Contacts of the helix formed by residues 485 - 506 (chain B) in PDB entry 1KPS
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 485 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B ARG* 3.2 6.0 - - + +
484B ASP* 1.3 74.2 - - - +
486B ALA* 1.3 59.0 + - - +
487B SER* 2.9 28.4 + - - -
488B VAL* 3.0 19.0 + - + -
489B LYS* 2.8 32.6 + - - +
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Residues in contact with ALA 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B ASP 3.1 6.8 + - - -
485B ASP* 1.3 73.9 + - - +
487B SER* 1.3 66.5 + - - +
489B LYS* 4.5 5.6 - - - -
490B THR* 3.0 27.4 + - - +
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Residues in contact with SER 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B LEU* 4.3 25.3 - - - +
485B ASP* 2.9 14.8 + - - -
486B ALA* 1.3 82.6 - - - +
488B VAL* 1.3 63.9 + - - +
490B THR* 3.5 3.3 + - - -
491B ALA* 3.3 17.0 + - - +
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Residues in contact with VAL 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B PRO* 4.1 21.5 - - + +
448B LEU* 4.7 3.4 - - + -
449B LEU* 4.2 22.0 - - + -
481B VAL* 3.4 27.8 - - + +
483B ARG* 4.2 14.4 - - + +
485B ASP* 3.0 20.8 + - + +
487B SER* 1.3 74.4 - - - +
489B LYS* 1.3 66.9 + - - +
491B ALA* 2.9 8.6 + - - +
492B VAL* 2.8 31.8 + - + +
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Residues in contact with LYS 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B PHE* 3.5 34.1 - - + -
483B ARG 3.3 15.6 + - - +
484B ASP* 4.3 8.3 - - - +
485B ASP 2.8 20.2 + - - +
486B ALA* 4.1 5.2 - - - +
488B VAL* 1.3 73.6 - - - +
490B THR* 1.3 69.0 + - - +
492B VAL* 4.1 0.7 - - - +
493B LEU* 3.2 52.9 + - + +
546B HIS* 6.2 0.2 - - - -
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Residues in contact with THR 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B ALA* 3.0 18.9 + - - +
487B SER* 3.7 4.0 - - - -
488B VAL 3.1 0.6 - - - -
489B LYS* 1.3 84.4 - - - +
491B ALA* 1.3 65.9 + - - +
493B LEU* 4.0 1.3 - - - -
494B ASP* 2.3 48.4 + - - +
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Residues in contact with ALA 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B LEU* 3.5 23.8 - - + -
449B LEU* 4.3 13.7 - - + -
455B VAL* 5.8 7.4 - - + +
487B SER 3.3 9.7 + - - +
488B VAL 2.9 8.8 + - - +
490B THR* 1.3 82.2 - - - +
492B VAL* 1.3 62.1 + - - +
494B ASP* 3.3 4.6 + - - +
495B ALA* 3.0 25.3 + - - +
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Residues in contact with VAL 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B LEU* 3.6 22.9 - - + -
478B VAL* 3.5 32.1 - - + +
481B VAL* 3.8 19.1 - - + -
482B PHE* 3.8 34.8 - - + +
488B VAL* 2.8 20.1 + - + +
489B LYS 4.2 2.0 - - - +
491B ALA* 1.3 71.8 - - - +
493B LEU* 1.3 61.3 + - - +
495B ALA* 3.8 1.6 - - - +
496B ILE* 2.9 37.9 + - + +
543B VAL* 4.3 8.7 - - + -
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B PHE* 4.6 11.4 - - + -
489B LYS* 3.2 47.3 + - + +
490B THR* 4.3 2.2 - - - +
492B VAL* 1.3 74.4 - - - +
494B ASP* 1.3 64.0 + - - +
496B ILE* 3.8 2.3 - - + +
497B ASP* 3.0 35.6 + - - +
542B MET 5.0 0.7 - - - +
543B VAL* 4.1 31.6 - - + -
546B HIS* 3.6 54.0 + - + +
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Residues in contact with ASP 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B SER* 4.2 15.3 + - - +
490B THR* 2.3 46.3 + - - +
491B ALA* 3.7 4.9 - - - +
493B LEU* 1.3 77.6 - - - +
495B ALA* 1.3 64.8 + - - +
497B ASP* 3.1 10.1 + - - +
498B ALA* 2.9 23.9 + - - +
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Residues in contact with ALA 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B LEU* 5.5 2.5 - - + -
455B VAL* 5.0 9.9 - - + +
456B SER* 4.3 12.7 + - - +
459B ILE* 4.4 23.2 - - + +
460B VAL* 5.1 0.7 - - - +
478B VAL* 4.1 17.3 - - + -
491B ALA 3.0 17.7 + - - +
492B VAL* 3.8 4.5 - - - +
494B ASP* 1.3 75.5 - - - +
496B ILE* 1.3 57.3 + - - +
498B ALA* 3.2 6.6 + - - +
499B LEU* 2.8 30.1 + - - +
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Residues in contact with ILE 496 (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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474B ALA 4.8 0.2 - - - +
475B PHE* 3.4 52.0 - - + +
478B VAL* 3.4 33.4 - - + -
479B ALA 4.3 2.5 - - - +
492B VAL* 2.9 27.0 + - + +
493B LEU* 3.8 5.6 - - + +
495B ALA* 1.3 73.2 - - - +
497B ASP* 1.3 60.9 + - - +
