Contacts of the helix formed by residues 491 - 507 (chain B) in PDB entry 5KJH
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 ALA 491 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490B GLU* 1.4 74.2 - - - +
492B LEU* 1.4 65.3 + - - +
494B GLN* 3.3 8.5 + - - +
495B LYS* 3.0 39.6 + - - +
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B GLU* 3.4 0.8 - - - -
491B ALA* 1.4 75.2 - - - +
493B MET* 1.3 75.3 + - + +
495B LYS* 3.2 20.1 + - - +
496B VAL* 3.0 35.4 + - + +
599B GLU* 3.7 44.0 - - + +
602B PHE* 4.4 18.6 - - + -
603B ALA* 5.2 1.1 - - + -
637B LEU* 4.2 14.6 - - + -
638B ARG 3.5 30.7 - - - +
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Residues in contact with MET 493 (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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490B GLU* 3.3 17.0 + - + +
492B LEU* 1.3 106.0 - - + +
494B GLN* 1.4 60.3 + - - +
496B VAL* 3.2 8.7 + - - +
497B ILE* 2.8 40.3 + - + +
538B LEU* 5.9 0.2 - - - -
539B MET* 3.6 30.1 - - + +
542B LEU* 4.7 4.3 - - - -
546B TRP* 3.9 13.2 - - + -
603B ALA* 3.9 25.8 - - + -
638B ARG 4.8 0.7 - - - +
639B LEU* 5.0 1.3 - - - -
640B PRO* 3.6 35.2 - - + -
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Residues in contact with GLN 494 (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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490B GLU* 3.0 15.1 + - + +
491B ALA* 3.3 10.7 + - - +
493B MET* 1.4 73.2 - - - +
495B LYS* 1.4 61.7 + - + +
497B ILE* 3.4 24.4 + - - +
498B ASP* 2.9 50.5 + - - +
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Residues in contact with LYS 495 (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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491B ALA* 3.0 37.8 + - - +
492B LEU* 3.3 17.8 - - - +
494B GLN* 1.4 77.2 - - - +
496B VAL* 1.4 55.9 + - - +
498B ASP* 3.3 8.3 + - - +
499B ALA* 2.9 30.0 + - - +
599B GLU* 3.7 35.5 + - - +
637B LEU* 6.3 0.2 - - - +
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Residues in contact with VAL 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 3.0 25.3 + - + +
493B MET* 3.2 12.1 + - - +
495B LYS* 1.4 72.0 - - + +
497B ILE* 1.3 65.8 + - - +
499B ALA* 3.1 9.0 + - - +
500B LEU* 3.0 29.9 + - + +
538B LEU* 4.0 18.4 - - + -
599B GLU* 3.9 11.9 - - + +
600B TRP* 3.7 43.5 - - + +
603B ALA* 4.1 16.8 - - + -
604B THR* 4.8 2.2 - - + -
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Residues in contact with ILE 497 (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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493B MET* 2.8 33.1 + - + +
494B GLN* 3.8 26.2 - - - +
496B VAL* 1.3 70.4 - - - +
498B ASP* 1.3 63.4 + - - +
500B LEU* 3.5 2.8 + - - +
501B GLY* 3.2 20.6 + - - -
504B THR* 5.2 1.2 + - - -
538B LEU* 3.9 30.5 - - + +
539B MET* 3.7 29.6 - - + -
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Residues in contact with ASP 498 (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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494B GLN* 2.9 44.4 + - - +
495B LYS* 3.5 8.0 + - - +
497B ILE* 1.3 75.4 - - - +
499B ALA* 1.3 61.0 + - - +
500B LEU 3.6 0.5 + - - -
501B GLY* 3.6 10.5 + - - -
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Residues in contact with ALA 499 (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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495B LYS 2.9 17.5 + - - +
496B VAL* 3.1 7.2 + - - +
498B ASP* 1.3 78.0 - - - +
500B LEU* 1.3 61.6 + - + +
501B GLY 3.4 0.6 + - - -
502B SER 5.2 1.0 + - - -
503B TYR* 5.1 6.4 - - - -
600B TRP* 3.4 38.6 - - + -
2603B GLU* 5.2 4.9 - - - +
