Contacts of the helix formed by residues 452 - 465 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384B THR* 3.8 19.6 - - - +
448B LYS* 5.4 2.0 + - - +
449B ASN* 2.9 34.0 + - + +
451B SER* 1.3 84.5 + - - +
453B LEU* 1.3 65.0 + - - +
454B GLN 3.3 2.5 - - - -
455B ASP* 3.1 13.6 + - + +
456B LEU* 3.0 36.5 + - + +
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B SER* 3.9 37.9 - - - +
388B ILE* 5.1 2.5 - - + -
446B THR* 3.9 37.7 - - + +
449B ASN* 3.4 21.3 - - + +
450B CYS* 3.2 17.7 + - + +
451B SER 3.5 0.4 - - - -
452B GLN* 1.3 77.5 - - - +
454B GLN* 1.3 63.3 + - - +
456B LEU* 3.1 8.7 + - + +
457B HIS* 3.0 37.0 + - + +
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Residues in contact with GLN 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B CYS 4.8 0.8 + - - -
451B SER 5.1 2.6 + - - +
452B GLN 3.3 1.0 - - - -
453B LEU* 1.3 78.7 - - - +
455B ASP* 1.3 63.3 + - - +
457B HIS* 3.3 4.0 + - - +
458B LYS* 2.9 26.9 + - + +
493B SER 3.9 13.7 - - - +
494B ALA* 3.4 30.1 + - - +
495B LYS* 3.8 20.7 - - + +
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Residues in contact with ASP 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B SER 5.2 4.5 - - - +
452B GLN* 3.1 12.2 + - + +
454B GLN* 1.3 82.8 + - - +
456B LEU* 1.3 63.9 + - + +
458B LYS* 3.7 17.4 - - - +
459B LYS* 3.0 25.6 + - - +
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Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B THR* 3.5 34.1 - - + +
385B ASP* 3.2 29.8 - - - +
387B SER* 4.0 13.9 - - - -
388B ILE* 3.3 21.7 - - + +
403B LEU* 4.9 1.2 - - - +
449B ASN* 5.0 0.9 - - + -
452B GLN* 3.0 39.8 + - + +
453B LEU* 3.1 8.3 + - + +
455B ASP* 1.3 77.2 - - + +
457B HIS* 1.3 65.7 + - - +
459B LYS* 3.0 26.1 + - + +
460B ILE* 3.2 9.0 + - - +
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Residues in contact with HIS 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE* 3.7 24.6 - - + +
453B LEU* 3.0 34.9 + - + +
454B GLN 3.6 7.0 - - - +
456B LEU* 1.3 76.1 - - - +
458B LYS* 1.3 62.1 + - - +
460B ILE* 3.2 23.1 + - - +
461B ILE* 3.3 9.9 + - - +
489B TYR* 3.7 26.8 + + - -
490B HIS* 2.8 48.3 + + - +
493B SER* 3.5 25.3 - - - -
494B ALA* 3.7 9.2 - - - +
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Residues in contact with LYS 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B GLN* 2.9 17.7 + - + +
455B ASP* 3.7 19.1 - - - +
456B LEU 3.3 0.2 - - - -
457B HIS* 1.3 76.5 - - - +
459B LYS* 1.3 57.5 + - - +
461B ILE* 3.4 2.3 + - - +
462B THR* 2.9 35.8 + - - +
494B ALA* 3.3 16.9 - - + +
496B MET* 4.0 29.8 - - + -
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Residues in contact with LYS 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B TYR* 5.8 0.4 - - - -
385B ASP* 2.5 42.4 + - - +
403B LEU* 3.6 24.4 - - + +
404B TRP* 3.9 11.5 - - - +
455B ASP 3.0 15.4 + - - +
456B LEU* 3.0 19.9 + - + +
458B LYS* 1.3 77.8 - - - +
460B ILE* 1.3 54.8 + - - +
462B THR* 3.4 5.9 + - - -
463B GLN* 2.9 41.6 + - + +
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Residues in contact with ILE 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B ILE* 3.8 23.1 - - + -
399B VAL* 4.0 19.1 - - + +
402B ILE* 4.9 0.4 - - + +
403B LEU* 3.7 30.2 - - + +
456B LEU 3.2 4.0 + - - -
457B HIS 3.2 20.0 - - - +
459B LYS* 1.3 78.4 - - - +
461B ILE* 1.3 55.4 + - + +
463B GLN* 3.4 2.5 + - + +
464B PHE* 2.8 35.9 + - - +
482B TYR* 4.5 2.0 - - - +
483B TRP* 3.8 26.9 - - + -
490B HIS* 3.6 41.5 - - + +
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Residues in contact with ILE 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B HIS 3.3 12.9 + - - +
458B LYS 3.7 6.1 - - - +
459B LYS 3.3 0.4 - - - -
460B ILE* 1.3 77.3 - - + +
462B THR* 1.3 66.5 + - - +
464B PHE* 3.2 5.6 + - + +
465B GLN* 3.0 42.2 + - + +
483B TRP* 5.4 2.2 - - + -
487B LEU* 3.6 29.2 - - + +
490B HIS* 3.8 18.8 - - + -
491B MET* 3.7 38.1 - - + +
496B MET* 3.8 29.6 - - + -
499B GLU* 4.8 0.7 - - + -
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Residues in contact with THR 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B LYS* 2.9 33.2 + - - +
459B LYS* 3.6 8.0 - - + -
461B ILE* 1.3 79.6 - - - +
463B GLN* 1.3 69.9 + - + +
465B GLN* 3.5 17.5 + - - +
466B ARG* 3.3 23.6 - - - +
496B MET* 4.9 4.0 - - - +
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Residues in contact with GLN 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B ILE* 2.9 35.3 + - + +
403B LEU* 2.9 26.9 + - - +
404B TRP 4.0 1.0 - - - -
405B ASP* 3.5 12.5 - - - +
459B LYS* 2.9 31.7 + - + +
460B ILE 3.7 3.6 - - - +
462B THR* 1.3 79.6 - - + +
464B PHE* 1.3 66.2 + - - +
466B ARG* 2.8 53.8 + - - +
467B TYR* 3.6 20.0 - - - -
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Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402B ILE* 3.7 10.0 - - - +
460B ILE 2.8 21.9 + - - +
461B ILE* 3.2 8.0 + - + +
463B GLN* 1.3 73.8 - - - +
465B GLN* 1.3 71.0 + - + +
467B TYR* 3.0 3.6 + - - +
468B HIS* 2.8 67.4 + + + +
469B GLN 4.3 0.7 - - - -
470B PRO* 4.2 23.1 - - + -
473B LEU* 4.3 4.0 - - + -
483B TRP* 3.5 55.4 - + + -
487B LEU* 3.6 35.2 - - + -
491B MET* 5.7 2.5 - - + -
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Residues in contact with GLN 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362A GLU* 4.5 8.3 - - - +
461B ILE* 3.0 30.5 + - + +
462B THR* 3.7 14.2 + - - +
463B GLN 3.3 0.4 - - - -
464B PHE* 1.3 85.6 - - + +
466B ARG* 1.3 58.8 + - + +
467B TYR 3.5 0.2 - - - -
468B HIS 3.7 15.0 - - - +
469B GLN* 5.7 1.2 - - - +
470B PRO* 6.5 0.4 - - + -
491B MET* 4.9 5.4 - - + +
496B MET* 5.4 1.9 - - - +
499B GLU* 3.8 28.0 + - - +
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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