Contacts of the helix formed by residues 467 - 481 (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 467 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B ASP* 3.3 15.9 + - - +
466B SER* 1.3 79.8 + - - +
468B PRO* 1.3 67.9 - - - +
469B GLU* 2.8 25.3 + - - +
470B LYS* 2.9 47.8 + - + +
471B VAL* 3.0 14.4 + - - +
509B PHE* 4.1 2.5 - - - -
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Residues in contact with PRO 468 (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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466B SER 3.3 10.3 - - - +
467B ASP* 1.3 86.5 - - - +
469B GLU* 1.3 59.5 + - - +
471B VAL* 3.5 1.4 + - - +
472B VAL* 3.0 31.7 + - - +
508B SER 5.9 0.2 - - - +
509B PHE* 3.2 29.6 - - + -
510B ASN* 4.0 17.9 - - + +
513B THR* 3.8 28.5 - - + +
514B PHE* 3.9 8.2 - - - +
517B ARG* 5.2 2.7 - - + -
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Residues in contact with GLU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ASP* 2.8 15.1 + - - +
468B PRO* 1.3 74.8 - - - +
470B LYS* 1.3 69.8 + - + +
472B VAL* 3.5 4.6 + - - +
473B SER* 3.2 18.7 + - - -
517B ARG* 3.0 43.9 + - + +
521B HIS* 3.0 31.3 + - - -
531B ILE* 5.5 1.0 - - - +
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Residues in contact with LYS 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B THR* 4.9 6.2 - - + +
464B ASP* 3.6 31.6 - - + +
467B ASP* 2.9 39.9 + - + +
469B GLU* 1.3 78.9 - - - +
471B VAL* 1.3 66.2 + - - +
473B SER* 3.0 17.9 + - - -
474B ALA* 3.1 11.8 + - - +
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B THR* 4.7 3.1 - - + -
464B ASP 3.9 1.8 + - - +
465B THR* 3.9 27.1 - - - -
467B ASP 3.0 13.3 + - - +
468B PRO 4.0 3.4 - - - +
470B LYS* 1.3 75.0 - - - +
472B VAL* 1.3 53.0 + - - +
474B ALA* 3.2 7.4 + - - +
475B PHE* 2.7 32.7 + - - +
499B LEU* 4.0 14.8 - - + -
500B MET* 3.3 39.5 - - + -
503B ALA* 4.1 13.2 - - + -
509B PHE* 4.1 11.9 - - + -
514B PHE* 3.9 5.2 - - + -
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Residues in contact with VAL 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B PRO 3.0 26.8 + - - +
469B GLU* 3.6 6.5 - - - +
470B LYS 3.1 0.2 - - - -
471B VAL* 1.3 74.9 - - - +
473B SER* 1.3 56.6 + - - +
475B PHE* 3.4 2.3 - - - +
476B LEU* 2.9 39.9 + - + +
514B PHE* 3.4 43.7 - - + +
517B ARG* 4.0 7.4 - - + -
518B LEU* 3.9 17.0 - - + +
521B HIS* 3.1 35.0 - - + -
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Residues in contact with SER 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B GLU 3.2 9.6 + - - -
470B LYS* 3.0 12.0 + - - -
472B VAL* 1.3 80.7 - - - +
474B ALA* 1.3 63.9 + - - +
475B PHE 3.2 0.2 + - - -
476B LEU* 3.9 5.1 - - - +
477B LYS* 3.0 52.3 + - - +
521B HIS* 5.6 3.6 - - - -
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Residues in contact with ALA 474 (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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440B LEU* 5.2 9.2 - - + -
459B ILE* 4.8 6.3 - - + -
463B THR* 4.2 24.9 - - + +
470B LYS 3.1 8.9 + - - +
471B VAL 3.7 3.4 - - - +
473B SER* 1.3 77.7 - - - +
475B PHE* 1.3 59.5 + - - +
477B LYS* 4.0 6.2 - - - +
478B VAL* 2.9 33.5 + - + +
499B LEU* 3.7 18.4 - - + -
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Residues in contact with PHE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B VAL 2.7 17.6 + - - +
