Contacts of the helix formed by residues 559 - 571 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B ASP* 4.0 27.9 + - + +
430B THR* 5.7 0.2 - - - +
490B HIS* 3.5 40.6 - - + +
513B ASN* 3.8 6.5 - - - +
546B ALA* 3.6 26.7 - - + -
547B VAL* 3.7 21.8 - - + +
557B GLY 3.3 12.3 + - - +
558B ARG* 1.3 72.1 - - - +
560B ASN* 1.3 68.6 + - - +
561B MET 3.3 2.2 - - - -
562B ILE* 3.1 8.7 + - - +
563B MET* 3.0 27.9 + - + +
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Residues in contact with ASN 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211A ALA* 4.0 18.9 - - - +
428B ASP 3.7 16.2 + - - +
429B GLY* 4.1 17.9 - - - +
430B THR* 5.6 0.9 - - - +
433B ALA* 4.5 9.7 - - + +
558B ARG* 3.6 25.9 + - - +
559B ILE* 1.3 81.0 - - - +
561B MET* 1.3 69.2 + - - +
563B MET* 3.4 4.1 + - - +
564B GLN* 2.9 28.4 + - - +
591B TYR* 4.3 14.0 + - - -
602B ASN* 5.2 1.4 + - - -
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Residues in contact with MET 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555B LEU* 4.7 4.5 - - + -
558B ARG 4.9 1.2 + - - +
559B ILE 3.3 0.6 - - - -
560B ASN* 1.3 85.2 + - - +
562B ILE* 1.3 61.2 + - + +
564B GLN* 3.5 15.1 + - + +
565B THR* 2.9 28.6 + - - -
583B LEU* 3.2 34.8 - - + -
586B SER* 5.8 0.2 - - - +
587B ILE* 4.1 20.0 - - + -
591B TYR* 5.0 8.3 - - - -
602B ASN* 3.6 48.7 - - - +
605B ALA* 4.0 11.9 - - + -
606B VAL* 3.9 11.4 - - + -
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Residues in contact with ILE 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ILE* 3.8 27.6 - - + -
546B ALA* 3.6 29.2 - - + +
549B ILE* 3.8 22.4 - - + -
550B ALA* 3.9 22.4 - - + +
555B LEU* 5.1 1.8 - - + -
558B ARG 3.9 21.1 - - - +
559B ILE 3.1 7.3 + - - +
561B MET* 1.3 81.1 - - + +
563B MET* 1.3 59.7 + - - +
565B THR* 3.1 7.9 + - - -
566B ALA* 2.9 24.6 + - - +
605B ALA* 4.3 16.2 - - + -
609B ALA* 4.1 11.4 - - + +
613B LEU* 4.8 0.5 - - - +
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Residues in contact with MET 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B PHE* 5.4 1.6 - - - -
433B ALA* 6.0 0.2 - - - -
486B TYR* 4.5 1.4 + - - -
488B ALA* 5.1 0.2 - - + -
490B HIS* 3.4 53.9 + - + +
511B VAL* 3.5 31.6 - - + -
512B LEU 4.7 0.2 - - - -
513B ASN* 3.9 14.4 - - + +
544B ILE* 3.8 16.8 - - + -
546B ALA* 3.7 23.1 - - - -
559B ILE* 3.0 27.7 + - + +
560B ASN* 4.2 4.3 - - - +
562B ILE* 1.3 73.9 - - - +
564B GLN* 1.3 64.8 + - - +
566B ALA* 3.3 7.5 + - + +
567B PHE* 3.3 19.8 + - - +
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Residues in contact with GLN 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B ALA* 2.9 47.2 + - + +
434B ASN* 4.8 1.7 + - - +
436B GLN* 4.0 7.7 - - - +
437B ALA* 3.8 13.8 - - - +
440B ILE* 5.2 3.0 - - - +
560B ASN 2.9 18.2 + - - +
561B MET* 3.5 15.6 - - + +
563B MET* 1.3 77.3 - - - +
565B THR* 1.3 62.2 + - - +
567B PHE* 3.2 10.4 + - - +
568B PHE* 3.0 47.6 + - + -
583B LEU* 3.5 24.8 - - + +
586B SER* 5.9 0.2 + - - -
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Residues in contact with THR 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561B MET 2.9 15.6 + - - -
