Contacts of the helix formed by residues 473 - 484 (chain F) in PDB entry 5CBZ
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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458E ALA* 5.7 0.2 - - + -
472E ASN* 4.4 6.7 - - + +
456F LEU 4.9 0.2 - - - -
457F CYS* 3.8 20.9 - - - -
458F ALA 4.9 0.4 - - - -
463F CYS* 4.0 14.8 - - + -
465F ILE* 4.0 6.1 - - + +
469F ARG 4.3 1.4 + - - -
470F ARG 4.2 3.8 + - - -
471F LYS 3.4 0.4 - - - -
472F ASN* 1.3 83.4 - - + +
474F PRO* 1.3 66.1 - - - +
475F ALA* 3.1 5.8 + - - -
476F CYS* 3.2 13.6 + - + -
477F ARG* 3.0 21.3 + - - +
502F ZN 2.3 37.9 - - - -
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Residues in contact with PRO 474 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472E ASN* 5.1 6.1 - - - +
444F PHE* 3.5 28.3 - - + -
455F TYR* 3.8 33.0 - - + -
470F ARG 5.1 0.7 - - - +
471F LYS 3.8 9.2 - - - +
472F ASN 3.5 8.7 - - - +
473F CYS* 1.3 87.6 - - - +
475F ALA* 1.3 57.2 + - - +
477F ARG* 4.0 4.3 - - + -
478F LEU* 2.9 33.4 + - - +
11G G 5.3 1.3 - - - +
12G T 4.0 12.1 - - - +
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Residues in contact with ALA 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455F TYR* 3.5 31.9 - - + +
456F LEU 4.2 0.9 - - - +
457F CYS* 3.9 21.5 - - + +
461F ASN* 4.8 6.1 - - - +
473F CYS* 3.1 13.1 - - - -
474F PRO* 1.3 80.8 - - - +
476F CYS* 1.3 58.2 + - - +
478F LEU* 3.6 2.4 + - - +
479F ARG* 3.0 27.4 + - - +
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Residues in contact with CYS 476 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457F CYS* 3.8 1.3 - - - -
461F ASN* 3.4 26.5 - - - -
463F CYS* 3.3 29.2 - - + +
465F ILE* 3.9 10.7 - - + +
473F CYS* 3.2 5.5 + - - -
475F ALA* 1.3 78.4 - - - +
477F ARG* 1.3 61.3 + - - +
479F ARG* 3.3 20.2 + - - +
480F LYS* 2.9 27.9 + - - +
502F ZN 2.4 35.9 - - - -
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Residues in contact with ARG 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423F VAL* 4.2 6.4 - - + +
440F SER* 3.1 26.9 + - - -
441F CYS* 3.2 31.5 - - - +
444F PHE* 3.5 44.9 - - + +
465F ILE* 3.6 24.8 - - + +
470F ARG* 3.6 38.1 + - - +
471F LYS* 4.9 0.4 - - - +
473F CYS 3.0 17.0 + - - +
474F PRO* 3.2 5.4 + - + +
476F CYS* 1.3 78.1 - - - +
478F LEU* 1.3 56.6 + - - +
480F LYS* 3.1 4.8 + - - +
481F CYS* 2.8 32.6 + - - -
12G T 4.5 7.7 + - - -
13G G 2.9 22.4 + - - -
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Residues in contact with LEU 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444F PHE* 3.6 13.1 - - + -
445F PHE* 4.0 22.0 - - + -
448F ALA* 4.1 22.7 - - + +
449F VAL* 4.3 8.5 - - + -
453F HIS 5.8 1.3 - - - +
455F TYR* 4.1 23.3 - - + -
474F PRO 2.9 17.3 + - - +
475F ALA 3.9 2.9 - - - +
477F ARG* 1.3 74.0 - - - +
479F ARG* 1.3 65.2 + - - +
481F CYS* 3.2 2.4 + - - +
482F LEU* 3.0 44.7 + - + +
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Residues in contact with ARG 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461F ASN* 2.8 37.2 + - - -
462F ASP* 3.5 20.0 - - - +
463F CYS 4.3 3.6 + - - -
465F ILE* 5.9 0.6 - - - +
475F ALA 3.0 19.4 + - - +
476F CYS* 3.3 25.0 + - - +
478F LEU* 1.3 77.1 - - - +
480F LYS* 1.3 75.1 + - - +
482F LEU* 3.5 8.3 + - - +
483F GLN* 3.0 61.1 + - + +
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Residues in contact with LYS 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422F LEU 4.1 11.0 + - - +
423F VAL* 2.6 38.7 + - + +
424F CYS* 4.9 0.8 - - - +
463F CYS 5.7 0.7 - - - +
465F ILE* 3.4 34.6 + - + +
476F CYS 2.9 18.1 + - - +
477F ARG* 3.1 5.6 + - - +
479F ARG* 1.3 84.4 - - - +
481F CYS* 1.3 67.3 + - - +
483F GLN* 3.4 8.7 + - + +
484F ALA* 3.1 26.1 + - + +
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Residues in contact with CYS 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423F VAL* 3.9 21.2 - - - +
441F CYS* 4.6 5.4 - - - -
444F PHE* 4.4 12.6 - - - -
445F PHE* 3.6 31.4 - - + -
477F ARG* 2.8 23.0 + - - -
478F LEU* 3.3 10.5 - - - +
480F LYS* 1.3 73.5 - - - +
482F LEU* 1.3 62.8 + - - +
484F ALA* 3.3 8.0 + - - +
485F GLY 3.5 0.2 + - - -
486F MET* 3.2 47.4 + - - +
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Residues in contact with LEU 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445F PHE* 3.6 24.5 - - + -
449F VAL* 4.9 4.9 - - + -
478F LEU* 3.0 40.9 + - + +
479F ARG* 4.0 7.4 - - - +
481F CYS* 1.3 77.1 - - - +
483F GLN* 1.3 55.6 + - + +
485F GLY* 2.8 26.3 + - - -
486F MET 3.9 12.4 - - - +
487F ASN* 5.7 0.9 - - + -
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Residues in contact with GLN 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479F ARG* 3.0 58.1 + - + +
480F LYS* 3.8 9.1 - - + +
482F LEU* 1.3 79.2 - - + +
484F ALA* 1.3 58.7 + - - +
485F GLY* 3.2 0.9 + - - -
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Residues in contact with ALA 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422F LEU* 5.1 11.2 - - + +
423F VAL* 5.0 7.2 - - + -
435F VAL* 3.3 30.1 - - + +
480F LYS* 3.1 17.5 + - + +
481F CYS* 3.6 7.6 - - - +
482F LEU 3.0 1.0 - - - -
483F GLN* 1.3 76.9 - - - +
485F GLY* 1.3 58.4 + - - +
486F MET* 3.7 0.7 - - + -
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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