Contacts of the helix formed by residues 465 - 481 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A TYR* 3.6 22.0 - - + -
380A ARG* 3.8 38.0 - - + +
381A MET* 3.9 14.1 - - - -
384A ALA* 4.0 12.6 - - - -
434A ASP* 2.5 13.8 + - - -
436A VAL* 4.5 6.7 - - - -
464A HIS* 1.3 79.2 - - - +
466A LEU* 1.3 65.6 + - - +
467A PRO 3.4 1.8 - - - -
468A GLU* 3.3 11.5 - - - +
469A ILE* 3.0 23.5 + - - +
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Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PHE* 3.8 38.4 - - + -
377A TYR* 3.8 7.8 - - + -
428A ILE* 4.0 23.3 - - + -
433A ILE 3.8 11.4 - - - +
434A ASP* 3.4 10.6 + - - +
435A PRO* 4.4 3.6 - - + -
465A CYS* 1.3 77.3 - - - +
467A PRO* 1.3 79.0 - - + +
469A ILE* 2.8 32.5 + - + -
470A VAL* 2.8 18.6 + - + +
499A PHE* 4.2 13.5 - - + -
503A LEU* 4.1 17.7 - - + -
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Residues in contact with PRO 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ILE* 3.6 5.6 - - + +
429A ARG* 4.0 19.0 - - + +
432A LEU* 3.4 48.0 - - + -
433A ILE 3.7 10.5 - - - +
434A ASP* 3.8 8.7 - - + -
464A HIS* 4.0 8.1 - - + +
465A CYS 3.8 1.3 - - - -
466A LEU* 1.3 95.8 - - + +
468A GLU* 1.3 62.1 + - - +
470A VAL* 3.4 4.2 + - + +
471A THR* 2.3 36.5 + - + +
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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
----------------------------------------------------------
380A ARG* 3.9 24.5 - - - +
464A HIS* 2.7 47.0 + - - +
465A CYS* 3.3 17.9 - - - +
467A PRO* 1.3 76.2 - - - +
469A ILE* 1.3 65.1 + - - +
471A THR* 3.1 9.6 - - + -
472A ASN* 2.9 33.0 + - - +
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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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376A LEU* 3.5 42.0 - - + +
377A TYR* 4.2 13.2 - - + +
380A ARG* 3.1 41.3 - - - +
465A CYS 3.0 13.4 + - - +
466A LEU* 2.8 28.7 + - + +
468A GLU* 1.3 74.2 - - - +
470A VAL* 1.3 61.7 + - - +
472A ASN* 3.7 3.3 + - - +
473A ILE* 3.2 27.0 + - + +
499A PHE* 4.1 15.3 - - + -
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Residues in contact with VAL 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A PRO* 3.9 10.8 - - + +
428A ILE* 3.9 20.4 - - + -
429A ARG* 3.7 17.0 - - + -
466A LEU* 2.8 30.7 - - + +
467A PRO 3.7 3.8 - - - +
469A ILE* 1.3 74.2 - - - +
471A THR* 1.3 65.8 + - - +
472A ASN 3.2 0.4 - - - -
473A ILE* 3.4 7.9 - - - +
474A TRP* 3.0 19.6 + - - +
496A MET* 3.7 25.5 - - + +
499A PHE* 4.2 17.0 - - + -
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Residues in contact with THR 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG* 3.6 36.3 - - + +
467A PRO* 2.3 37.1 + - + +
468A GLU* 3.1 17.9 - - + -
470A VAL* 1.3 73.6 - - - +
472A ASN* 1.3 75.7 + - - +
474A TRP* 3.0 2.9 + - - +
475A HIS* 2.8 39.4 + - - -
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Residues in contact with ASN 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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380A ARG* 3.4 23.8 + - - +
468A GLU* 2.9 21.7 + - - +
469A ILE* 3.9 5.6 - - - +
471A THR* 1.3 85.7 + - - +
473A ILE* 1.3 58.0 + - + +
475A HIS* 3.8 11.2 - - - +
476A GLY* 2.9 25.3 + - - -
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Residues in contact with ILE 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 5.3 4.7 - - + -
469A ILE* 3.2 19.2 + - + +
470A VAL* 3.3 9.2 + - - +
471A THR 3.0 0.4 - - - -
472A ASN* 1.3 79.3 - - + +
474A TRP* 1.3 55.9 + - - +
476A GLY 3.5 0.3 + - - -
477A ARG* 2.8 30.1 + - - +
492A LEU* 3.5 39.9 - - + +
495A ILE* 3.7 23.3 - - + -
