Contacts of the helix formed by residues 485 - 506 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D LEU* 5.2 0.3 - - - +
483D ARG* 3.2 4.8 - - + +
484D ASP* 1.3 76.5 - - - +
486D ALA* 1.3 66.4 + - - +
487D SER* 3.0 16.7 + - - -
488D VAL* 2.7 44.5 + - + +
489D LYS* 2.9 19.7 + - - +
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Residues in contact with ALA 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484D ASP 3.2 6.6 + - - -
485D ASP* 1.3 72.9 + - - +
487D SER* 1.3 65.8 + - - +
489D LYS* 4.2 8.3 - - - -
490D THR* 2.9 34.8 + - - +
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Residues in contact with SER 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449D LEU* 3.8 26.2 - - - +
485D ASP* 3.0 16.0 + - - -
486D ALA* 1.3 78.8 - - - +
488D VAL* 1.3 65.0 + - - +
490D THR* 3.8 5.0 - - - -
491D ALA* 3.4 16.5 + - - +
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Residues in contact with VAL 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D PRO* 3.7 22.9 - - + +
448D LEU* 5.2 1.8 - - + -
449D LEU* 4.0 23.1 - - + -
481D VAL* 3.6 30.1 - - + +
483D ARG* 3.9 17.5 - - + +
485D ASP* 2.7 26.9 + - + +
487D SER* 1.3 69.0 - - - +
489D LYS* 1.3 68.5 + - - +
491D ALA* 2.8 18.4 + - - +
492D VAL* 2.9 23.5 + - + -
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Residues in contact with LYS 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482D PHE* 3.4 34.3 - - + -
483D ARG 3.5 11.1 + - - +
484D ASP* 4.4 11.7 - - - +
485D ASP 2.9 20.0 + - - +
486D ALA* 3.5 8.3 - - - +
488D VAL* 1.3 74.4 - - - +
490D THR* 1.3 65.3 + - - +
492D VAL* 3.1 2.5 + - - +
493D LEU* 2.9 51.6 + - + +
542D MET* 5.8 3.8 - - - -
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Residues in contact with THR 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486D ALA* 2.9 24.6 + - - +
487D SER* 3.8 5.4 - - - -
489D LYS* 1.3 74.0 - - - +
491D ALA* 1.3 64.0 + - - +
493D LEU* 4.9 4.5 - - - -
494D ASP* 2.5 47.7 + - - +
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Residues in contact with ALA 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D LEU* 4.0 22.2 - - + +
449D LEU* 4.5 14.6 - - + -
455D VAL* 5.5 8.2 - - + +
456D SER* 5.1 1.0 + - - -
487D SER 3.4 9.2 + - - +
488D VAL* 2.8 14.7 + - - +
490D THR* 1.3 75.7 - - - +
492D VAL* 1.3 53.0 + - - +
494D ASP* 3.1 7.2 + - - +
495D ALA* 2.8 35.2 + - - +
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Residues in contact with VAL 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D LEU* 3.6 23.5 - - + +
478D VAL* 3.6 18.6 - - + +
481D VAL* 3.7 10.5 - - + -
482D PHE* 3.9 28.3 - - + -
488D VAL* 2.9 33.1 + - + +
489D LYS 3.5 6.5 - - - +
491D ALA* 1.3 73.5 - - - +
493D LEU* 1.3 60.3 + - - +
495D ALA* 3.0 5.9 + - - +
496D ILE* 2.8 45.1 + - + +
543D VAL* 4.2 7.6 - - + -
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Residues in contact with LEU 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D PHE* 4.6 14.6 - - + -
489D LYS* 2.9 57.8 + - + +
490D THR* 4.1 4.7 - - - +
492D VAL* 1.3 72.4 - - - +
494D ASP* 1.3 57.4 + - - +
496D ILE* 4.3 2.9 - - - -
497D ASP* 2.7 41.7 + - - +
542D MET 5.4 0.2 - - - +
543D VAL* 4.6 18.2 - - + -
546D HIS* 3.6 54.7 - - + +
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Residues in contact with ASP 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456D SER* 4.2 14.4 + - - +
490D THR* 2.5 45.7 + - - +
491D ALA* 3.3 6.5 - - - +
493D LEU* 1.3 79.1 - - - +
495D ALA* 1.3 57.0 + - - +
497D ASP* 3.9 6.0 - - - +
498D ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448D LEU* 5.3 5.6 - - + -
455D VAL* 5.0 12.3 - - + +
456D SER* 4.3 9.1 + - - +
459D ILE* 3.6 23.9 - - + +
478D VAL* 4.0 15.5 - - + -
491D ALA 2.8 15.5 + - - +
492D VAL* 3.4 7.6 - - - +
494D ASP* 1.3 70.2 - - - +
496D ILE* 1.3 67.2 + - - +
498D ALA* 2.9 8.0 + - - +
499D LEU* 2.8 23.4 + - - +
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Residues in contact with ILE 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D PHE* 3.8 36.6 - - + +
478D VAL* 3.6 31.4 - - + -
479D ALA 4.2 2.9 - - - +
492D VAL* 2.8 28.7 + - + +
493D LEU* 3.6 5.8 - - - +
495D ALA* 1.3 72.9 - - - +
497D ASP* 1.3 67.7 + - - +
