Contacts of the helix formed by residues 452 - 465 (chain A) in PDB entry 1Z6T
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 GLN 452 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A THR* 3.6 21.7 + - - +
448A LYS* 5.3 1.6 - - - +
449A ASN* 3.0 32.4 + - + +
451A SER* 1.3 80.1 - - - +
453A LEU* 1.3 64.6 + - - +
454A GLN 3.3 2.0 - - - -
455A ASP* 3.0 24.8 + - + +
456A LEU* 3.0 27.0 + - + +
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Residues in contact with LEU 453 (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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387A SER* 3.6 42.4 - - - +
388A ILE* 4.8 3.1 - - + +
446A THR* 3.8 39.0 - - + +
449A ASN 3.3 17.7 + - - +
450A CYS* 3.3 17.8 + - + +
451A SER 3.4 0.2 - - - -
452A GLN* 1.3 76.4 - - - +
454A GLN* 1.3 63.1 + - - +
456A LEU* 3.2 10.4 + - + +
457A HIS* 3.0 37.9 + - + +
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Residues in contact with GLN 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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450A CYS 4.9 0.4 + - - -
451A SER 5.1 2.2 + - - +
452A GLN 3.2 0.8 + - - -
453A LEU* 1.3 78.2 - - - +
455A ASP* 1.3 58.0 + - - +
457A HIS* 3.3 3.8 + - - +
458A LYS* 2.8 28.9 + - - +
493A SER 3.3 23.8 - - - +
494A ALA* 3.7 10.8 + - - +
495A LYS* 3.3 42.4 - - + +
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Residues in contact with ASP 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A SER 5.2 3.0 - - - +
452A GLN* 3.0 16.7 + - + +
454A GLN* 1.3 78.8 - - - +
456A LEU* 1.3 58.6 + - + +
458A LYS* 3.5 15.8 + - - +
459A LYS* 2.9 26.7 + - - +
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Residues in contact with LEU 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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384A THR* 3.6 28.7 - - + +
385A ASP* 3.1 35.7 - - - +
387A SER* 3.9 16.8 - - - -
388A ILE* 3.3 23.4 - - + +
403A LEU* 4.9 1.0 - - - +
449A ASN* 4.9 1.3 - - + -
452A GLN* 3.0 33.9 + - + +
453A LEU* 3.2 15.5 + - + +
455A ASP* 1.3 74.8 - - + +
457A HIS* 1.3 64.0 + - - +
459A LYS* 3.1 24.8 + - + +
460A ILE* 3.2 9.2 + - - +
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Residues in contact with HIS 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A ILE* 3.8 28.2 - - + +
453A LEU* 3.0 33.4 + - + +
454A GLN 3.6 7.4 - - - +
456A LEU* 1.3 76.8 - - - +
458A LYS* 1.3 59.5 + - - +
460A ILE* 3.0 25.3 - - - +
461A ILE* 3.4 10.2 + - - +
489A TYR* 3.7 25.7 + + - -
490A HIS* 2.9 43.5 + + - +
493A SER* 3.4 26.5 - - - -
494A ALA* 3.7 9.4 - - - +
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Residues in contact with LYS 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 GLN 2.8 20.8 + - - +
455A ASP* 3.6 17.3 - - - +
457A HIS* 1.3 72.0 - - - +
459A LYS* 1.3 53.7 + - - +
461A ILE* 3.4 2.4 + - - +
462A THR* 2.6 44.8 + - - +
494A ALA* 3.4 17.3 - - + +
496A MET* 3.9 29.8 - - + -
499A GLU* 5.7 0.4 - - - -
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Residues in contact with LYS 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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382A TYR* 5.7 2.0 - - - -
385A ASP* 2.8 36.8 + - - +
403A LEU* 3.7 29.8 - - + -
404A TRP* 4.2 5.6 - - - +
455A ASP 2.9 15.0 + - - +
456A LEU* 3.1 17.0 + - + +
458A LYS* 1.3 76.4 - - - +
460A ILE* 1.3 57.2 + - - +
462A THR* 3.3 6.4 + - - -
463A GLN* 2.9 43.0 + - + +
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Residues in contact with ILE 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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388A ILE* 3.6 29.4 - - + -
399A VAL* 4.0 20.2 - - + +
402A ILE* 4.8 0.8 - - + +
403A LEU* 4.0 23.5 - - + +
456A LEU 3.2 1.8 + - - -
457A HIS 3.0 22.9 - - - +
459A LYS* 1.3 78.6 - - - +
461A ILE* 1.3 58.7 + - + +
463A GLN* 3.9 1.9 - - - +
464A PHE* 2.8 31.4 + - - +
482A TYR* 4.8 1.1 - - + +
483A TRP* 3.6 29.2 - - + -
490A HIS* 3.7 38.6 - - + +
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Residues in contact with ILE 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 HIS 3.6 12.3 - - - +
458A LYS 3.4 7.1 + - - +
459A LYS 3.3 0.2 - - - -
460A ILE* 1.3 78.0 - - + +
462A THR* 1.3 64.0 + - - +
464A PHE* 3.3 3.6 + - - +
465A GLN* 3.0 45.1 + - + +
483A TRP* 5.3 2.2 - - + -
487A LEU* 3.5 28.9 - - + -
490A HIS* 3.6 23.6 - - + -
491A MET* 3.6 35.0 - - + +
496A MET* 3.8 30.1 - - + -
499A GLU* 4.8 0.7 - - + -
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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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458A LYS* 2.6 36.0 + - - +
459A LYS* 3.5 7.7 - - - -
461A ILE* 1.3 77.6 - - - +
463A GLN* 1.3 66.7 + - - +
465A GLN* 3.4 16.7 + - - +
466A ARG* 3.2 41.7 + - - +
496A MET* 4.8 4.6 - - - +
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Residues in contact with GLN 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 ILE* 3.2 23.7 + - + +
403A LEU* 3.5 20.6 + - - +
405A ASP* 2.7 44.7 + - - +
459A LYS* 2.9 31.0 + - + +
460A ILE 3.9 2.9 - - - +
462A THR* 1.3 78.8 - - - +
464A PHE* 1.3 66.4 + - - +
466A ARG* 3.2 30.6 + - - +
467A TYR* 3.5 19.5 - - - -
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Residues in contact with PHE 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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402A ILE* 3.7 9.5 - - - +
460A ILE 2.8 23.0 + - - +
461A ILE* 3.6 7.2 - - + +
463A GLN* 1.3 74.0 - - - +
465A GLN* 1.3 68.6 + - + +
466A ARG 3.1 1.4 + - - -
467A TYR* 3.1 2.0 + - - -
468A HIS* 2.9 60.6 + + + -
469A GLN 4.4 1.6 - - - -
470A PRO* 4.2 24.7 - - + -
473A LEU* 5.1 4.5 - - + -
483A TRP* 3.3 63.5 - + + -
487A LEU* 3.9 33.4 - - + -
491A MET* 5.9 1.1 - - + -
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Residues in contact with GLN 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ILE* 3.0 32.5 + - + +
462A THR* 3.8 11.7 - - - +
463A GLN 3.3 0.4 - - - -
464A PHE* 1.3 84.7 - - + +
466A ARG* 1.3 60.2 + - - +
468A HIS 3.7 15.0 - - - +
469A GLN* 5.9 0.2 - - - +
470A PRO* 6.3 2.0 - - + -
491A MET* 4.5 7.6 - - + +
496A MET* 5.3 2.1 - - - +
499A GLU* 3.7 31.1 - - - +
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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