472B VAL* 3.4 7.2 - - - +
474B ALA* 1.3 76.8 - - - +
476B LEU* 1.3 61.1 + - + +
478B VAL* 3.8 1.6 - - - +
479B ALA* 2.7 44.9 + - + +
496B ILE* 3.4 33.1 - - + +
499B LEU* 3.7 8.0 - - + +
500B MET* 3.8 28.7 - - + -
514B PHE* 4.4 8.5 - + + -
518B LEU* 4.1 28.0 - - + -
540B PRO* 4.9 7.0 - - + -
543B VAL* 4.0 15.0 - - + -
544B LEU* 3.8 34.3 - - + -
547B VAL* 4.0 7.2 - - + -
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Residues in contact with LEU 476 (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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472B VAL* 2.9 32.9 + - + +
473B SER* 3.9 4.0 - - - +
475B PHE* 1.3 72.8 - - + +
477B LYS* 1.3 53.8 + - + +
479B ALA* 3.2 5.9 + - - +
480B SER* 2.8 34.8 + - - -
518B LEU* 4.0 12.6 - - + -
521B HIS* 3.1 36.8 - - + -
522B MET* 3.9 16.2 - - + -
534B ILE* 3.8 41.1 - - + -
540B PRO* 4.2 13.6 - - + +
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Residues in contact with LYS 477 (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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439B PHE* 4.9 1.6 - - + -
440B LEU* 2.9 54.2 + - + +
441B SER* 5.0 1.2 - - - +
443B PRO* 3.8 25.3 - - + +
473B SER* 3.0 38.4 + - - +
474B ALA* 4.0 4.9 - - - +
476B LEU* 1.3 74.1 - - + +
478B VAL* 1.3 67.1 + - - +
480B SER* 2.7 25.7 + - - -
481B VAL* 3.5 3.3 + - - +
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Residues in contact with VAL 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B PHE* 4.4 22.7 - - + -
440B LEU* 5.2 2.2 - - + -
448B LEU* 4.8 7.0 - - + -
459B ILE* 4.6 24.7 - - + -
474B ALA* 2.9 24.1 + - - +
477B LYS* 1.3 75.6 - - + +
479B ALA* 1.3 62.7 + - - +
481B VAL* 3.0 18.5 + - - +
492B VAL* 3.5 29.7 - - + +
495B ALA* 4.1 13.7 - - + -
496B ILE* 3.4 24.5 - - + -
499B LEU* 5.4 0.9 - - + -
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Residues in contact with ALA 479 (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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475B PHE* 2.7 30.2 + - + +
476B LEU* 3.4 8.3 - - - +
478B VAL* 1.3 75.3 - - - +
480B SER* 1.3 57.5 + - - +
481B VAL 3.1 1.4 + - - -
482B PHE* 3.5 7.8 + - - +
492B VAL* 4.4 2.0 - - - -
496B ILE* 4.3 3.3 - - + +
539B GLY* 3.2 24.5 - - - -
540B PRO* 3.9 25.8 - - + -
543B VAL* 4.0 20.2 - - + -
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Residues in contact with SER 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B PRO* 3.6 17.0 - - - +
476B LEU 2.8 16.7 + - - -
477B LYS* 2.7 20.6 + - - -
479B ALA* 1.3 74.3 - - - +
481B VAL* 1.3 59.5 + - - +
482B PHE 3.4 1.4 - - - +
483B ARG* 3.3 17.8 + - - -
535B PRO* 6.3 3.8 - - - -
536B SER 6.1 1.1 - - - -
539B GLY* 4.9 2.0 - - - -
540B PRO* 4.9 8.3 - - - -
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Residues in contact with VAL 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B PHE* 3.6 13.2 - - + -
443B PRO* 3.7 12.8 - - + -
444B SER* 3.1 40.4 - - - +
445B PRO* 3.2 25.7 - - + +
448B LEU* 3.9 12.6 - - + -
477B LYS 4.0 0.7 - - - +
478B VAL 3.0 10.6 + - - +
480B SER* 1.3 77.9 - - - +
482B PHE* 1.3 63.6 + - - +
483B ARG* 2.9 14.8 + - - +
488B VAL* 3.4 11.1 - - + +
492B VAL* 3.8 15.5 - - + -
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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