Contacts of the helix formed by residues 461 - 475 (chain B) in PDB entry 3KN5
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 MET 461 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436B SER* 3.7 25.8 - - - +
437B PHE* 3.6 44.0 - - + -
438B SER* 6.1 0.2 - - - -
457B ILE* 3.8 16.8 - - + -
458B SER 2.9 10.9 + - - +
460B ARG* 1.3 80.6 - - - +
462B GLU* 1.3 56.3 + - - +
463B ALA 3.3 2.2 - - - -
464B ASN* 2.9 46.5 + - + +
465B THR* 3.0 13.0 + - + +
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Residues in contact with GLU 462 (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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458B SER 4.6 0.5 - - - +
459B LYS* 3.1 39.7 + - + +
460B ARG 3.3 2.2 + - - -
461B MET* 1.3 76.7 - - - +
463B ALA* 1.3 62.1 + - - +
465B THR* 3.5 13.8 + - - +
466B GLN* 3.1 47.4 + - - +
469B ILE* 5.7 0.7 - - - +
489B HIS* 3.4 19.4 + - - -
494B THR* 3.0 27.4 + - - -
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Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B MET 3.1 1.0 + - - -
462B GLU* 1.3 74.3 - - - +
464B ASN* 1.3 66.1 + - - +
466B GLN* 3.4 14.2 + - - +
467B LYS* 3.2 19.8 + - - +
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Residues in contact with ASN 464 (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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461B MET* 2.9 33.5 + - + +
463B ALA* 1.3 81.3 - - - +
465B THR* 1.3 58.0 + - - +
467B LYS* 3.1 27.9 + - - +
468B GLU* 2.9 27.7 + - - +
567B GLY* 2.9 30.3 + - - +
570B ARG* 4.9 3.5 + - - -
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Residues in contact with THR 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ILE* 3.6 41.7 - - + -
458B SER 4.8 0.2 - - - +
461B MET* 3.0 27.1 + - + +
462B GLU* 3.5 23.7 + - - +
464B ASN* 1.3 74.4 - - + +
466B GLN* 1.3 61.6 + - - +
468B GLU* 3.6 12.1 - - - +
469B ILE* 2.9 39.3 + - - +
494B THR* 4.0 14.2 + - - +
496B LEU* 5.3 0.4 - - - -
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Residues in contact with GLN 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B GLU* 3.1 37.9 + - - +
463B ALA* 3.5 13.6 - - - +
465B THR* 1.3 75.3 + - - +
467B LYS* 1.3 63.1 + - - +
469B ILE* 3.8 9.9 - - + +
470B THR* 2.8 31.6 + - - +
489B HIS* 6.2 0.2 - - - +
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Residues in contact with LYS 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463B ALA 3.2 9.1 + - - +
464B ASN* 3.1 33.5 + - - +
466B GLN* 1.3 76.6 - - - +
468B GLU* 1.3 61.7 + - - +
470B THR* 3.2 7.9 + - - -
471B ALA* 2.9 26.8 + - + +
566B PHE 3.8 6.7 - - - -
567B GLY 3.0 27.3 + - - -
568B PHE 3.6 1.4 - - - -
569B ALA* 2.7 40.3 + - + +
570B ARG* 3.2 15.2 - - - +
571B LEU* 4.4 20.4 - - + +
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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
----------------------------------------------------------
455B LYS* 2.7 38.4 + - - +
457B ILE* 4.3 8.7 - - - +
464B ASN* 2.9 17.1 + - - +
465B THR* 3.6 13.9 - - - +
466B GLN 3.3 0.2 - - - -
467B LYS* 1.3 86.4 - - - +
469B ILE* 1.3 57.0 + - - +
471B ALA* 3.4 4.1 + - - +
472B LEU* 3.0 38.6 + - + +
496B LEU* 3.7 16.3 - - + +
565B ASP* 5.1 0.3 - - - -
566B PHE* 3.7 29.4 + - + +
567B GLY* 3.9 14.5 + - - -
