Contacts of the helix formed by residues 467 - 481 (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 467 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464D ASP* 2.9 21.6 + - - +
465D THR 3.6 0.4 - - - -
466D SER* 1.3 78.6 + - - +
468D PRO* 1.3 67.7 - - - +
469D GLU* 3.4 14.4 + - - +
470D LYS* 3.1 41.8 + - + +
471D VAL* 2.8 30.0 + - - +
509D PHE* 3.8 2.0 - - - -
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Residues in contact with PRO 468 (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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466D SER 3.6 9.0 - - - +
467D ASP* 1.3 85.1 - - - +
469D GLU* 1.3 66.1 + - - +
471D VAL* 3.0 3.1 + - - +
472D VAL* 2.9 29.3 + - - +
508D SER 5.8 0.7 - - - +
509D PHE* 3.7 17.5 - - + -
510D ASN* 4.0 27.4 - - + +
513D THR* 4.0 20.0 - - + +
514D PHE* 4.0 21.4 - - - +
517D ARG* 5.3 0.7 - - + -
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Residues in contact with GLU 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D ASP* 3.4 11.0 + - - +
468D PRO* 1.3 78.3 - - - +
470D LYS* 1.3 63.9 + - + +
472D VAL* 3.5 4.6 + - - +
473D SER* 3.2 20.8 + - - -
513D THR* 5.8 0.2 - - - +
517D ARG* 2.7 52.1 + - - +
521D HIS* 2.9 32.9 + - - -
531D ILE* 5.6 2.1 - - - +
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Residues in contact with LYS 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D THR* 5.4 5.7 - - - -
464D ASP* 3.9 26.5 + - + +
467D ASP* 3.1 42.3 + - + +
468D PRO 3.1 0.4 - - - -
469D GLU* 1.3 82.2 - - + +
471D VAL* 1.3 62.5 + - - +
473D SER* 3.1 16.4 + - - -
474D ALA* 3.1 12.6 + - - +
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Residues in contact with VAL 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D THR* 5.3 1.8 - - - +
464D ASP 4.0 13.0 - - - +
465D THR* 4.3 4.9 - - - -
467D ASP 2.8 24.5 + - - +
468D PRO 3.7 3.1 - - - +
470D LYS* 1.3 68.5 - - - +
472D VAL* 1.3 61.9 + - - +
474D ALA* 3.0 5.8 + - - +
475D PHE* 2.8 32.9 + - - +
499D LEU* 4.0 16.4 - - + -
500D MET* 3.4 35.0 - - + -
503D ALA* 3.9 11.7 - - + -
509D PHE* 3.3 22.7 - - + -
514D PHE* 3.8 8.3 - - + -
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Residues in contact with VAL 472 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D PRO 2.9 15.9 + - - +
469D GLU* 3.8 6.7 - - - +
471D VAL* 1.3 74.8 - - - +
473D SER* 1.3 58.7 + - - +
475D PHE* 4.3 2.2 - - - -
476D LEU* 2.9 49.5 + - + +
514D PHE* 3.3 47.8 - - + +
517D ARG* 4.0 8.1 - - + -
518D LEU* 3.7 17.9 - - + +
521D HIS* 3.8 27.1 - - + +
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Residues in contact with SER 473 (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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469D GLU 3.2 9.4 + - - -
470D LYS* 3.1 13.8 + - - -
471D VAL 3.0 0.6 - - - -
472D VAL* 1.3 79.3 - - - +
474D ALA* 1.3 63.7 + - - +
476D LEU* 4.3 2.4 - - - +
477D LYS* 3.0 50.7 + - - +
521D HIS* 6.3 3.6 - - - -
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Residues in contact with ALA 474 (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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440D LEU* 5.1 10.1 - - + -
459D ILE* 5.7 2.2 - - + -
463D THR* 4.1 26.2 - - + +
470D LYS 3.1 10.2 + - - +
471D VAL* 3.0 9.2 + - - +
473D SER* 1.3 75.1 - - - +
475D PHE* 1.3 68.8 + - - +
477D LYS* 3.8 2.9 - - - +
478D VAL* 2.9 34.9 + - + +
499D LEU* 3.8 17.3 - - + -
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Residues in contact with PHE 475 (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 2.8 20.8 + - - +
