Contacts of the helix formed by residues 466 - 482 (chain B) in PDB entry 6KNC
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 VAL 466 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358B ARG* 3.7 24.7 - - - +
359B LEU 5.4 2.5 - - - +
360B ARG* 4.7 13.0 - - + +
464B ASN* 3.0 13.3 + - + +
465B TYR* 1.3 80.2 - - - +
467B GLU* 1.3 63.3 + - - +
468B GLU* 3.2 19.6 + - + +
469B TRP* 3.6 15.3 - - + +
470B TRP* 3.5 17.0 + - - +
541B PRO* 4.2 3.2 - - - +
656B ARG* 4.0 5.2 - - - +
1022B TYR* 5.5 1.1 - - + -
1027B TYR* 3.3 38.1 - - + +
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Residues in contact with GLU 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ARG* 5.3 3.1 + - - -
466B VAL* 1.3 72.7 - - - +
468B GLU* 1.3 66.5 + - - +
469B TRP 3.6 0.2 - - - -
470B TRP* 3.8 10.0 - - + +
471B VAL* 3.2 25.8 + - - +
518B PRO* 3.9 18.4 - - + +
519B LEU* 5.2 8.9 - - - +
522B LYS* 2.8 39.4 + - - -
540B HIS* 4.1 10.5 - - + +
541B PRO* 3.6 19.7 - - + -
542B TYR* 4.0 9.4 + - - -
656B ARG* 3.3 33.2 + - - -
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Residues in contact with GLU 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B ARG* 3.3 30.6 + - - -
466B VAL* 3.2 22.3 - - + +
467B GLU* 1.3 83.8 + - - +
469B TRP* 1.3 66.8 + - - +
470B TRP 3.1 1.3 - - - -
471B VAL* 3.1 18.2 + - - +
472B GLN* 3.1 9.2 + - - +
489B PHE* 3.5 40.7 - - + -
518B PRO* 4.8 13.9 - - + +
519B LEU* 4.5 15.9 + - - +
1020B ARG* 5.5 3.7 - - + -
1022B TYR* 4.1 19.1 - - + -
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Residues in contact with TRP 469 (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 TYR* 3.5 25.8 - + - -
466B VAL* 3.6 15.1 - - + +
468B GLU* 1.3 78.1 - - - +
470B TRP* 1.3 59.3 + - - +
472B GLN* 3.2 14.5 + - + +
473B GLU* 2.8 54.6 + - + +
476B GLN* 6.0 0.7 - - - -
489B PHE* 5.4 0.9 - - - -
654B ARG* 3.5 19.1 - - - -
1022B TYR 5.9 1.1 - - - -
1023B PRO 4.7 1.1 - - - -
1024B LEU* 3.4 32.6 - - + +
1027B TYR* 3.4 65.5 - + + +
1028B LYS* 4.4 16.4 - - + -
1031B TYR* 4.6 16.6 - + - -
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Residues in contact with TRP 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B TYR* 3.1 27.1 + + + +
466B VAL 3.5 15.2 + - - +
467B GLU* 3.8 18.8 - - + +
469B TRP* 1.3 77.5 - - - +
471B VAL* 1.3 69.3 + - + +
473B GLU* 3.2 15.9 + - + +
474B LEU* 2.9 39.3 + - + +
514B LEU* 4.5 12.6 - - + -
518B PRO* 6.1 0.7 - - + -
523B PRO* 4.1 18.4 - - + -
528B ALA* 6.0 4.9 - - + -
531B LEU* 6.5 1.3 - - + -
537B ILE* 4.5 19.2 - - + +
538B PRO* 4.2 16.2 + - + -
539B PHE 4.5 4.6 + - - -
540B HIS* 3.4 41.7 - + + -
541B PRO* 4.1 13.5 - - + -
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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
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467B GLU 3.2 17.5 - - - +
468B GLU* 3.1 10.2 + - - +
470B TRP* 1.3 80.4 - - + +
472B GLN* 1.3 60.3 + - - +
474B LEU* 3.1 8.9 + - + +
475B VAL* 2.9 28.7 + - + +
488B PRO* 3.7 21.5 - - + -
489B PHE* 4.8 4.5 - - + +
514B LEU* 4.0 18.2 - - + -
515B LEU* 3.7 23.8 - - + -
518B PRO* 3.7 27.4 - - + -
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Residues in contact with GLN 472 (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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468B GLU 3.1 11.5 + - - +
469B TRP* 3.2 17.0 + - + +
471B VAL* 1.3 77.1 - - - +
473B GLU* 1.3 56.0 + - - +
475B VAL* 3.2 24.4 - - - +
476B GLN* 3.0 36.5 + - - +
488B PRO* 3.1 25.6 - - - +
489B PHE* 3.9 11.1 - - + -
1022B TYR 5.1 2.6 - - - +
1023B PRO* 6.1 0.3 - - - +
1024B LEU* 3.7 37.1 - - + +
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Residues in contact with GLU 473 (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 TYR* 2.4 37.2 + - - -
469B TRP* 2.8 35.7 + - + +
470B TRP* 3.2 15.1 + - + +
472B GLN* 1.3 75.3 - - - +
474B LEU* 1.3 57.8 + - - +
476B GLN* 3.2 24.2 + - - +