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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
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462B GLU* 5.7 0.7 - - - +
465B THR* 2.9 38.2 + - - +
466B GLN* 3.8 9.4 - - + +
468B GLU* 1.3 72.6 - - - +
470B THR* 1.3 66.2 + - - +
472B LEU* 3.4 9.4 + - - +
473B LYS* 3.1 46.9 + - + +
484B LEU* 4.2 7.0 - - + -
487B VAL* 4.0 28.3 - - + -
489B HIS* 5.1 6.1 - - + +
494B THR* 4.4 3.8 - - + -
496B LEU* 4.1 24.9 - - + -
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Residues in contact with THR 470 (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 GLN* 2.8 22.4 + - - +
467B LYS* 3.5 3.9 - - - -
469B ILE* 1.3 74.7 - - - +
471B ALA* 1.3 61.2 + - - +
473B LYS* 3.2 5.9 + - - +
474B LEU* 2.9 48.8 + - + +
571B LEU* 3.8 23.1 - - + +
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Residues in contact with ALA 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 LYS 2.9 16.1 + - - +
468B GLU* 3.5 7.6 - - - +
469B ILE 3.3 0.2 - - - -
470B THR* 1.3 78.8 - - - +
472B LEU* 1.3 61.9 + - - +
474B LEU* 3.4 2.3 + - - +
475B CYS* 3.1 28.0 + - - -
540B VAL* 4.0 24.2 - - + -
566B PHE* 4.2 8.3 - - + -
569B ALA* 4.0 17.3 - - + -
571B LEU* 4.0 14.5 - - + +
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Residues in contact with LEU 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* 3.0 37.4 + - + +
469B ILE* 3.7 4.9 - - - +
470B THR 3.2 0.2 - - - -
471B ALA* 1.3 77.1 - - - +
473B LYS* 1.3 58.7 + - - +
475B CYS* 3.5 6.9 + - - +
476B GLU* 3.2 25.4 + - - +
481B ILE* 5.0 1.9 - - + +
482B VAL* 3.8 40.0 - - + +
484B LEU* 4.3 29.9 + - + +
496B LEU* 4.5 11.2 - - + -
498B MET* 4.3 12.3 - - + -
566B PHE* 3.8 25.8 - - + +
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Residues in contact with LYS 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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469B ILE* 3.1 35.6 + - + +
470B THR* 3.2 5.1 + - - +
472B LEU* 1.3 74.1 - - - +
474B LEU* 1.3 66.9 + - - +
475B CYS 3.1 2.0 - - - -
476B GLU* 3.2 38.9 + - - +
484B LEU* 4.1 26.9 + - + +
485B HIS 5.2 4.2 + - - -
486B GLU* 5.6 2.0 - - - +
487B VAL* 4.7 8.0 - - - +
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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
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470B THR* 2.9 38.0 + - + +
471B ALA 3.6 5.4 - - - +
473B LYS* 1.3 78.1 - - - +
475B CYS* 1.3 57.5 + - - +
476B GLU 4.6 2.1 - - - +
534B HIS* 4.3 1.9 + - - -
538B VAL* 3.7 40.8 - - + +
539B GLY 4.7 2.0 - - - +
540B VAL* 3.7 26.0 - - + -
571B LEU* 4.1 12.1 - - + -
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Residues in contact with CYS 475 (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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471B ALA 3.1 19.4 + - - +
472B LEU 3.8 4.7 - - - +
473B LYS 3.1 0.6 - - - -
474B LEU* 1.3 75.8 - - - +
476B GLU* 1.3 69.2 - - - +
477B GLY 3.1 2.4 + - - -
478B HIS* 3.4 13.7 + - - +
481B ILE* 3.8 27.8 - - + +
534B HIS* 3.6 15.5 + - + -
535B MET* 4.0 25.4 - - - -
538B VAL* 4.3 5.6 - - - -
540B VAL* 4.3 14.4 - - - -
566B PHE* 4.4 10.3 - - - -
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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