Contacts of the helix formed by residues 460 - 472 (chain A) in PDB entry 3CPE
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 ASN 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A ASP* 4.2 1.1 + - - -
402A CYS* 2.9 30.8 + - - +
403A SER 3.1 13.9 + - - -
404A GLU* 3.5 19.1 + - - +
458A GLU* 2.9 26.6 + - - +
459A LEU* 1.3 73.0 - - - +
461A SER* 1.3 69.8 + - - +
462A THR 4.1 1.1 - - - -
463A GLY* 2.7 37.2 + - - -
464A VAL* 2.9 14.2 + - - +
491A GLN* 3.8 16.4 - - - +
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Residues in contact with SER 461 (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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404A GLU* 3.4 25.4 + - - +
460A ASN* 1.3 75.6 - - - +
462A THR* 1.3 70.1 + - - +
464A VAL* 3.9 5.9 + - - +
465A SER* 3.7 15.2 + - - -
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Residues in contact with THR 462 (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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402A CYS* 3.7 17.9 - - + -
403A SER 3.9 12.6 - - - +
404A GLU* 3.5 27.1 + - - +
411A HIS* 4.5 7.2 - - + -
436A HIS* 3.4 38.2 - - + -
460A ASN* 3.2 1.8 + - - -
461A SER* 1.3 78.8 + - - +
463A GLY* 1.3 58.5 + - - +
465A SER* 3.3 7.9 + - - -
466A VAL* 3.0 28.4 + - + +
569A PO4 5.5 0.2 - - - +
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Residues in contact with GLY 463 (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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402A CYS* 4.0 9.4 - - - +
457A ILE* 3.8 13.1 - - - +
458A GLU 3.3 14.1 - - - -
459A LEU* 4.6 0.9 - - - -
460A ASN* 2.7 26.5 + - - -
462A THR* 1.3 71.9 - - - +
464A VAL* 1.3 53.5 + - - -
466A VAL* 3.0 2.9 + - - +
467A ALA* 2.7 35.6 + - - +
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Residues in contact with VAL 464 (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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459A LEU* 3.9 38.3 - - + +
460A ASN 2.9 21.6 + - - +
461A SER* 4.0 5.8 - - - +
463A GLY* 1.3 70.0 - - - +
465A SER* 1.3 63.8 + - - +
467A ALA* 3.3 3.9 + - - +
468A LYS* 3.1 47.6 + - + +
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Residues in contact with SER 465 (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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436A HIS* 3.8 24.7 + - - -
437A LEU* 5.5 2.4 - - - +
461A SER 3.7 9.6 + - - -
462A THR* 3.3 10.3 + - - -
463A GLY 3.2 0.2 - - - -
464A VAL* 1.3 79.7 - - - +
466A VAL* 1.3 62.0 + - - +
468A LYS* 3.1 20.3 + - - +
469A SER* 3.2 17.3 + - - -
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Residues in contact with VAL 466 (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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400A LEU* 3.8 26.0 - - + -
402A CYS* 3.8 17.5 - - - -
436A HIS* 4.0 17.7 - - + +
439A LEU* 3.9 16.4 - - + -
440A PRO* 4.3 19.7 - - + +
443A VAL* 5.9 0.4 - - + -
457A ILE* 4.2 7.4 - - + -
462A THR* 3.0 22.2 + - + +
463A GLY 3.0 7.9 + - - +
465A SER* 1.3 75.4 - - - +
467A ALA* 1.3 65.6 + - - +
469A SER* 3.2 4.4 + - - -
470A LEU* 3.0 28.3 + - + +
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Residues in contact with ALA 467 (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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457A ILE* 3.8 17.9 - - + +
459A LEU* 4.4 2.9 - - + -
463A GLY 2.7 16.5 + - - +
464A VAL* 3.4 12.8 - - - +
466A VAL* 1.3 73.8 - - - +
468A LYS* 1.3 61.8 + - + +
470A LEU* 3.9 1.3 - - - +
471A TYR* 3.0 28.1 + - - +
479A VAL* 4.8 2.4 - - + +
487A LEU* 3.3 38.8 - - + +
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Residues in contact with LYS 468 (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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464A VAL* 3.1 35.5 + - + +
465A SER* 3.1 11.4 + - - +
467A ALA* 1.3 75.7 - - - +
469A SER* 1.3 57.9 + - - +
472A MET* 2.8 68.3 + - + +
473A ASP* 3.5 3.7 + - - +
485A THR 4.7 12.1 + - - -
487A LEU* 4.6 9.7 - - + +
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Residues in contact with SER 469 (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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437A LEU 5.7 0.2 + - - -
440A PRO* 3.5 31.6 - - - +
465A SER* 3.2 11.0 + - - -
466A VAL 3.2 4.1 + - - -
468A LYS* 1.3 78.3 - - - +
470A LEU* 1.3 55.8 + - - +
473A ASP* 3.3 24.4 + - - +
474A LEU* 2.6 39.7 + - - +
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Residues in contact with LEU 470 (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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400A LEU* 5.4 0.2 - - + -
440A PRO* 3.4 31.2 - - + +
443A VAL* 4.5 10.1 - - + -
444A MET* 3.8 29.8 - - + -
447A LEU* 4.2 9.2 - - + -
455A VAL* 4.0 18.4 - - + -
457A ILE* 3.8 26.7 - - + -
466A VAL* 3.0 20.1 + - + +
467A ALA* 3.9 3.6 - - - +
469A SER* 1.3 76.9 - - - +
471A TYR* 1.3 54.0 + - - +
474A LEU* 3.5 3.5 - - + -
475A GLU 3.2 6.2 + - - -
476A TYR* 2.8 40.1 + - + +
479A VAL* 4.2 8.3 - - + -
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Residues in contact with TYR 471 (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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467A ALA 3.0 16.6 + - - +
470A LEU* 1.3 78.4 - - - +
472A MET* 1.3 72.2 + - + +
475A GLU* 3.5 16.7 - - - -
476A TYR 3.3 19.2 - - - +
477A GLU* 3.5 30.5 + - + -
479A VAL* 3.4 33.4 - - + -
481A CYS* 5.1 5.8 - - - -
484A TYR* 5.3 11.1 - + - -
487A LEU* 4.1 28.0 - - + -
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Residues in contact with MET 472 (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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468A LYS* 2.8 40.4 + - + +
471A TYR* 1.3 93.3 - - + +
473A ASP* 1.3 71.0 + - - +
474A LEU 3.4 1.1 - - - -
475A GLU* 3.4 19.1 - - - +
487A LEU* 3.7 26.2 - - + -
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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