Contacts of the helix formed by residues 465 - 484 (chain B) in PDB entry 3K5N
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 CYS 465 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B TYR* 3.5 22.0 - - + +
380B ARG* 3.8 39.7 + - + +
381B MET* 3.9 12.6 - - - -
384B ALA* 4.1 9.4 - - - -
434B ASP* 3.2 3.6 + - - -
436B VAL* 3.4 22.0 - - - -
464B HIS* 1.3 83.9 - - - +
466B LEU* 1.3 63.3 + - - +
467B PRO* 3.7 0.7 - - - -
468B GLU* 3.3 9.2 - - - +
469B ILE* 2.9 30.3 + - + +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B PHE* 3.3 39.5 - - + -
377B TYR* 3.9 10.1 - - + -
428B ILE* 4.0 11.0 - - + -
433B ILE 3.8 9.4 - - - +
434B ASP* 3.8 9.4 + - + -
435B PRO* 5.2 2.9 - - + -
465B CYS* 1.3 75.2 - - - +
467B PRO* 1.3 68.2 - - + +
468B GLU 2.9 2.0 - - - -
469B ILE* 2.5 38.4 + - + -
470B VAL* 2.6 31.0 + - + -
499B PHE* 4.4 12.8 - - + -
503B LEU* 5.3 6.3 - - + -
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Residues in contact with PRO 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B ILE* 3.7 5.8 - - + +
429B ARG* 3.6 27.8 - - + +
432B LEU* 3.5 37.7 - - + -
433B ILE 3.7 8.5 - - - +
434B ASP* 3.7 7.9 - - + -
464B HIS* 3.9 12.8 - - + -
466B LEU* 1.3 93.4 - - + +
468B GLU* 1.3 56.5 + - + +
470B VAL* 4.1 4.3 - - + -
471B THR* 2.4 45.8 + - + +
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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
----------------------------------------------------------
380B ARG* 3.7 24.8 + - - +
462B GLU 4.5 2.7 - - - +
464B HIS* 2.3 75.3 + - + +
465B CYS* 3.3 6.7 - - - +
467B PRO* 1.3 72.4 - - + +
469B ILE* 1.3 58.1 + - - +
471B THR* 2.5 22.5 + - - -
472B ASN* 3.4 18.2 + - - +
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Residues in contact with ILE 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B LEU* 3.9 37.0 - - + +
377B TYR* 4.2 19.7 - - + +
380B ARG* 3.7 25.8 - - + +
465B CYS 2.9 18.2 + - - +
466B LEU* 2.5 27.2 + - + +
468B GLU* 1.3 69.7 - - - +
470B VAL* 1.3 65.5 + - - +
471B THR 3.2 0.2 - - - -
472B ASN* 3.3 5.0 + - - +
473B ILE* 2.9 44.3 + - + +
499B PHE* 4.1 11.0 - - + -
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Residues in contact with VAL 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B PRO* 3.6 34.3 - - + -
428B ILE* 4.1 13.2 - - + -
429B ARG* 4.0 9.6 - - + -
466B LEU* 2.6 54.4 + - + +
467B PRO* 3.9 2.7 - - + +
469B ILE* 1.3 72.2 - - + +
471B THR* 1.3 55.4 + - - +
473B ILE* 3.1 5.9 + - - +
474B TRP* 2.6 37.4 + - - +
496B MET* 3.5 16.6 - - + +
499B PHE* 4.5 11.2 - - + -
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Residues in contact with THR 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ARG* 2.9 48.0 - - + +
467B PRO* 2.4 40.3 + - + +
468B GLU* 2.5 25.8 + - - -
470B VAL* 1.3 76.9 - - - +
472B ASN* 1.3 63.1 + - - -
474B TRP* 3.0 4.5 + - - +
475B HIS* 3.0 32.1 + - - -
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Residues in contact with ASN 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ARG* 4.9 12.1 - - - +
468B GLU 3.6 14.5 + - - +
469B ILE* 3.3 9.5 + - - +
470B VAL 3.3 0.6 - - - -
471B THR* 1.3 82.3 + - - +
473B ILE* 1.3 64.1 + - + +
475B HIS* 3.1 16.5 + - - +
476B GLY* 3.1 17.2 + - - -
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Residues in contact with ILE 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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358B VAL* 5.4 4.7 - - + -
376B LEU* 5.0 7.4 - - + -
469B ILE* 2.9 34.0 + - + +
470B VAL* 3.5 6.1 - - - +
472B ASN* 1.3 73.9 - - + +
474B TRP* 1.3 68.7 + - - +
476B GLY* 2.9 12.7 + - - +
477B ARG* 3.1 12.2 + - + +
492B LEU* 3.6 33.2 - - + +
495B ILE* 4.4 11.9 - - + -
496B MET* 4.3 17.3 - - + -
499B PHE* 4.0 22.7 - - + -
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Residues in contact with TRP 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LYS* 3.6 42.6 - - + -
422B SER* 3.7 24.7 - - - -
