Contacts of the helix formed by residues 465 - 474 (chain F) in PDB entry 4CYM
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 THR 465 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456F PRO 4.0 12.8 - - - +
457F PHE* 4.8 3.4 - - - +
458F SER 3.5 12.8 - - - +
459F ARG* 3.7 26.2 - - - +
463F GLY 3.5 0.6 + - - -
464F HIS* 1.3 73.2 - - - +
466F PRO* 1.3 73.1 - - - +
467F LEU* 3.6 12.1 + - - +
468F HIS* 2.8 45.9 + - - +
469F VAL* 3.1 13.6 + - - +
488F MET* 5.1 2.9 + - + +
491F ALA* 4.2 13.8 - - + +
499F PRO* 4.8 0.2 - - - +
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Residues in contact with PRO 466 (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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454F VAL* 5.4 2.9 - - + -
455F THR 3.8 20.4 - - - +
456F PRO* 3.9 9.6 - - + +
458F SER* 3.4 24.5 - - - +
464F HIS 4.4 1.1 - - - +
465F THR* 1.3 84.0 - - - +
467F LEU* 1.3 58.8 + - - +
469F VAL* 2.9 11.0 + - + +
470F ALA* 2.7 31.0 + - - +
482F LEU* 3.6 26.2 - - + +
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Residues in contact with LEU 467 (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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456F PRO 5.2 0.6 + - - -
465F THR* 3.2 11.8 + - - +
466F PRO* 1.3 78.4 - - - +
468F HIS* 1.3 62.8 + - - +
470F ALA* 4.3 0.4 - - - -
471F ALA* 3.0 23.2 + - - +
479F ILE* 4.1 30.1 - - + -
482F LEU* 3.4 28.6 - - + +
483F VAL* 4.3 6.7 - - + -
487F ALA* 4.4 13.2 - - + +
488F MET 3.8 10.5 - - - +
489F VAL* 3.7 37.0 - - + +
499F PRO* 3.9 18.0 - - + +
515F LEU* 4.7 7.2 - - + -
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Residues in contact with HIS 468 (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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459F ARG* 4.6 0.2 - - - -
463F GLY 3.9 8.5 - - - -
464F HIS* 3.8 22.6 - + + -
465F THR* 2.8 40.7 + - - +
467F LEU* 1.3 74.8 - - - +
469F VAL* 1.3 63.6 + - - +
471F ALA* 3.2 1.4 + - - +
472F VAL* 3.0 20.7 + - - +
491F ALA* 3.3 29.3 + - + -
493F ASP* 3.7 12.2 + - + -
497F ALA 2.7 27.9 + - - -
498F THR 3.8 0.4 - - - -
499F PRO* 3.5 22.1 - - + +
502F LEU* 3.5 32.0 - - + +
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Residues in contact with VAL 469 (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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464F HIS* 4.7 13.5 - - + +
465F THR 3.1 15.7 + - - +
466F PRO* 2.9 9.5 + - + +
468F HIS* 1.3 73.0 - - - +
470F ALA* 1.3 68.1 + - - +
472F VAL* 3.0 20.3 + - + +
473F CYS* 3.0 31.5 + - - -
475F GLN* 5.8 0.7 - - - +
478F LEU* 6.4 0.9 - - + -
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Residues in contact with ALA 470 (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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466F PRO 2.7 17.8 + - - +
467F LEU 3.9 3.8 - - - +
469F VAL* 1.3 74.4 - - - +
471F ALA* 1.3 60.8 + - - +
473F CYS* 3.6 4.4 + - - +
474F GLY 3.1 16.1 + - - -
475F GLN* 3.1 13.3 + - - +
478F LEU* 3.9 33.3 - - + +
479F ILE* 4.0 17.6 - - + +
482F LEU* 3.9 14.6 - - + -
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Residues in contact with ALA 471 (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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467F LEU 3.0 19.5 + - - +
468F HIS 3.5 4.7 - - - +
469F VAL 3.1 0.2 - - - -
470F ALA* 1.3 76.1 - - - +
472F VAL* 1.3 64.9 + - - +
474F GLY* 3.2 13.9 + - - -
479F ILE* 4.3 11.6 - - + +
499F PRO* 3.8 31.0 - - + +
502F LEU* 4.7 0.4 - - + -
503F ALA* 4.7 6.7 - - - +
508F TYR* 3.8 9.7 - - - -
511F VAL* 4.3 18.2 - - + +
515F LEU* 4.6 2.0 - - + -
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Residues in contact with VAL 472 (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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468F HIS 3.0 12.1 + - - +
469F VAL* 3.0 17.4 + - + +
471F ALA* 1.3 78.1 - - - +
473F CYS* 1.3 67.6 + - - +
502F LEU* 4.2 33.0 - - + +
505F GLN* 6.1 1.8 - - - +
506F LYS* 3.4 42.1 - - + -
508F TYR* 3.5 4.5 + - - -
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Residues in contact with CYS 473 (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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469F VAL* 3.0 35.5 + - - +
470F ALA 3.9 1.3 - - - +
472F VAL* 1.3 82.5 - - - +
474F GLY* 1.3 57.1 + - - +
475F GLN* 3.3 34.0 - - + +
508F TYR* 3.2 14.5 + - - -
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Residues in contact with GLY 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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470F ALA 3.1 5.5 + - - -
471F ALA 3.2 7.0 + - - -
473F CYS* 1.3 77.1 - - - +
475F GLN* 1.3 60.1 + - - +
476F ALA* 2.8 11.8 + - - +
508F TYR* 3.4 23.6 - - - -
511F VAL* 4.0 13.2 - - - +
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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