Contacts of the helix formed by residues 453 - 467 (chain A) in PDB entry 1CEZ
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 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A PRO* 3.6 1.9 - - - -
452A ILE* 1.3 74.7 - - - +
454A LYS* 1.3 59.6 + - - -
455A GLU 3.5 0.7 - - - -
457A TYR* 3.0 30.3 + - - +
526A LEU* 2.8 34.2 + - - -
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Residues in contact with LYS 454 (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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453A GLY* 1.3 68.1 - - - -
455A GLU* 1.3 101.1 + - - +
457A TYR* 3.2 7.8 + - + +
458A TYR* 3.0 44.2 + - - +
526A LEU* 3.3 21.4 - - + +
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Residues in contact with GLU 455 (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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453A GLY 3.5 0.2 - - - -
454A LYS* 1.3 103.2 + - - +
456A GLY* 1.3 62.9 + - - +
458A TYR* 3.1 12.6 + - - +
459A TRP* 3.2 52.4 + - + -
818A PRO 5.8 0.4 - - - +
819A ALA 6.0 1.8 - - - +
822A ALA* 3.5 20.9 - - + +
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Residues in contact with GLY 456 (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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452A ILE* 3.4 25.2 + - - -
454A LYS 3.4 0.4 - - - -
455A GLU* 1.3 79.9 - - - +
457A TYR* 1.3 57.2 + - - +
459A TRP* 3.5 3.6 + - - +
460A LEU* 3.0 22.5 + - - +
818A PRO* 3.4 38.0 - - - +
819A ALA* 4.3 1.6 - - - +
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Residues in contact with TYR 457 (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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452A ILE* 3.4 9.4 - - + +
453A GLY 3.0 20.9 + - - +
454A LYS* 3.5 6.5 - - - +
455A GLU 3.2 0.2 - - - -
456A GLY* 1.3 73.8 - - - +
458A TYR* 1.3 65.2 + - - +
460A LEU* 3.7 8.0 - - + +
461A LYS* 3.4 52.1 + - + +
518A TYR* 3.9 17.5 + + - -
521A VAL* 3.4 38.6 - - + -
522A GLN* 2.7 27.8 + - - -
526A LEU* 4.2 18.6 - - + -
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Residues in contact with TYR 458 (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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454A LYS* 3.0 29.9 + - - +
455A GLU* 3.1 8.9 + - - +
457A TYR* 1.3 79.1 - - - +
459A TRP* 1.3 97.5 + + - +
461A LYS* 3.1 23.4 + - - +
462A ILE* 3.1 26.7 + - + +
475A PHE* 3.3 32.3 - + + +
476A PRO* 4.9 2.0 - - + +
479A ILE* 3.6 31.1 - - + +
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Residues in contact with TRP 459 (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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455A GLU* 3.2 58.6 + - + +
456A GLY* 4.2 2.2 - - - +
458A TYR* 1.3 97.8 - + - +
460A LEU* 1.3 66.7 + - - +
461A LYS 3.0 1.3 - - - -
462A ILE* 3.7 21.9 - - + +
463A HIS* 2.9 24.8 + - - +
475A PHE* 5.2 8.4 - + - -
534A LEU* 3.7 16.6 - - + +
536A PHE* 3.8 28.3 - + + -
821A ALA* 4.1 15.0 - - + -
822A ALA* 3.5 25.1 - - + -
825A PHE* 4.2 29.9 - + - -
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Residues in contact with LEU 460 (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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452A ILE* 4.0 19.7 - - + -
456A GLY 3.0 17.5 + - - +
457A TYR* 3.8 13.5 - - + +
458A TYR 3.2 0.6 - - - -
459A TRP* 1.3 77.2 - - - +
461A LYS* 1.3 57.3 + - - +
463A HIS* 3.3 3.0 + - - +
464A GLY 3.0 21.0 + - - -
514A PHE* 3.3 18.1 - - + -
517A GLU* 4.3 12.1 - - + -
518A TYR* 4.1 23.1 - - + +
521A VAL* 4.1 17.7 - - + -
532A LEU* 4.1 18.6 - - + -