472D VAL* 3.8 4.9 - - - +
474D ALA* 1.3 73.7 - - - +
476D LEU* 1.3 73.1 + - + +
478D VAL* 3.7 1.6 - - - +
479D ALA* 2.8 42.6 + - + +
496D ILE* 3.8 30.8 - - + +
499D LEU* 3.9 11.8 - - + +
500D MET* 3.9 26.0 - - + -
514D PHE* 4.4 10.8 - + + -
518D LEU* 4.1 18.4 - - + -
540D PRO* 4.7 5.4 - - + -
543D VAL* 3.9 16.8 - - + -
544D LEU* 4.0 29.6 - - + -
547D VAL* 4.0 10.3 - - + -
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Residues in contact with LEU 476 (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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472D VAL* 2.9 29.7 + - + +
473D SER* 4.3 3.1 - - - +
475D PHE* 1.3 79.9 - - + +
477D LYS* 1.3 53.1 + - + +
479D ALA* 3.2 2.2 + - - +
480D SER* 2.7 35.9 + - - -
518D LEU* 3.9 20.9 - - + -
521D HIS* 3.5 37.2 - - + +
522D MET* 4.2 2.5 - - + -
534D ILE* 3.9 42.2 - - + +
540D PRO* 4.1 17.1 - - + +
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Residues in contact with LYS 477 (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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439D PHE* 5.0 0.9 - - + -
440D LEU* 3.0 47.5 + - + +
441D SER* 5.2 3.2 + - - +
443D PRO* 3.9 26.8 - - + +
473D SER* 3.0 34.5 + - - +
474D ALA* 3.3 3.2 + - - +
476D LEU* 1.3 77.1 - - + +
478D VAL* 1.3 64.2 + - - +
480D SER* 2.7 26.4 + - - -
481D VAL* 3.5 3.1 + - - +
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Residues in contact with VAL 478 (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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439D PHE* 4.5 22.4 - - + -
440D LEU* 4.9 6.1 - - + -
448D LEU* 4.9 8.1 - - + -
459D ILE* 4.8 19.7 - - + -
474D ALA* 2.9 27.3 + - + +
475D PHE* 3.7 2.9 - - - +
477D LYS* 1.3 75.7 - - - +
479D ALA* 1.3 61.4 + - - +
481D VAL* 3.4 17.8 + - - +
492D VAL* 3.6 17.2 - - + +
495D ALA* 4.0 19.3 - - + -
496D ILE* 3.6 26.7 - - + -
499D LEU* 5.3 0.7 - - + -
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Residues in contact with ALA 479 (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* 2.8 27.1 + - + +
476D LEU* 3.6 5.8 - - - +
478D VAL* 1.3 74.9 - - - +
480D SER* 1.3 64.1 + - - +
481D VAL 3.0 2.7 + - - -
482D PHE* 3.2 11.1 + - - +
492D VAL* 4.4 2.9 - - - -
496D ILE* 4.5 1.1 - - + -
539D GLY* 3.2 19.0 - - - -
540D PRO* 4.1 17.9 - - + -
543D VAL* 3.8 29.6 - - + -
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Residues in contact with SER 480 (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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443D PRO* 4.0 13.2 - - - +
476D LEU 2.7 19.0 + - - -
477D LYS* 2.7 20.8 + - - -
479D ALA* 1.3 74.8 - - - +
481D VAL* 1.3 57.6 + - - +
482D PHE 3.6 0.9 + - - +
483D ARG* 3.1 17.5 + - - -
534D ILE* 6.5 0.7 - - - -
536D SER 5.9 2.7 - - - -
539D GLY* 4.9 6.1 - - - -
540D PRO* 5.1 4.3 - - - -
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Residues in contact with VAL 481 (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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439D PHE* 4.0 7.0 - - + -
443D PRO* 3.8 13.9 - - + -
444D SER* 3.1 44.2 - - - +
445D PRO* 3.4 19.8 - - + +
448D LEU* 3.8 14.6 - - + -
477D LYS 4.2 0.9 - - - +
478D VAL 3.5 9.0 - - - +
479D ALA 3.0 0.6 - - - -
480D SER* 1.3 78.8 + - - +
482D PHE* 1.3 64.9 + - - +
483D ARG* 2.8 23.1 + - - +
488D VAL* 3.6 3.3 - - + +
492D VAL* 3.7 18.4 - - + -
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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