Contacts of the helix formed by residues 455 - 469 (chain A) in PDB entry 5ZR1
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 GLU 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A ALA 4.3 2.4 - - - +
452A ARG* 3.4 42.0 + - + -
453A GLU 3.2 2.6 + - - -
454A ASN* 1.3 85.2 + - - +
456A PHE* 1.3 64.0 + - - +
457A ALA 3.3 0.2 - - - -
458A SER* 4.0 4.3 - - - +
459A ILE* 3.3 31.6 + - - +
488A THR* 5.2 1.1 - - + -
622A ILE* 4.4 9.2 - - + -
623A MET 4.8 6.0 - - - +
624A PHE* 3.5 43.1 - - + -
625A THR 5.5 1.4 + - - -
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Residues in contact with PHE 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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449A LEU* 5.2 2.7 - - + -
452A ARG 3.5 20.8 + - - +
453A GLU* 3.5 7.4 + - + +
455A GLU* 1.3 78.6 - - - +
457A ALA* 1.3 61.5 + - + +
459A ILE 3.4 0.7 + - - -
460A TYR* 2.9 51.4 + + + +
488A THR* 3.9 18.0 + - - +
491A GLU* 3.3 37.0 - - + -
492A VAL* 3.6 21.1 - - + +
495A GLU* 3.9 31.0 - - + -
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Residues in contact with ALA 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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453A GLU* 3.0 26.0 + - - +
454A ASN* 3.7 8.9 + - - +
455A GLU 3.3 0.2 - - - -
456A PHE* 1.3 80.9 - - + +
458A SER* 1.3 57.3 + - - +
460A TYR* 4.7 5.3 - - - -
461A LEU* 3.3 28.0 + - - +
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Residues in contact with SER 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 ASN 2.8 22.5 + - - -
455A GLU* 4.0 4.7 - - - -
456A PHE 3.2 0.8 - - - -
457A ALA* 1.3 78.5 - - - +
459A ILE* 1.3 62.4 - - - +
460A TYR 3.4 0.2 - - - -
461A LEU* 3.7 3.2 + - - +
462A SER* 3.0 29.5 + - - -
622A ILE* 3.8 24.6 - - - +
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Residues in contact with ILE 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLU 3.3 18.9 + - - +
458A SER* 1.3 73.9 - - - +
460A TYR* 1.3 65.9 + - - +
462A SER 3.5 0.5 + - - -
463A ALA* 3.1 23.8 + - + +
475A ILE* 3.9 24.8 - - + +
477A VAL* 4.8 7.4 - - + -
488A THR* 4.7 5.4 - - + -
489A VAL* 4.0 25.8 - - + -
492A VAL* 3.8 26.9 - - + -
596A ILE* 4.4 14.6 - - + -
622A ILE* 3.7 19.5 - - + -
624A PHE* 4.1 22.4 - - + -
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Residues in contact with TYR 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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456A PHE* 2.9 36.3 + + + +
457A ALA* 4.7 3.4 - - - -
459A ILE* 1.3 78.7 - - - +
461A LEU* 1.3 60.9 + - + +
464A TYR* 2.9 57.5 + + + +
492A VAL* 3.8 15.2 - - + +
495A GLU* 3.6 33.7 + - + +
496A LEU* 3.6 34.8 - - + -
499A SER* 4.1 11.3 + - - -
504A GLU* 5.6 0.3 + - - -
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Residues in contact with LEU 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 ALA 3.3 22.2 + - - +
458A SER* 3.7 3.1 + - - +
459A ILE 3.3 0.2 - - - -
460A TYR* 1.3 84.2 - - + +
462A SER* 1.3 62.7 + - - +
464A TYR* 4.2 8.9 - - + +
465A SER* 3.4 26.2 + - - -
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Residues in contact with SER 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 SER 3.0 19.1 + - - -
459A ILE 4.0 0.2 - - - -
461A LEU* 1.3 79.6 - - - +
463A ALA* 1.3 58.8 + - - +
465A SER* 3.2 16.9 + - - -
466A ALA* 3.7 11.6 + - - +
473A THR* 4.2 8.4 - - - +
475A ILE* 3.7 25.8 - - - -
620A THR* 4.2 19.3 + - - +
622A ILE* 5.9 0.9 - - - +
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Residues in contact with ALA 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 ILE 3.1 18.2 + - - +
462A SER* 1.3 76.5 - - - +
464A TYR* 1.3 64.0 + - - +
465A SER 3.3 1.6 - - - -
467A ILE* 3.2 33.4 + - + +
475A ILE* 4.4 10.8 - - + -
492A VAL* 4.9 3.1 - - + -
493A VAL* 6.5 0.4 - - + -
496A LEU* 3.8 20.6 - - + -
562A VAL* 6.0 2.5 - - + -
594A ILE* 4.0 19.6 - - + +
596A ILE* 5.4 5.4 - - + -
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Residues in contact with TYR 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 TYR* 2.9 49.5 + + + +
461A LEU* 3.6 11.0 + - + +
463A ALA* 1.3 77.3 - - - +
465A SER* 1.3 64.4 + - - +
467A ILE* 5.0 2.5 - - - -
468A GLU* 3.2 33.4 + - + +
496A LEU* 4.4 3.3 - - - +
499A SER* 3.6 18.8 - - - -
504A GLU* 3.7 21.5 + - + +
505A ILE* 3.5 32.4 - - + +
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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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461A LEU* 3.4 15.1 + - - -
462A SER* 3.2 14.4 + - - -
464A TYR* 1.3 84.6 - - - +
466A ALA* 1.3 59.1 + - - +
468A GLU* 3.6 3.9 + - - +
469A SER* 3.2 31.0 + - - -
471A SER* 5.1 0.2 - - - -
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Residues in contact with ALA 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 SER 3.7 6.0 + - - +
463A ALA 3.7 1.0 + - - -
464A TYR 3.4 0.2 - - - -
465A SER* 1.3 80.9 + - - +
467A ILE* 1.3 63.4 + - - +
470A ASP* 3.3 2.1 + - - -
471A SER* 2.8 53.0 + - - +
473A THR* 3.8 22.4 - - + -
560A THR* 5.1 0.5 - - - +
594A ILE* 3.7 22.9 - - + -
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Residues in contact with ILE 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 ALA* 3.2 21.5 + - + +
464A TYR 4.3 0.9 - - - +
466A ALA* 1.3 76.1 - - - +
468A GLU* 1.3 63.8 + - - +
469A SER 3.4 0.5 + - - -
470A ASP* 3.5 10.2 + - - +
496A LEU* 3.8 28.7 - - + -
505A ILE* 3.8 28.3 - - + -
506A PRO* 3.5 34.5 - - + +
508A PHE* 4.4 7.6 - - + -
560A THR* 4.2 23.0 - - - +
562A VAL* 4.1 18.8 - - + -
594A ILE* 3.6 14.4 - - + -
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Residues in contact with GLU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A TYR* 3.2 31.5 + - + +
465A SER* 4.1 4.2 - - - +
467A ILE* 1.3 77.5 - - - +
469A SER* 1.3 63.4 + - - +
470A ASP* 3.4 2.8 + - - -
504A GLU 4.1 10.2 - - - +
505A ILE* 3.8 21.9 - - + +
506A PRO* 4.4 7.0 - - + +
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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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465A SER 3.2 18.4 + - - -
468A GLU* 1.3 80.1 - - - +
470A ASP* 1.3 69.7 + - - +
471A SER* 3.4 13.0 + - - -
555A LYS* 4.8 2.9 + - - -
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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