496A MET* 3.6 17.7 - - + -
499A PHE* 4.0 28.5 - - + -
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Residues in contact with TRP 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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421A LYS* 3.6 44.7 - - + +
422A SER* 3.6 24.7 - - - -
425A PRO 4.4 0.2 - - - -
426A SER* 3.5 39.7 - - - -
429A ARG* 3.0 37.5 - - - +
470A VAL 3.0 7.5 + - - +
471A THR 3.3 4.3 - - - +
473A ILE* 1.3 74.9 - - - +
475A HIS* 1.3 74.6 + + - +
477A ARG* 2.9 7.8 + - - +
478A ASP* 2.7 37.1 + - - +
496A MET* 3.1 31.6 - - + -
589A ALA 4.3 8.7 - - - -
591A GLU* 4.1 10.8 + - - -
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Residues in contact with HIS 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG* 4.2 21.5 + - - -
471A THR* 2.8 31.5 + - - +
472A ASN* 3.8 10.3 - - - +
474A TRP* 1.3 82.8 - + - +
476A GLY* 1.3 64.1 + - - +
478A ASP* 3.5 4.3 + - - +
479A GLU* 2.8 24.5 + - - +
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Residues in contact with GLY 476 (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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472A ASN 2.9 18.2 + - - -
473A ILE* 3.8 1.6 - - - -
475A HIS* 1.3 77.9 - - - +
477A ARG* 1.3 52.2 + - - +
479A GLU* 2.9 10.2 + - - +
480A ALA* 2.8 34.8 + - - +
488A LEU* 5.7 0.2 - - - +
492A LEU* 3.9 11.2 - - - +
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Residues in contact with ARG 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LYS* 4.5 16.6 - - - +
422A SER* 5.9 0.2 + - - -
473A ILE* 2.8 19.0 + - + +
474A TRP* 2.9 9.6 + - + +
476A GLY* 1.3 75.4 - - - +
478A ASP* 1.3 85.3 + - - +
480A ALA* 3.0 11.7 + - - -
481A LYS* 3.4 26.5 + - - +
489A SER* 3.4 27.2 + - - +
490A GLN* 4.8 1.2 - - - +
492A LEU* 3.6 28.6 - - + +
493A LYS* 3.5 50.9 - - + +
496A MET* 5.2 1.8 - - - -
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Residues in contact with ASP 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A LYS* 3.0 29.6 + - - -
474A TRP* 2.7 32.5 + - + +
475A HIS* 4.1 3.8 - - - +
477A ARG* 1.3 94.0 + - - +
479A GLU* 1.3 58.8 + - - +
481A LYS* 2.8 36.9 - - + +
482A ARG* 3.9 5.7 - - - +
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Residues in contact with GLU 479 (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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475A HIS 2.8 16.0 + - - +
476A GLY* 2.9 17.3 - - - +
477A ARG 2.9 0.2 - - - -
478A ASP* 1.3 74.5 - - - +
480A ALA* 1.3 54.0 - - - +
481A LYS 2.2 26.8 - - - +
482A ARG* 3.1 30.0 + - - +
483A GLN* 3.0 26.1 + - - +
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Residues in contact with ALA 480 (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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476A GLY 2.8 14.1 + - - +
477A ARG 3.0 4.9 + - - +
479A GLU* 1.3 70.4 - - - +
481A LYS* 1.3 66.8 + - - +
483A GLN* 2.8 24.6 - - - +
485A ASN* 3.1 18.6 + - + +
488A LEU* 4.1 22.7 - - + -
489A SER* 2.7 33.7 - - - +
492A LEU* 4.5 1.8 - - + -
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Residues in contact with LYS 481 (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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477A ARG* 3.4 28.5 + - - +
478A ASP* 2.8 41.7 - - + +
479A GLU 2.2 32.1 - - - +
480A ALA* 1.3 76.3 - - - +
482A ARG* 1.3 75.1 + - + +
483A GLN 2.8 0.7 - - - -
484A GLY* 3.9 8.7 - - - +
485A ASN 4.6 1.1 - - - +
486A LYS* 5.8 2.3 - - - +
489A SER* 3.4 8.6 + - - +
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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