Contacts of the helix formed by residues 462 - 478 (chain F) in PDB entry 6CP3
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 GLY 462 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139F LYS* 5.6 0.4 - - - -
413F PHE* 4.4 4.7 - - - -
432F VAL* 3.9 10.3 - - - +
436F ASP* 3.6 19.5 - - - -
437F THR* 6.4 0.2 - - - -
440F SER* 4.4 2.2 - - - -
460F VAL* 4.1 0.2 - - - +
461F GLY* 1.3 74.3 - - - -
463F ILE* 1.3 60.1 + - - -
464F GLU* 3.2 3.8 - - - -
465F ASP* 3.1 12.2 + - - +
466F VAL* 3.0 28.2 + - - +
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Residues in contact with ILE 463 (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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413F PHE* 4.5 2.9 - - + -
436F ASP* 4.3 5.9 + - - +
439F ALA 5.5 0.7 - - - -
440F SER* 3.3 36.1 + - - +
443F ALA* 5.0 2.7 - - + -
444F VAL* 3.9 26.5 - - + -
449F TYR* 3.7 41.5 - - + +
457F PHE* 4.8 1.6 - - + -
462F GLY* 1.3 69.4 - - - -
464F GLU* 1.3 70.6 + - + +
466F VAL* 3.1 24.7 + - + +
467F VAL* 2.9 29.4 + - + +
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Residues in contact with GLU 464 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436F ASP* 4.4 15.2 - - - +
462F GLY* 3.2 1.7 - - - -
463F ILE* 1.3 85.9 - - + +
465F ASP* 1.3 61.1 + - - +
467F VAL* 3.3 8.6 + - - +
468F ALA* 2.9 27.3 + - - +
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Residues in contact with ASP 465 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430F LYS* 2.8 35.4 + - - -
460F VAL* 3.6 14.8 - - + +
461F GLY 4.1 3.1 - - - +
462F GLY 3.1 18.2 + - - +
464F GLU* 1.3 79.2 - - - +
466F VAL* 1.3 61.0 + - - +
468F ALA* 3.8 9.6 - - - +
469F LYS* 2.8 32.1 + - - +
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Residues in contact with VAL 466 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413F PHE* 3.5 29.8 - - + -
452F ILE* 4.6 14.1 - - + -
456F ALA 4.3 13.5 - - - +
457F PHE* 3.9 29.4 - - + -
460F VAL* 3.7 17.0 - - + -
462F GLY 3.0 14.6 + - - +
463F ILE* 3.1 19.9 + - + +
465F ASP* 1.3 74.3 - - - +
467F VAL* 1.3 60.3 + - - +
469F LYS* 3.8 0.7 - - - +
470F ALA* 2.9 30.0 + - - +
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Residues in contact with VAL 467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449F TYR* 4.0 30.3 - - + +
452F ILE* 5.2 5.2 - - + -
463F ILE* 2.9 18.3 + - + +
464F GLU* 3.6 9.2 - - - +
466F VAL* 1.3 75.4 - - + +
468F ALA* 1.3 58.3 + - - +
470F ALA* 3.7 5.3 - - - +
471F GLU* 2.9 33.3 + - + +
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Residues in contact with ALA 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464F GLU 2.9 18.1 + - - +
465F ASP* 3.8 13.0 - - - +
466F VAL 3.3 0.2 - - - -
467F VAL* 1.3 78.5 - - - +
469F LYS* 1.3 57.1 + - - +
471F GLU* 3.2 14.5 + - - +
472F LYS* 2.9 35.1 + - + +
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Residues in contact with LYS 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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427F ILE* 5.2 5.7 - - - +
455F HIS* 4.6 13.0 + - - -
456F ALA* 3.9 19.3 - - - +
458F TYR* 2.5 32.2 + - - +
459F MET* 3.3 17.0 + - - +
460F VAL* 4.5 8.7 - - + -
465F ASP 2.8 21.3 + - - +
466F VAL 4.1 2.2 - - - +
468F ALA* 1.3 70.5 - - - +
470F ALA* 1.3 61.2 + - - +
472F LYS* 3.4 11.1 - - + +
473F LEU* 2.9 43.4 + - + +
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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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452F ILE* 4.1 19.7 - - + -
453F PRO* 5.4 4.5 - - + -
456F ALA* 3.8 22.5 - - + +
466F VAL 2.9 19.2 + - - +
467F VAL* 3.7 6.7 - - - +
469F LYS* 1.3 75.8 - - - +
471F GLU* 1.3 57.8 + - - +
473F LEU* 3.5 3.4 + - - +
474F ALA* 2.8 29.5 + - - +
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Residues in contact with GLU 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 VAL* 2.9 19.9 + - + +
468F ALA* 3.2 15.3 + - - +
470F ALA* 1.3 75.7 - - - +
472F LYS* 1.3 59.7 + - + +
474F ALA* 3.5 7.3 - - + +
475F ALA* 2.9 30.7 + - + +
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Residues in contact with LYS 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 ALA* 2.9 23.4 + - + +
469F LYS* 3.2 16.1 + - + +
471F GLU* 1.3 76.6 - - + +
473F LEU* 1.3 61.9 + - + +
475F ALA* 3.2 7.0 + - + +
476F GLU* 2.9 39.1 + - - +
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Residues in contact with LEU 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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455F HIS* 3.8 29.6 - - + +
456F ALA* 4.2 21.5 - - + +
469F LYS* 2.9 29.9 + - + +
470F ALA* 4.1 4.3 - - - +
472F LYS* 1.3 74.2 - - + +
474F ALA* 1.3 60.8 + - - +
476F GLU* 3.5 23.1 - - + +
477F ALA* 2.9 33.3 + - + +
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Residues in contact with ALA 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 2.8 19.1 + - - +
471F GLU* 3.5 10.3 - - + +
472F LYS 3.2 0.2 - - - -
473F LEU* 1.3 77.6 - - - +
475F ALA* 1.3 57.0 + - - +
477F ALA* 5.2 0.7 - - - -
478F ASN* 2.9 32.4 + - - +
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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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471F GLU* 2.9 18.3 + - + +
472F LYS* 3.2 6.5 + - + +
474F ALA* 1.3 76.3 - - - +
476F GLU* 1.3 60.0 + - + +
478F ASN* 2.8 27.1 + - - +
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Residues in contact with GLU 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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472F LYS* 2.9 23.3 + - - +
473F LEU* 3.5 26.3 - - + +
474F ALA 3.2 0.2 - - - -
475F ALA* 1.3 79.6 - - + +
477F ALA* 1.3 65.2 + - - +
478F ASN* 3.6 8.8 + - - -
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Residues in contact with ALA 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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415B SER* 5.5 12.3 - - - +
473F LEU* 2.9 20.5 + - + +
474F ALA* 5.2 0.9 - - - -
476F GLU* 1.3 74.2 - - - +
478F ASN* 1.3 70.7 + - - +
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Residues in contact with ASN 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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474F ALA* 2.9 21.4 + - - +
475F ALA* 2.8 32.0 + - - +
476F GLU 3.6 9.1 + - - -
477F ALA* 1.3 81.6 - - - +
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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