562B ILE 3.1 8.3 + - - -
564B GLN* 1.3 74.8 - - - +
566B ALA* 1.3 64.0 + - - +
568B PHE* 3.2 2.1 + - + -
569B LYS* 2.9 24.0 + - + +
583B LEU* 3.2 27.1 - - + +
606B VAL* 3.5 16.8 - - - +
609B ALA* 3.8 19.6 - - + +
610B VAL* 3.5 33.2 - - + +
613B LEU* 4.2 4.3 - - + -
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Residues in contact with ALA 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486B TYR* 3.5 13.2 - - - +
511B VAL* 4.1 20.6 - - + -
562B ILE 2.9 12.6 + - - +
563B MET* 3.5 16.2 - - + +
564B GLN 3.2 0.4 - - - -
565B THR* 1.3 76.3 - - - +
567B PHE* 1.3 54.9 + - - +
569B LYS* 4.7 0.4 - - - +
570B LEU* 2.8 39.3 + - + +
613B LEU* 3.8 25.4 - - + +
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Residues in contact with PHE 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420B CYS* 3.8 17.3 - - - -
422B PHE* 3.6 33.4 - + + -
437B ALA* 3.9 14.8 - - + -
441B ILE* 3.8 20.6 - - + -
468B LEU* 5.0 1.3 - - + -
470B PHE* 3.6 26.7 - + - -
486B TYR* 3.3 10.9 + + - -
563B MET 3.3 8.3 + - - +
564B GLN* 3.2 16.8 + - - +
566B ALA* 1.3 76.3 - - - +
568B PHE* 1.3 81.6 - + - +
571B ALA* 2.9 51.8 + - + +
573B VAL* 3.9 13.3 + - + +
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Residues in contact with PHE 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ALA* 4.0 15.0 - - + -
440B ILE* 4.0 21.5 - - + -
441B ILE* 4.1 15.9 - - + -
564B GLN* 3.0 51.5 + - + +
565B THR 3.9 2.7 - - - +
567B PHE* 1.3 93.6 - + - +
569B LYS* 1.4 61.7 + - - +
571B ALA 4.6 1.0 + - - -
572B GLY 5.2 2.1 + - - -
573B VAL 5.7 0.5 + - - -
574B LEU* 3.9 33.8 + - + +
576B PHE* 5.9 0.2 - - - -
579B ALA* 3.5 42.9 - - + +
580B VAL* 5.9 0.7 - - + -
582B LEU* 4.4 10.3 - - + -
583B LEU* 3.8 26.9 - - + -
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Residues in contact with LYS 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565B THR* 2.9 23.1 + - + +
566B ALA* 4.1 2.9 - - - +
568B PHE* 1.4 79.4 - - - +
570B LEU* 1.3 70.4 + - + +
571B ALA 3.9 0.2 - - - -
572B GLY 5.0 2.0 + - - -
574B LEU 5.6 1.6 - - - +
576B PHE* 4.5 27.4 - - + +
579B ALA* 5.2 2.5 - - - -
580B VAL* 6.1 2.5 - - + -
610B VAL* 2.7 48.3 + - + +
613B LEU* 2.9 39.0 + - + -
614B GLN* 3.8 9.3 + - - +
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Residues in contact with LEU 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486B TYR* 4.0 10.2 - - + -
509B THR* 4.0 21.0 - - - +
511B VAL* 4.5 9.0 - - + -
540B LYS* 6.0 0.7 - - - +
542B TYR* 3.8 55.9 - - + +
566B ALA* 2.8 24.8 + - - +
569B LYS* 1.3 99.2 - - + +
571B ALA* 1.3 60.4 + - - +
572B GLY* 3.1 6.9 + - - -
613B LEU* 3.8 28.0 - - + -
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Residues in contact with ALA 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B ILE* 3.4 19.1 - - - +
420B CYS* 4.1 2.0 - - - -
485B ASP* 5.1 2.8 - - - +
486B TYR* 3.7 28.8 - - + +
567B PHE* 2.9 53.7 + - + +
568B PHE 4.6 0.4 + - - -
569B LYS 3.9 0.2 - - - -
570B LEU* 1.3 72.2 - - - +
572B GLY* 1.3 62.1 + - - +
573B VAL* 4.1 5.8 - - + +
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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