Contacts of the helix formed by residues 473 - 485 (chain A) in PDB entry 6BSF
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 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A LEU 4.4 2.9 - - - -
457A CYS* 3.9 17.0 - - - -
458A ALA 4.8 0.7 - - - -
463A CYS* 4.0 13.5 - - + -
465A ILE* 3.9 6.7 - - + +
469A ARG 4.0 2.0 + - - -
470A ARG 3.9 5.0 + - - -
471A LYS 3.5 0.8 - - - -
472A ASN* 1.3 80.9 - - + +
474A PRO* 1.3 68.3 - - - +
475A ALA 3.2 4.4 + - - -
476A CYS* 3.4 17.7 - - + -
477A ARG* 2.9 22.7 + - - +
601A ZN 2.4 36.3 - - - -
472B ASN* 4.4 3.1 - - - +
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Residues in contact with PRO 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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444A PHE* 3.4 20.5 - - + -
447A ARG* 5.9 2.5 - - - +
455A TYR* 3.3 40.6 - - + -
456A LEU 5.4 0.9 - - - +
470A ARG 4.7 1.1 - - - +
471A LYS 3.9 9.0 - - - +
472A ASN 3.5 8.3 - - - +
473A CYS* 1.3 87.5 - - - +
475A ALA* 1.3 58.5 + - - +
477A ARG* 4.2 1.1 - - + -
478A TYR* 2.7 34.7 + - - +
472B ASN* 4.7 10.1 - - - +
15D G 6.1 0.7 - - - +
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Residues in contact with ALA 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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455A TYR* 3.6 21.7 - - + +
456A LEU 3.8 28.4 + - - -
457A CYS* 3.9 8.5 - - + +
461A ASN* 5.4 2.2 - - - +
473A CYS* 3.2 5.4 - - - -
474A PRO* 1.3 81.4 - - - +
476A CYS* 1.3 58.1 + - - +
478A TYR* 3.4 3.9 + - - +
479A ARG* 2.9 28.5 + - - +
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Residues in contact with CYS 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A CYS* 3.9 1.1 - - - -
461A ASN* 3.4 18.6 - - - -
463A CYS* 3.3 21.3 - - + -
465A ILE* 4.0 15.2 - - + +
473A CYS* 3.3 8.3 + - - +
475A ALA* 1.3 78.8 - - - +
477A ARG* 1.3 58.2 + - - +
479A ARG* 3.3 29.8 + - - +
480A LYS* 3.0 29.1 + - - +
601A ZN 2.5 34.1 - - - -
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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
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423A VAL* 4.0 7.7 - - + +
440A SER* 3.1 33.3 + - - -
441A CYS* 3.3 31.3 - - - -
444A PHE* 3.6 47.9 - - + +
465A ILE* 3.9 27.3 - - + +
470A ARG* 3.3 42.4 + - - +
471A LYS* 5.0 1.4 - - - +
473A CYS 2.9 19.0 + - - +
474A PRO* 3.6 3.6 - - + +
476A CYS* 1.3 73.3 - - - +
478A TYR* 1.3 60.5 + - - +
480A LYS* 3.2 5.9 + - - +
481A CYS* 2.9 30.5 + - - -
15D G 5.2 7.1 + - - -
16D C 5.2 1.8 + - - -
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Residues in contact with TYR 478 (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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444A PHE* 3.5 13.1 - + + -
445A PHE* 3.7 30.5 - + - -
448A ALA* 3.5 32.1 - - + -
449A VAL* 4.2 12.2 - - - +
453A HIS* 3.3 49.4 + + + -
455A TYR* 4.5 6.5 - + + -
474A PRO 2.7 20.8 + - - +
475A ALA* 3.9 2.9 - - - +
477A ARG* 1.3 70.4 - - - +
479A ARG* 1.3 67.5 + - - +
481A CYS* 3.3 3.6 + - - +
482A LEU* 3.1 54.4 + - + +
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Residues in contact with ARG 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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461A ASN* 3.3 30.5 + - - +
462A ASP* 3.7 10.8 - - - +
463A CYS 4.0 7.3 + - - +
465A ILE* 5.3 0.4 - - - +
475A ALA 2.9 17.0 + - - +
476A CYS* 3.4 34.1 + - - +
477A ARG 3.2 0.2 - - - -
478A TYR* 1.3 80.2 - - - +
480A LYS* 1.3 70.9 + - - +
482A LEU* 3.2 8.7 + - - +
483A GLN* 2.4 70.7 + - + +
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Residues in contact with LYS 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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422A LEU 4.4 9.4 + - - +
423A VAL* 2.7 40.3 + - + +
424A CYS* 4.8 1.2 - - - +
425A SER* 5.4 3.2 + - - -
463A CYS 5.9 0.2 - - - +
465A ILE* 3.8 29.8 + - + +
476A CYS 3.0 14.0 + - - +
477A ARG* 3.2 5.8 + - - +
479A ARG* 1.3 91.3 - - - +
481A CYS* 1.3 64.7 + - - +
483A GLN* 3.1 15.2 + - + +
484A ALA* 2.9 26.2 + - - +
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Residues in contact with CYS 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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423A VAL* 4.0 21.5 - - - +
441A CYS* 4.7 4.5 - - - -
444A PHE* 4.2 18.6 - - - -
445A PHE* 3.7 32.5 - - + -
477A ARG 2.9 18.3 + - - -
478A TYR* 3.3 10.1 + - - +
480A LYS* 1.3 77.8 - - - +
482A LEU* 1.3 61.1 + - - +
484A ALA* 3.4 1.2 + - - +
485A GLY 3.2 5.5 + - - -
486A MET* 3.1 45.5 + - - +
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Residues in contact with LEU 482 (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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445A PHE* 4.2 7.9 - - + -
449A VAL* 6.3 0.2 - - + -
478A TYR* 3.1 53.8 + - + +
479A ARG* 3.5 10.1 - - - +
481A CYS* 1.3 75.7 - - - +
483A GLN* 1.3 67.0 + - + +
485A GLY* 3.0 14.4 + - - +
486A MET 4.1 17.5 - - - +
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Residues in contact with GLN 483 (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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479A ARG* 2.4 61.9 + - + +
480A LYS* 3.1 16.6 + - + +
482A LEU* 1.3 78.4 - - + +
484A ALA* 1.3 60.1 + - - +
485A GLY* 3.5 0.7 + - - -
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Residues in contact with ALA 484 (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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422A LEU* 4.5 14.1 - - + +
423A VAL* 4.4 9.9 - - + -
435A VAL* 3.2 34.7 - - + +
480A LYS 2.9 16.2 + - - +
481A CYS 3.7 5.4 - - - +
483A GLN* 1.3 77.4 - - - +
485A GLY* 1.3 55.1 + - - +
486A MET 3.7 0.9 - - - -
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Residues in contact with GLY 485 (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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433A TYR 3.9 1.7 - - - +
434A GLY* 5.1 1.2 - - - -
435A VAL* 3.7 6.1 - - - +
481A CYS 3.2 0.4 + - - -
482A LEU 3.0 14.0 + - - -
483A GLN 3.2 1.5 - - - -
484A ALA* 1.3 78.8 - - - +
486A MET* 1.3 68.6 + - - +
487A ASN* 3.1 17.9 + - - +
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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