477B ALA* 2.9 29.3 + - - +
537B ILE* 4.7 8.6 - - + +
538B PRO* 4.2 10.2 - - + +
654B ARG* 3.0 33.0 + - - -
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Residues in contact with LEU 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B TRP* 2.9 29.1 + - + +
471B VAL* 3.1 13.9 + - + +
473B GLU* 1.3 76.4 - - - +
475B VAL* 1.3 63.5 + - + +
477B ALA* 3.1 3.6 + - - +
478B ILE* 3.0 31.8 + - + +
486B LEU* 6.1 3.1 - - + -
504B LEU* 4.9 14.8 - - + -
511B LEU* 4.9 13.2 - - + -
514B LEU* 4.7 21.8 - - + -
515B LEU* 5.9 1.6 - - + -
531B LEU* 5.6 8.7 - - + -
535B LEU* 4.1 25.1 - - + -
537B ILE* 4.5 15.3 - - + -
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Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B VAL* 2.9 18.5 + - + +
472B GLN* 3.2 26.7 - - - +
474B LEU* 1.3 80.2 - - + +
476B GLN* 1.3 57.1 + - - +
478B ILE* 3.5 9.2 - - - +
479B LYS* 2.7 32.2 + - + +
484B VAL 4.2 1.0 - - - +
486B LEU* 3.2 39.6 + - + +
488B PRO* 3.6 35.4 - - + -
515B LEU* 4.4 11.7 - - + -
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Residues in contact with GLN 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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469B TRP* 6.0 1.0 - - - -
472B GLN* 3.0 21.2 + - - +
473B GLU* 3.2 33.4 + - - +
475B VAL* 1.3 77.2 - - + +
477B ALA* 1.3 62.1 + - - +
479B LYS* 3.8 10.5 - - + -
480B ASP* 2.9 44.5 + - - +
1024B LEU* 3.6 24.9 - - - +
1028B LYS* 5.0 9.0 + - - +
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Residues in contact with ALA 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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473B GLU 2.9 21.0 + - - +
474B LEU* 3.1 6.2 + - - +
476B GLN* 1.3 78.1 - - + +
478B ILE* 1.3 58.1 + - - +
480B ASP* 4.8 1.8 - - - -
481B LEU* 2.8 40.2 + - + +
535B LEU* 4.5 16.4 - - + +
537B ILE* 3.8 25.4 - - + -
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Residues in contact with ILE 478 (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 LEU* 3.0 21.6 + - + +
475B VAL* 3.5 7.6 - - - +
477B ALA* 1.3 74.8 - - - +
479B LYS* 1.3 61.2 + - - +
482B TYR* 2.9 32.9 + - + +
483B GLU 2.8 24.3 + - - -
484B VAL* 3.0 26.1 + - + +
486B LEU* 3.6 22.2 - - + -
500B ALA* 3.7 24.5 - - + -
503B TYR* 5.1 1.6 - - + -
504B LEU* 3.7 36.1 - - + -
535B LEU* 4.8 6.1 - - + +
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Residues in contact with LYS 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 VAL* 2.7 25.1 + - + +
476B GLN* 3.8 9.6 - - + +
477B ALA 3.2 0.2 - - - -
478B ILE* 1.3 79.4 - - - +
480B ASP* 1.3 66.8 + - - +
483B GLU* 3.2 20.5 - - - +
484B VAL 3.4 18.4 - - - +
485B GLU* 3.2 31.6 - - - +
486B LEU 5.7 2.2 - - - +
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Residues in contact with ASP 480 (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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476B GLN* 2.9 32.8 + - - +
477B ALA* 4.2 2.9 - - - +
479B LYS* 1.3 90.3 + - - +
481B LEU* 1.3 67.9 + - + +
483B GLU 4.6 0.4 - - - -
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Residues in contact with LEU 481 (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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477B ALA* 2.8 23.1 + - + +
480B ASP* 1.3 89.1 - - + +
482B TYR* 1.3 72.5 + - + +
483B GLU* 3.4 2.1 + - - +
534B VAL 4.8 3.4 - - - +
535B LEU* 3.6 42.4 - - + +
536B ASP* 5.8 1.1 - - + +
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Residues in contact with TYR 482 (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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478B ILE* 2.9 33.0 + - + +
481B LEU* 1.3 79.7 - - + +
483B GLU* 1.3 75.0 + - - +
484B VAL* 3.0 16.2 + - + +
503B TYR* 3.5 52.8 + + + -
504B LEU* 4.5 9.6 - - + -
534B VAL* 4.1 19.5 - - + +
535B LEU* 3.6 31.2 - - + -
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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