Contacts of the helix formed by residues 462 - 477 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413E PHE* 4.5 7.2 - - - -
432E VAL* 5.0 1.1 - - - -
436E ASP* 3.5 19.3 - - - -
440E SER* 4.5 1.6 - - - -
461E GLY* 1.3 76.5 + - - +
463E ILE* 1.3 61.9 + - - -
464E GLU* 3.2 3.8 - - - -
465E ASP* 3.5 9.1 + - - +
466E VAL* 2.9 31.7 + - - +
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Residues in contact with ILE 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E PHE* 5.1 2.2 - - + -
436E ASP* 4.1 10.6 + - - +
439E ALA* 4.9 1.6 - - + +
440E SER* 3.4 37.8 + - - +
443E ALA* 3.8 19.7 - - + -
444E VAL* 5.1 4.9 - - + -
449E TYR* 3.6 42.2 - - + +
462E GLY* 1.3 69.5 - - - -
464E GLU* 1.3 68.6 + - + +
466E VAL* 3.3 14.9 - - + +
467E VAL* 2.9 28.6 + - + +
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Residues in contact with GLU 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436E ASP* 4.8 10.2 - - - +
462E GLY* 3.2 1.5 - - - -
463E ILE* 1.3 85.7 - - + +
465E ASP* 1.3 64.8 + - - +
467E VAL* 3.1 9.5 + - - +
468E ALA* 2.9 26.2 + - - +
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Residues in contact with ASP 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430E LYS* 3.4 39.4 - - - +
460E VAL* 4.7 5.6 - - + +
461E GLY 4.3 7.9 - - - +
462E GLY* 3.5 16.6 + - - +
464E GLU* 1.3 77.5 - - - +
466E VAL* 1.3 59.7 + - - +
468E ALA* 3.7 10.4 - - + +
469E LYS* 2.9 31.7 + - - +
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Residues in contact with VAL 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E PHE* 3.7 24.5 - - + -
444E VAL* 6.4 1.3 - - + -
449E TYR* 5.1 9.0 - - + -
452E ILE* 4.9 4.7 - - + -
456E ALA* 4.6 6.5 - - - +
457E PHE* 3.5 34.1 - - + -
460E VAL* 3.7 17.0 - - + -
462E GLY 2.9 18.3 + - - +
463E ILE* 3.3 20.9 - - + +
464E GLU 3.2 0.2 - - - -
465E ASP* 1.3 76.3 - - - +
467E VAL* 1.3 61.9 + - + +
469E LYS* 3.8 1.8 - - - +
470E ALA* 2.9 28.6 + - - +
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Residues in contact with VAL 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449E TYR* 4.0 32.5 - - + +
452E ILE* 6.4 0.7 - - + -
463E ILE* 2.9 20.0 + - + +
464E GLU* 3.1 10.5 + - - +
466E VAL* 1.3 76.7 - - + +
468E ALA* 1.3 58.8 + - - +
470E ALA* 3.2 7.6 + - + +
471E GLU* 2.9 46.0 + - + +
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Residues in contact with ALA 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464E GLU 2.9 14.6 + - - +
465E ASP* 3.7 14.1 - - + +
466E VAL 3.3 0.2 - - - -
467E VAL* 1.3 78.5 - - - +
469E LYS* 1.3 57.2 + - - +
471E GLU* 3.3 10.8 + - - +
472E LYS* 2.9 46.7 + - - +
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Residues in contact with LYS 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455E HIS* 3.1 30.7 + - - -
456E ALA* 3.5 21.3 - - + +
458E TYR* 2.8 30.9 + - - +
459E MET 5.1 0.6 + - - +
460E VAL* 3.8 11.0 - - + -
465E ASP 2.9 18.4 + - - +
466E VAL 4.0 2.9 - - - +
468E ALA* 1.3 73.6 - - - +
470E ALA* 1.3 60.9 + - - +
472E LYS* 3.8 9.8 - - + -
473E LEU* 2.9 46.5 + - + +
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Residues in contact with ALA 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452E ILE* 3.9 36.6 - - + -
453E PRO* 5.5 3.6 - - + -
456E ALA* 4.3 8.9 - - - +
466E VAL 2.9 19.2 + - - +
467E VAL* 3.2 9.8 + - + +
469E LYS* 1.3 77.1 - - - +
471E GLU* 1.3 57.2 + - + +
473E LEU* 3.8 1.7 - - - +
474E ALA* 2.9 29.1 + - - +
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Residues in contact with GLU 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E VAL* 2.9 31.5 + - + +
468E ALA* 3.7 10.2 - - - +
470E ALA* 1.3 76.8 - - + +
472E LYS* 1.3 60.1 + - + +
474E ALA* 3.3 7.8 + - - +
475E ALA* 2.9 28.1 + - - +
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Residues in contact with LYS 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E ALA* 2.9 32.5 + - - +
469E LYS* 3.9 9.2 - - + +
470E ALA 3.3 0.4 - - - -
471E GLU* 1.3 78.9 - - + +
473E LEU* 1.3 59.6 + - + +
475E ALA* 3.2 7.4 + - - +
476E GLU* 2.9 38.3 + - + +
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Residues in contact with LEU 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453E PRO* 5.6 7.6 - - + -
455E HIS* 3.6 35.4 - - + +
456E ALA* 3.8 27.1 - - + +
469E LYS* 2.9 31.3 + - + +
470E ALA* 4.2 2.5 - - - +
472E LYS* 1.3 73.7 - - + +
474E ALA* 1.3 65.0 + - - +
476E GLU* 3.6 26.1 - - + +
477E ALA* 3.2 24.9 + - - +
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Residues in contact with ALA 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470E ALA 2.9 19.1 + - - +
471E GLU* 3.5 9.2 - - - +
473E LEU* 1.3 78.6 - - - +
475E ALA* 1.3 60.5 + - - +
477E ALA* 3.6 7.4 + - - +
478E ASN* 3.2 28.9 + - - +
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Residues in contact with ALA 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471E GLU 2.9 16.3 + - - +
472E LYS* 3.6 8.3 - - - +
474E ALA* 1.3 78.6 - - - +
476E GLU* 1.3 58.1 + - + +
478E ASN* 3.1 25.7 + - - +
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Residues in contact with GLU 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472E LYS* 2.9 23.6 + - + +
473E LEU* 3.6 25.3 + - + +
474E ALA 3.4 0.2 - - - -
475E ALA* 1.3 77.2 - - + +
477E ALA* 1.3 58.7 + - - +
478E ASN* 3.3 2.7 + - - +
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Residues in contact with ALA 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473E LEU 3.2 18.8 + - - +
474E ALA* 3.6 5.8 + - - +
475E ALA 3.2 0.6 - - - -
476E GLU* 1.3 76.7 - - - +
478E ASN* 1.3 69.9 + - - +
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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