425B PRO* 4.4 0.4 - - + -
426B SER* 3.8 20.9 - - - -
429B ARG* 3.0 38.5 - - - +
470B VAL 2.6 12.4 + - - +
471B THR 3.0 10.1 + - - +
473B ILE* 1.3 74.8 - - - +
475B HIS* 1.3 67.6 + + - +
476B GLY 3.2 0.2 + - - -
477B ARG* 3.2 3.4 + - - +
478B ASP* 2.3 53.9 + - - +
496B MET* 3.1 40.6 - - + +
589B ALA 4.6 7.9 - - - -
591B GLU* 4.0 18.5 + - + -
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Residues in contact with HIS 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ARG* 4.1 21.3 + - - -
471B THR* 3.0 21.1 + - - -
472B ASN* 3.1 16.1 + - - +
474B TRP* 1.3 83.3 - + - +
476B GLY* 1.3 59.0 + - - +
478B ASP* 3.4 3.0 + - - +
479B GLU* 2.7 37.1 + - + +
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Residues in contact with GLY 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ASN 3.1 9.4 + - - -
473B ILE* 2.9 10.2 + - - -
475B HIS* 1.3 74.4 - - - +
477B ARG* 1.3 52.1 + - - -
479B GLU* 4.8 2.5 - - - -
480B ALA* 2.4 42.7 + - - +
492B LEU* 3.2 15.0 - - - -
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Residues in contact with ARG 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LYS* 4.6 17.5 - - - +
473B ILE* 3.1 11.0 + - + +
474B TRP* 3.2 4.9 + - - +
476B GLY* 1.3 72.3 - - - +
478B ASP* 1.3 65.8 + - - +
480B ALA* 3.0 2.2 - - - +
481B LYS* 2.3 53.2 + - - +
489B SER* 3.6 19.4 + - - +
492B LEU* 3.1 28.2 - - + +
493B LYS* 4.2 34.7 - - - +
496B MET* 5.7 6.5 - - - -
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Residues in contact with ASP 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B LYS* 3.3 26.1 + - - -
474B TRP* 2.3 47.5 + - - +
475B HIS* 3.4 4.7 + - - +
476B GLY 3.2 0.2 - - - -
477B ARG* 1.3 77.3 - - - +
479B GLU* 1.3 74.8 + - - +
480B ALA 2.9 0.9 - - - -
481B LYS* 2.9 15.7 + - - +
482B ARG* 3.2 11.3 + - - +
591B GLU* 5.3 0.9 - - - +
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Residues in contact with GLU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B HIS* 2.7 23.6 + - + +
476B GLY* 4.2 2.2 - - - +
478B ASP* 1.3 78.4 - - - +
480B ALA* 1.3 65.0 + - - +
482B ARG* 3.1 3.3 + - - +
483B GLN* 3.1 31.6 + - + +
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Residues in contact with ALA 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B GLY* 2.4 35.7 + - - +
477B ARG* 3.0 7.9 - - - +
479B GLU* 1.3 75.3 - - - +
481B LYS* 1.3 49.6 + - - -
483B GLN* 3.1 6.6 + - - +
484B GLY* 2.6 35.9 + - - -
485B ASN* 4.3 2.9 + - - +
488B LEU* 4.0 19.7 - - + -
489B SER* 3.8 9.8 + - - +
492B LEU* 4.0 9.6 - - + -
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Residues in contact with LYS 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 ARG* 2.3 46.2 + - - +
478B ASP* 2.9 9.8 + - - +
480B ALA* 1.3 69.2 - - - +
482B ARG* 1.3 55.5 + - - +
484B GLY* 2.6 28.3 + - - +
486B LYS* 4.2 29.5 - - - +
489B SER* 3.5 14.8 + - - +
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Residues in contact with ARG 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B ASP 3.2 6.1 + - - +
479B GLU* 3.1 7.1 + - - +
481B LYS* 1.3 77.6 - - + +
483B GLN* 1.3 59.3 + - - +
484B GLY 3.0 4.9 - - - +
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Residues in contact with GLN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B GLU* 3.1 24.7 + - + +
480B ALA* 3.8 6.4 - - - +
482B ARG* 1.3 78.0 - - - +
484B GLY* 1.3 68.1 + - - +
485B ASN* 3.4 16.5 + - - +
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Residues in contact with GLY 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B ALA 2.6 12.2 + - - -
481B LYS* 2.6 27.4 + - - +
482B ARG 3.0 1.1 - - - -
483B GLN 1.3 81.2 - - - +
485B ASN* 1.3 64.0 + - - -
486B LYS* 3.5 3.1 - - - -
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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) + - + + + + + -
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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