Contacts of the helix formed by residues 461 - 475 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436A SER* 3.9 18.8 - - - +
437A PHE* 3.4 48.2 - - + -
457A ILE* 3.9 12.8 - - + -
458A SER 2.8 11.4 + - - +
460A ARG* 1.3 75.7 - - - +
462A GLU* 1.3 63.7 + - - +
463A ALA* 3.3 3.1 - - - -
464A ASN* 3.0 39.4 + - + +
465A THR* 2.9 15.5 + - + +
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Residues in contact with GLU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458A SER 3.9 0.5 + - - +
459A LYS* 3.0 36.6 + - + +
460A ARG 3.3 2.0 + - - -
461A MET* 1.3 76.7 - - - +
463A ALA* 1.3 63.2 + - - +
465A THR* 3.3 12.8 + - - +
466A GLN* 3.0 50.1 + - + +
469A ILE* 5.6 0.2 - - - +
489A HIS* 3.7 16.3 + - - -
494A THR* 3.0 21.7 + - - +
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Residues in contact with ALA 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460A ARG 5.1 0.6 + - - -
461A MET 3.1 1.2 + - - -
462A GLU* 1.3 79.5 - - - +
464A ASN* 1.3 63.3 + - - +
466A GLN* 3.5 7.7 + - - +
467A LYS* 3.5 16.5 + - - +
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Residues in contact with ASN 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A MET* 3.0 34.2 + - + +
463A ALA* 1.3 80.9 - - - +
465A THR* 1.3 57.9 + - - +
467A LYS* 3.1 31.4 + - - +
468A GLU* 3.0 26.2 + - - +
567A GLY* 2.9 29.7 + - - +
570A ARG* 4.2 7.4 + - - -
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Residues in contact with THR 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A ILE* 3.7 41.3 - - + +
458A SER 4.9 0.7 - - - +
461A MET* 2.9 26.7 - - + +
462A GLU* 3.3 20.2 + - - +
464A ASN* 1.3 72.1 - - + +
466A GLN* 1.3 59.9 + - - +
467A LYS 3.1 1.1 - - - -
468A GLU* 3.8 12.5 - - - +
469A ILE* 2.8 45.1 + - - +
494A THR* 4.1 7.2 - - - +
496A LEU* 4.6 0.6 - - - +
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Residues in contact with GLN 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A GLU* 3.0 42.3 + - + +
463A ALA* 3.7 7.4 - - - +
465A THR* 1.3 76.6 + - - +
467A LYS* 1.3 57.7 + - - +
469A ILE* 3.7 14.5 - - - +
470A THR* 3.0 35.8 + - - -
489A HIS* 4.3 13.5 + - - -
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Residues in contact with LYS 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A ALA 3.5 9.0 + - - +
464A ASN* 3.1 28.6 + - - +
466A GLN* 1.3 75.3 - - - +
468A GLU* 1.3 65.7 + - - +
470A THR* 3.3 3.4 + - - -
471A ALA* 2.8 33.7 + - + +
566A PHE 3.7 7.6 - - - -
567A GLY 3.0 27.1 + - - -
569A ALA* 2.7 41.7 + - + +
570A ARG* 3.1 15.0 - - - +
571A LEU* 4.2 25.6 - - + +
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Residues in contact with GLU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A LYS* 2.8 36.7 + - - +
457A ILE* 4.1 13.2 - - - +
464A ASN* 3.0 17.8 + - - +
465A THR* 3.8 8.9 - - - +
467A LYS* 1.3 84.0 - - - +
469A ILE* 1.3 62.3 + - - +
471A ALA* 3.4 3.9 + - - +
472A LEU* 3.0 38.1 + - + +
496A LEU* 4.1 15.9 - - + +
565A ASP* 4.0 1.2 - - - +