499D LEU* 3.1 6.4 + - + +
500D MET* 2.9 25.6 + - + +
543D VAL* 3.7 23.1 - - + -
546D HIS* 5.4 1.1 - - + -
547D VAL* 3.6 31.6 - - + -
552D TYR* 4.2 2.0 - - - +
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Residues in contact with ASP 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D LEU* 2.7 26.8 + - - +
494D ASP* 3.9 6.1 + - - +
496D ILE* 1.3 71.8 - - - +
498D ALA* 1.3 65.2 + - - +
501D LYS* 3.0 30.2 + - - +
546D HIS* 2.6 37.7 + - - -
550D GLN* 3.9 3.6 - - - +
552D TYR* 2.7 41.7 + - + -
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Residues in contact with ALA 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D SER* 3.4 31.2 - - - +
459D ILE* 5.1 0.2 - - + -
460D VAL* 3.8 11.0 - - + +
494D ASP 2.9 17.1 + - - +
495D ALA* 3.2 10.5 - - - +
497D ASP* 1.3 79.5 - - - +
499D LEU* 1.3 63.9 + - - +
501D LYS* 3.8 4.8 - - - +
502D LYS* 3.5 13.2 + - - +
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Residues in contact with LEU 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459D ILE* 3.8 22.9 - - + +
460D VAL* 3.9 10.7 - - - +
463D THR* 4.3 17.7 - - - +
465D THR* 4.7 12.3 - - + +
471D VAL* 4.0 20.0 - - + -
474D ALA* 3.8 26.9 - - + -
475D PHE* 3.9 21.3 - - + +
478D VAL* 5.3 1.3 - - + -
495D ALA 2.8 14.5 + - - +
496D ILE* 3.4 13.5 - - + +
498D ALA* 1.3 70.9 - - - +
500D MET* 1.3 75.2 + - - +
502D LYS* 3.0 15.2 + - - +
503D ALA 3.0 10.4 + - - -
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Residues in contact with MET 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471D VAL* 3.4 27.8 - - + -
475D PHE* 3.9 33.4 - - + -
496D ILE* 2.9 22.0 + - + +
499D LEU* 1.3 73.9 - - + +
501D LYS* 1.3 68.6 + - - +
503D ALA* 4.3 5.4 - - + -
504D PHE* 2.7 62.8 + - + +
509D PHE* 4.8 0.7 - - + -
514D PHE* 3.3 29.8 - - + -
547D VAL* 4.8 3.1 - - + -
552D TYR* 3.6 22.2 - - + +
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Residues in contact with LYS 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497D ASP* 3.0 20.8 + - + +
498D ALA* 3.8 5.4 - - - +
500D MET* 1.3 78.7 - - - +
502D LYS* 1.3 61.7 + - - +
504D PHE* 3.8 1.9 - - - +
505D SER* 2.8 33.7 + - - +
552D TYR* 3.9 36.4 - - + +
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Residues in contact with LYS 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D VAL* 3.1 46.2 + - + +
461D GLN* 4.7 8.3 - - - +
465D THR* 3.4 21.1 + - + -
498D ALA 3.5 7.5 + - - +
499D LEU 3.0 9.6 + - - +
501D LYS* 1.3 78.1 - - - +
503D ALA* 1.3 58.4 + - - +
505D SER* 2.7 29.1 + - - -
506D CYS* 2.9 14.2 + - + +
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Residues in contact with ALA 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D THR* 3.0 30.4 - - + +
471D VAL* 3.9 18.2 - - + -
499D LEU* 3.0 9.8 + - + +
500D MET* 3.9 6.1 - - + +
502D LYS* 1.3 78.3 - - - +
504D PHE* 1.3 60.1 + - - +
506D CYS* 3.5 3.7 + - - +
509D PHE* 2.9 51.7 - - + +
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Residues in contact with PHE 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500D MET* 2.7 59.4 + - + +
501D LYS 3.8 3.4 - - - +
503D ALA* 1.3 71.3 - - - +
505D SER* 1.3 62.5 + - - +
506D CYS 4.2 3.8 - - - +
507D SER* 5.5 0.3 - - - -
509D PHE* 4.2 17.4 - + - +
511D SER* 4.0 22.7 - - - -
514D PHE* 4.1 13.9 - + - -
547D VAL* 4.5 3.1 - - + -
552D TYR* 3.4 37.7 - + + +
553D PHE* 4.0 24.7 - + - -
554D PRO* 3.9 20.6 - - + -
557D LEU* 4.1 6.3 - - + -
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Residues in contact with SER 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D LYS* 2.8 25.3 + - - +
502D LYS* 2.7 18.3 + - - -
504D PHE* 1.3 72.4 - - - +
506D CYS* 1.3 51.6 + - - -
507D SER* 2.8 20.8 + - - -
552D TYR* 5.9 0.3 - - - +
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Residues in contact with CYS 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D THR* 4.0 10.5 - - + +
466D SER* 3.6 21.1 - - - -
502D LYS* 2.9 11.5 + - + +
503D ALA 3.6 11.1 - - - +
504D PHE 3.4 3.2 - - - +
505D SER* 1.3 72.9 - - - +
507D SER* 1.3 53.4 - - - +
508D SER* 3.0 33.7 - - - -
509D PHE* 2.8 35.0 + - + +
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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