499B LEU* 3.1 6.6 + - + -
500B MET* 2.8 33.6 + - + +
543B VAL* 3.6 24.7 - - + -
546B HIS* 6.1 0.7 - - + -
547B VAL* 3.7 12.6 - - + -
552B TYR* 4.3 0.4 - - - +
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Residues in contact with ASP 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B LEU 3.0 27.1 + - - +
494B ASP* 3.1 9.0 + - - +
496B ILE* 1.3 75.6 - - - +
498B ALA* 1.3 58.3 + - - +
501B LYS* 2.9 37.7 + - + +
546B HIS* 3.3 26.5 + - - -
550B GLN* 3.7 7.1 - - - +
552B TYR* 3.0 33.5 + - + -
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Residues in contact with ALA 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B SER* 3.9 19.1 - - - +
460B VAL* 3.4 24.5 - - + +
494B ASP 2.9 12.5 + - - +
495B ALA 3.4 7.9 - - - +
497B ASP* 1.3 77.1 - - - +
499B LEU* 1.3 61.9 + - - +
501B LYS* 4.0 3.8 - - - +
502B LYS* 3.2 24.8 + - - +
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Residues in contact with LEU 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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459B ILE* 4.6 15.7 - - + +
460B VAL* 3.8 7.7 - - - +
463B THR* 4.0 20.0 - - + +
465B THR* 3.9 22.2 - - + +
471B VAL* 4.0 16.6 - - + +
474B ALA* 3.7 13.7 - - + +
475B PHE* 3.7 36.1 - - + +
478B VAL* 5.4 0.4 - - + -
495B ALA 2.8 19.5 + - - +
496B ILE* 3.6 9.2 - - + +
498B ALA* 1.3 74.7 - - - +
500B MET* 1.3 67.5 + - - +
502B LYS* 3.6 3.4 + - - +
503B ALA* 3.1 26.0 + - - +
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Residues in contact with MET 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B VAL* 3.3 28.9 - - + -
475B PHE* 3.8 36.8 - - + -
496B ILE* 2.8 24.5 + - + +
499B LEU* 1.3 75.2 - - + +
501B LYS* 1.3 66.8 + - - +
503B ALA* 4.0 7.2 - - + -
504B PHE* 2.8 56.6 + - + -
509B PHE* 4.5 0.7 - - + -
514B PHE* 3.3 28.3 - - + -
547B VAL* 4.9 2.5 - - + -
552B TYR* 3.5 22.2 - - + +
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Residues in contact with LYS 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ASP* 2.9 23.5 + - + +
498B ALA* 4.0 4.5 - - - +
500B MET* 1.3 77.0 - - - +
502B LYS* 1.3 62.9 + - - +
504B PHE* 3.6 2.1 + - - +
505B SER* 3.3 21.9 + - - -
552B TYR* 3.8 34.8 - - + +
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Residues in contact with LYS 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B VAL* 3.3 38.6 + - + +
461B GLN* 5.6 3.2 - - - +
465B THR* 3.3 25.0 + - + +
498B ALA 3.2 15.5 + - - +
499B LEU 3.9 3.4 - - - +
500B MET 3.2 0.4 - - - -
501B LYS* 1.3 81.9 - - - +
503B ALA* 1.3 61.6 - - - +
505B SER* 3.2 15.1 + - - -
506B CYS* 3.2 14.8 + - + +
604B SO4 3.7 38.4 + - - +
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Residues in contact with ALA 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B THR* 4.0 13.8 - - - -
471B VAL* 4.1 20.0 - - + -
499B LEU 3.1 18.2 + - - +
500B MET* 3.1 15.2 + - + +
502B LYS* 1.3 77.2 - - - +
504B PHE* 1.3 62.1 + - - +
505B SER 3.1 1.0 + - - -
506B CYS* 3.3 6.1 + - - +
509B PHE* 2.8 44.4 - - + +
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Residues in contact with PHE 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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500B MET* 2.8 41.3 + - + +
501B LYS 4.2 2.5 - - - +
503B ALA* 1.3 72.8 - - - +
505B SER* 1.3 59.2 + - - +
506B CYS 4.7 2.5 - - - +
509B PHE* 3.8 15.0 - + - -
511B SER* 4.1 15.9 - - - -
514B PHE* 3.8 28.3 - + - -
547B VAL* 4.7 2.0 - - + -
552B TYR* 3.3 53.8 - + + +
553B PHE* 3.9 17.9 - + - -
554B PRO* 3.7 27.4 - - + -
557B LEU* 4.2 0.9 - - + -
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Residues in contact with SER 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B LYS* 3.3 14.0 + - - -
502B LYS* 3.2 12.8 + - - -
503B ALA 3.0 0.8 - - - -
504B PHE* 1.3 78.2 - - - +
506B CYS* 1.3 65.6 + - - +
507B SER* 3.0 7.4 + - - -
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Residues in contact with CYS 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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465B THR* 3.8 17.3 - - - +
466B SER* 4.0 24.0 - - - -
502B LYS* 3.2 8.5 + - + +
503B ALA 3.3 6.4 + - - +
504B PHE 4.7 2.0 - - - +
505B SER* 1.3 76.1 - - - +
507B SER* 1.3 68.1 - - - +
508B SER* 3.2 15.0 - - - -
509B PHE* 2.9 24.2 + - + +
604B SO4 5.8 4.9 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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