566A PHE* 3.6 23.5 + - - +
567A GLY* 3.5 17.4 + - - +
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Residues in contact with ILE 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A GLU* 5.6 0.4 - - - +
465A THR* 2.8 42.0 + - - +
466A GLN* 3.7 20.6 - - - +
468A GLU* 1.3 69.1 - - - +
470A THR* 1.3 69.2 + - - +
472A LEU* 3.4 3.8 + - - +
473A LYS* 3.0 45.7 + - + +
484A LEU* 4.4 12.1 - - + -
487A VAL* 4.1 30.5 - - + -
489A HIS* 5.0 2.0 - - + +
494A THR* 4.3 4.9 - - + -
496A LEU* 4.1 25.1 - - + -
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Residues in contact with THR 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A GLN* 3.0 20.7 + - - -
467A LYS* 3.6 4.0 - - - -
469A ILE* 1.3 75.3 - - - +
471A ALA* 1.3 67.1 + - - +
473A LYS* 2.8 7.3 + - + +
474A LEU* 2.8 46.2 + - + +
571A LEU* 4.2 15.2 - - + +
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Residues in contact with ALA 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A LYS 2.8 18.0 + - - +
468A GLU* 3.5 6.7 - - - +
469A ILE 3.3 0.2 - - - -
470A THR* 1.3 77.2 - - - +
472A LEU* 1.3 62.2 + - - +
473A LYS 3.2 0.3 + - - -
474A LEU* 3.4 2.4 + - - +
475A CYS* 3.3 28.3 + - - -
540A VAL* 4.1 11.4 - - + -
566A PHE* 4.2 7.9 - - + -
569A ALA* 3.9 26.7 - - + -
571A LEU* 4.1 18.6 - - + +
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A GLU* 3.0 37.4 + - + +
469A ILE 3.8 4.9 - - - +
470A THR 3.2 0.4 - - - -
471A ALA* 1.3 75.7 - - - +
473A LYS* 1.3 60.5 + - - +
475A CYS* 3.8 5.9 + - - +
476A GLU* 3.4 17.7 + - - +
481A ILE* 4.9 2.6 - - + +
482A VAL* 3.7 36.7 - - + +
484A LEU* 4.2 27.7 + - + +
496A LEU* 4.7 8.3 - - + -
498A MET* 4.2 15.0 - - + -
566A PHE* 3.5 36.3 - - + +
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Residues in contact with LYS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469A ILE* 3.0 37.2 - - + +
470A THR* 2.8 7.8 + - + +
472A LEU* 1.3 76.7 - - - +
474A LEU* 1.3 67.4 + - - +
475A CYS 3.2 1.3 - - - -
476A GLU* 3.4 43.2 + - - +
483A LYS* 5.4 0.6 - - - +
484A LEU* 4.2 25.7 + - + +
487A VAL* 5.4 6.3 - - - -
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A THR* 2.8 36.8 + - + +
471A ALA 3.8 4.0 - - - +
473A LYS* 1.3 79.3 - - + +
475A CYS* 1.3 58.0 + - - +
476A GLU 3.3 3.7 + - - +
534A HIS* 4.4 2.6 + - - -
538A VAL* 3.8 47.3 - - + +
539A GLY 5.3 1.1 - - - +
540A VAL* 4.3 12.6 - - + -
571A LEU* 4.4 10.5 - - + -
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Residues in contact with CYS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471A ALA 3.3 16.9 + - - +
472A LEU* 3.8 5.6 + - - +
473A LYS 3.2 0.6 - - - -
474A LEU* 1.3 74.0 - - - +
476A GLU* 1.3 67.2 + - - +
477A GLY 3.4 1.6 + - - -
478A HIS* 3.6 12.5 + - - +
481A ILE* 3.9 26.8 - - + +
534A HIS* 3.6 14.8 + - + -
535A MET* 3.9 32.1 - - - -
538A VAL* 4.1 3.1 - - - -
540A VAL* 3.9 22.9 - - - -
566A PHE* 4.4 6.5 - - + -
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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