534A LEU* 3.6 28.4 - - + +
818A PRO* 4.6 5.8 - - + -
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Residues in contact with LYS 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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457A TYR* 3.4 48.9 + - + +
458A TYR* 3.1 11.3 + - - +
459A TRP 3.0 0.6 - - - -
460A LEU* 1.3 76.7 - - + +
462A ILE* 1.3 60.4 + - - +
464A GLY 3.1 0.9 + - - -
465A ALA 2.8 24.3 + - - -
479A ILE* 3.8 25.4 - - + +
482A ILE* 3.0 41.6 - - + +
483A GLU* 3.6 29.2 + - + +
514A PHE* 4.0 6.5 - - - -
518A TYR* 4.3 13.5 - - + +
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Residues in contact with ILE 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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458A TYR* 3.1 27.6 + - + +
459A TRP* 3.2 21.5 + - + +
461A LYS* 1.3 76.0 - - - +
463A HIS* 1.3 57.8 + - - +
465A ALA* 3.2 4.9 + - - +
466A ASN* 2.9 46.0 + - - +
475A PHE* 3.7 34.8 - - + +
478A ARG* 3.8 20.9 - - + +
479A ILE* 3.3 30.5 - - + -
536A PHE* 5.9 2.2 - - + -
882A PHE* 5.6 2.2 - - + -
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Residues in contact with HIS 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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459A TRP 2.9 17.1 + - - +
460A LEU 3.5 5.3 + - - +
462A ILE* 1.3 74.6 - - - +
464A GLY* 1.3 62.6 + - - +
466A ASN* 3.4 10.1 + - + +
467A CYS* 2.9 55.8 + - - -
510A CYS* 4.7 7.8 - - + +
514A PHE* 4.6 3.2 - - - +
532A LEU* 4.4 17.7 - - + +
533A PRO 3.5 17.4 + - - -
534A LEU* 3.4 21.8 - - + +
535A ALA* 3.2 37.3 + - + +
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Residues in contact with GLY 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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460A LEU 3.0 10.7 + - - -
461A LYS 3.1 1.3 + - - -
463A HIS* 1.3 75.4 - - - +
465A ALA* 1.3 63.1 + - - +
467A CYS* 3.2 6.3 + - - +
468A ALA 3.2 15.4 + - - -
482A ILE* 4.1 3.6 - - - -
511A PHE* 3.5 13.1 - - - -
514A PHE* 3.2 41.5 - - - -
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Residues in contact with ALA 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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461A LYS 2.8 6.8 + - - +
462A ILE 3.2 8.0 + - - +
464A GLY* 1.3 77.0 - - - +
466A ASN* 1.3 57.3 + - - +
468A ALA* 2.9 28.6 + - - +
470A VAL* 3.4 20.0 + - + +
478A ARG* 3.5 30.3 - - + +
481A PHE* 4.2 7.2 - - + -
482A ILE* 3.3 24.3 - - + +
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Residues in contact with ASN 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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462A ILE* 2.9 27.8 + - - +
463A HIS* 3.7 10.8 - - + +
465A ALA* 1.3 75.2 - - - +
467A CYS* 1.3 55.7 + - - +
468A ALA 2.5 18.2 - - - +
470A VAL 3.6 9.5 - - - +
471A ASP* 3.6 20.5 - - + +
478A ARG* 2.7 32.9 + - - +
506A ASP* 4.9 2.1 - - - +
507A SER* 5.0 1.6 + - - -
535A ALA 4.2 16.4 + - - -
536A PHE* 6.0 0.6 - - - -
882A PHE* 4.4 12.3 - - - -
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Residues in contact with CYS 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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463A HIS* 2.9 51.7 + - - +
464A GLY* 3.5 7.6 - - - +
465A ALA 3.1 0.4 - - - -
466A ASN* 1.3 72.0 - - - +
468A ALA* 1.3 64.6 + - - +
505A GLN* 4.4 0.5 - - - +
506A ASP* 3.3 1.6 + - - +
507A SER* 2.8 38.7 + - - +
510A CYS* 3.7 28.7 - - - -
511A PHE* 3.8 21.8 - - + +
514A PHE* 5.1 0.4 - - - -
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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