 + - + +
564A GLN* 3.4 11.1 - - + +
565A THR* 2.8 36.5 + - - -
583A LEU* 3.3 38.1 - - + -
587A ILE* 3.5 17.0 - - + -
591A TYR* 5.3 8.1 - - - +
602A ASN* 3.5 45.1 - - - +
605A ALA* 4.5 3.1 - - + -
606A VAL* 3.4 25.1 - - + -
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Residues in contact with ILE 562 (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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544A ILE* 3.6 37.2 - - + -
546A ALA* 3.9 18.4 - - + +
549A ILE* 4.1 22.0 - - + -
550A ALA* 4.2 17.5 - - + +
555A LEU* 4.9 1.3 - - + -
558A ARG 4.0 20.6 - - - +
559A ILE 3.2 6.7 + - - +
561A MET* 1.3 74.9 - - + +
563A MET* 1.3 64.6 + - - +
565A THR* 3.1 8.7 + - - -
566A ALA* 2.9 24.9 + - - +
605A ALA* 4.0 23.1 - - + +
609A ALA* 4.0 12.0 - - + +
613A LEU* 4.8 0.5 - - - +
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Residues in contact with MET 563 (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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422A PHE* 5.5 1.0 - - - -
486A TYR* 4.4 2.3 + - - -
488A ALA* 5.0 0.2 - - + -
489A CYS 4.7 0.4 - - - +
490A HIS* 3.5 45.4 + - + +
511A VAL* 3.4 32.8 - - + -
513A ASN* 4.0 15.0 - - + +
544A ILE* 3.9 21.5 - - + -
546A ALA* 4.0 16.2 - - - -
559A ILE* 3.1 35.4 + - + +
560A ASN* 3.9 4.5 - - - +
562A ILE* 1.3 76.5 - - - +
564A GLN* 1.3 62.1 + - - +
566A ALA* 3.1 7.0 + - + +
567A PHE* 3.1 20.6 + - - +
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Residues in contact with GLN 564 (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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433A ALA* 3.0 45.0 + - + +
434A ASN* 5.5 0.7 - - - +
436A GLN* 4.2 6.3 - - - +
437A ALA* 3.7 13.0 - - - +
440A ILE* 5.3 1.6 - - - +
560A ASN 2.9 19.1 + - - +
561A MET* 3.4 15.5 - - + +
563A MET* 1.3 76.3 - - - +
565A THR* 1.4 62.0 + - - +
567A PHE* 3.1 10.8 + - - +
568A PHE* 3.1 54.1 + - + -
583A LEU* 3.8 23.8 - - + +
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Residues in contact with THR 565 (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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561A MET 2.8 19.2 + - - -
562A ILE* 3.1 8.9 + - - -
564A GLN* 1.4 75.9 - - - +
566A ALA* 1.3 58.4 + - - +
568A PHE* 3.4 1.1 + - - +
569A LYS* 2.8 35.0 + - + +
580A VAL* 6.1 0.9 - - + -
583A LEU* 3.6 18.4 - - + +
606A VAL* 3.6 32.8 - - + +
609A ALA* 3.8 12.8 - - + -
610A VAL* 3.6 33.2 - - + +
613A LEU* 4.2 2.7 - - + -
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Residues in contact with ALA 566 (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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486A TYR* 3.6 10.8 + - - +
511A VAL* 4.1 22.2 - - + -
544A ILE* 5.4 0.7 - - + -
562A ILE 2.9 11.5 + - - +
563A MET* 3.1 14.1 + - + +
565A THR* 1.3 78.6 - - - +
567A PHE* 1.3 58.4 + - - +
569A LYS 4.6 0.2 - - - +
570A LEU* 2.8 35.4 + - + +
613A LEU* 3.5 29.1 - - + +
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Residues in contact with PHE 567 (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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420A CYS* 4.0 17.3 - - - -
422A PHE* 3.6 31.6 - + + -
437A ALA* 3.7 21.3 - - + -
441A ILE* 3.8 18.4 - - + -
468A LEU* 4.9 1.8 - - + -
470A PHE* 3.7 25.4 - + - -
486A TYR* 3.4 16.5 + + - +
563A MET 3.1 11.6 + - - +
564A GLN* 3.1 15.7 + - - +
566A ALA* 1.3 74.7 - - - +
568A PHE* 1.3 88.6 + + - +
571A ALA* 2.7 59.8 + - + +
573A VAL* 3.9 7.7 - - + +
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Residues in contact with PHE 568 (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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437A ALA* 3.9 26.2 - - + -
440A ILE* 4.0 26.5 - - + -
441A ILE* 3.9 21.8 - - + -
564A GLN* 3.1 52.5 + - + +
565A THR* 4.0 3.1 - - + +
567A PHE* 1.3 86.9 - + - +
569A LYS* 1.3 63.6 + - - +
571A ALA 4.4 1.2 + - - -
572A GLY 5.0 1.9 + - - -
573A VAL* 5.7 0.6 + - - -
574A LEU* 4.1 14.8 + - + +
576A PHE* 5.7 0.7 - - - -
579A ALA* 3.6 49.8 - - + +
580A VAL* 5.2 2.5 - - + +
582A LEU* 5.3 0.4 - - + -
583A LEU* 3.8 24.9 - - + -
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Residues in contact with LYS 569 (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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565A THR* 2.8 22.1 + - + +
566A ALA 4.2 1.3 - - - +
568A PHE* 1.3 80.6 - - - +
570A LEU* 1.3 73.6 + - + +
571A ALA 3.8 0.2 - - - -
572A GLY 4.9 1.7 + - - -
574A LEU 5.4 1.7 - - - +
576A PHE* 4.4 30.6 - - + +
579A ALA* 5.5 0.2 - - - -
580A VAL* 5.3 6.3 - - + -
610A VAL* 2.5 47.8 + - + +
613A LEU* 3.1 42.7 + - + +
614A GLN* 4.0 7.3 + - - +
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Residues in contact with LEU 570 (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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486A TYR* 4.0 13.7 - - + -
509A THR* 4.2 16.6 + - + +
511A VAL* 4.4 9.9 - - + -
542A TYR* 3.4 67.3 - - + +
566A ALA 2.8 18.9 + - - +
569A LYS* 1.3 101.2 - - + +
571A ALA* 1.3 59.3 + - - -
572A GLY 3.3 4.5 + - - -
613A LEU* 4.2 15.3 - - + -
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Residues in contact with ALA 571 (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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418A ILE* 3.6 17.7 - - - +
420A CYS* 4.5 3.1 - - - -
485A ASP* 5.5 1.6 - - - +
486A TYR* 3.8 25.5 - - + +
567A PHE* 2.7 53.8 + - + +
569A LYS 3.8 0.2 - - - -
570A LEU* 1.3 73.2 - - - +
572A GLY* 1.3 62.9 + - - +
573A VAL* 3.3 6.8 + - + -
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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