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Residues in contact with LEU 500 (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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496B VAL* 3.0 36.5 + - + +
497B ILE* 3.9 4.5 - - - +
499B ALA* 1.3 78.9 - - - +
501B GLY* 1.3 63.6 + - - +
502B SER 3.4 2.5 - - - -
503B TYR* 3.0 30.3 + - + +
504B THR* 3.1 24.4 + - + -
538B LEU* 4.2 20.9 - - + -
600B TRP* 4.2 30.5 - - + +
604B THR* 4.2 14.4 - - + -
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Residues in contact with GLY 501 (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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497B ILE 3.2 13.4 + - - -
498B ASP 3.6 7.4 + - - -
499B ALA 3.4 3.8 - - - -
500B LEU* 1.3 75.2 - - - +
502B SER* 1.3 56.0 + - - +
504B THR* 3.3 6.4 + - - -
505B THR* 2.9 37.3 + - - -
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Residues in contact with SER 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B ALA 5.2 1.0 + - - -
500B LEU 3.4 1.0 - - - -
501B GLY* 1.3 73.4 - - - +
503B TYR* 1.3 65.1 + - - +
505B THR* 4.6 2.9 - - - -
506B LEU* 3.1 35.9 + - - +
514B HIS* 4.3 2.3 - - - -
2598B ASP 5.0 2.1 + - - -
2599B LEU* 3.4 22.8 - - - +
2603B GLU* 3.0 37.8 + - - -
2607B LEU* 4.8 5.4 - - - -
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Residues in contact with TYR 503 (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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499B ALA 5.1 4.3 - - - -
500B LEU* 3.0 25.0 + - + +
502B SER* 1.3 83.1 - - - +
504B THR* 1.3 61.4 + - + +
507B GLY* 3.0 27.0 + - - +
514B HIS* 3.7 20.7 + + - -
2603B GLU* 4.4 21.4 + - + +
2606B PHE* 3.4 38.1 - + - +
2607B LEU* 3.5 28.0 - - + +
2648B GLU 6.0 2.3 - - - -
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Residues in contact with THR 504 (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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497B ILE 5.2 1.4 + - - -
500B LEU* 3.1 27.0 + - + +
501B GLY* 3.3 13.9 + - - -
503B TYR* 1.3 77.3 - - + +
505B THR* 1.4 60.5 + - - +
531B SER* 3.3 3.5 - - - -
532B LEU* 3.2 58.4 + - + -
533B GLU* 3.2 25.4 + - - -
538B LEU* 4.4 21.1 + - + +
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Residues in contact with THR 505 (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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501B GLY* 2.9 24.6 + - - -
502B SER* 4.2 4.0 - - - -
504B THR* 1.4 78.3 + - - +
506B LEU* 1.4 67.8 + - + +
529B CYS* 3.5 10.6 - - - +
531B SER* 2.8 16.9 + - - -
533B GLU* 3.4 25.4 + - + +
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Residues in contact with LEU 506 (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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502B SER* 3.1 18.5 + - - +
505B THR* 1.4 91.7 - - + +
507B GLY* 1.3 65.3 - - - +
508B CYS* 3.1 5.9 + - - +
513B SER 3.5 8.1 - - - +
514B HIS* 3.6 32.5 - - + +
516B CYS* 5.9 0.3 - - - -
529B CYS* 3.8 29.4 - - - +
531B SER* 4.1 2.2 - - - -
2593B LEU* 4.3 8.1 - - + -
2596B PHE* 4.5 21.1 - - + -
2599B LEU* 3.9 35.4 - - + -
2607B LEU* 4.8 4.0 - - + -
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Residues in contact with GLY 507 (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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503B TYR 3.0 21.6 + - - +
505B THR 3.9 0.2 - - - -
506B LEU* 1.3 72.9 - - - +
508B CYS* 1.3 64.9 + - - -
509B LEU* 3.6 2.6 + - - +
512B PHE* 5.2 2.5 - - - -
513B SER 4.0 1.6 - - - -
514B HIS* 3.3 20.9 - - - -
531B SER* 3.3 20.9 - - - -
532B LEU* 4.1 3.1 + - - +
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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