Contacts of the helix formed by residues 452 - 465 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384D THR* 3.9 18.9 + - - +
448D LYS* 5.7 0.4 + - - +
449D ASN* 3.0 29.7 + - + +
451D SER* 1.3 86.5 + - - +
453D LEU* 1.3 64.4 + - - +
454D GLN 3.3 2.2 - - - -
455D ASP* 3.1 16.1 + - + +
456D LEU* 3.1 36.8 + - + +
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Residues in contact with LEU 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D SER* 3.8 39.7 - - - +
388D ILE* 5.0 2.9 - - + +
446D THR* 3.8 39.5 - - + +
449D ASN 3.3 18.6 + - - +
450D CYS* 3.4 19.6 + - + +
451D SER 3.4 0.2 - - - -
452D GLN* 1.3 76.4 - - - +
454D GLN* 1.3 58.2 + - - +
456D LEU* 3.2 9.1 + - + +
457D HIS* 3.0 43.9 + - + +
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Residues in contact with GLN 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D CYS 4.9 0.4 + - - -
451D SER 5.1 2.2 + - - +
452D GLN 3.3 0.4 - - - -
453D LEU* 1.3 79.8 - - - +
455D ASP* 1.3 65.1 + - - +
457D HIS 3.4 1.0 + - - -
458D LYS* 2.9 31.5 + - - +
493D SER 3.5 21.1 - - - +
494D ALA* 3.3 28.8 + - - +
495D LYS* 3.3 22.4 - - - +
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Residues in contact with ASP 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D SER 5.2 3.7 + - - +
452D GLN* 3.1 16.7 + - + +
454D GLN* 1.3 83.7 + - - +
456D LEU* 1.3 62.9 + - + +
458D LYS* 3.5 13.5 + - - +
459D LYS* 2.9 26.9 + - - +
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Residues in contact with LEU 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384D THR* 3.6 35.7 - - + +
385D ASP* 3.3 31.2 - - - +
387D SER* 3.8 16.4 - - - -
388D ILE* 3.4 25.4 - - + +
403D LEU* 4.7 1.2 - - - +
449D ASN* 4.8 1.8 - - + -
452D GLN* 3.1 34.8 + - + +
453D LEU* 3.2 11.0 + - + +
455D ASP* 1.3 76.3 - - + +
457D HIS* 1.3 63.3 + - - +
459D LYS* 3.1 25.1 + - + +
460D ILE 3.2 5.5 + - - -
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Residues in contact with HIS 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388D ILE* 3.7 27.7 - - + +
453D LEU* 3.0 34.6 + - + +
454D GLN* 3.6 7.9 - - - +
456D LEU* 1.3 76.4 - - - +
458D LYS* 1.3 58.4 + - - +
460D ILE* 3.1 24.7 - - - +
461D ILE* 3.4 11.1 + - - +
489D TYR* 3.7 25.3 + + - -
490D HIS* 3.0 43.4 + - - +
493D SER* 3.5 25.0 + - - -
494D ALA* 3.6 9.2 - - - +
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Residues in contact with LYS 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D GLN* 2.9 20.9 + - - +
455D ASP* 3.7 14.6 - - - +
457D HIS* 1.3 72.5 - - - +
459D LYS* 1.3 59.3 + - - +
461D ILE* 3.3 2.4 + - - +
462D THR* 2.5 40.4 + - - +
494D ALA* 3.3 16.9 - - + +
496D MET* 3.9 32.7 - - + +
499D GLU* 5.5 1.1 - - - -
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Residues in contact with LYS 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ASP* 6.4 0.2 - - - +
382D TYR* 5.7 2.2 - - - -
385D ASP* 2.9 37.1 + - - +
403D LEU* 3.8 28.7 - - + -
404D TRP* 4.2 6.4 - - - +
455D ASP 2.9 15.1 + - - +
456D LEU* 3.1 16.8 - - + +
458D LYS* 1.3 77.2 - - - +
460D ILE* 1.3 57.6 + - - +
462D THR* 3.3 6.6 + - - -
463D GLN* 2.9 41.6 + - + +
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Residues in contact with ILE 460 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D ILE* 3.6 25.4 - - + -
399D VAL* 4.0 20.0 - - + +
402D ILE* 4.9 0.8 - - + +
403D LEU* 3.6 27.3 - - + +
456D LEU 3.2 1.6 + - - -
457D HIS 3.1 21.5 - - - +
459D LYS* 1.3 78.6 - - - +
461D ILE* 1.3 60.3 + - + +
463D GLN* 3.8 1.8 - - - +
464D PHE* 2.8 29.8 + - - +
482D TYR* 4.6 1.3 - - - +
483D TRP* 3.7 29.4 - - + -
490D HIS* 3.7 39.3 - - + +
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Residues in contact with ILE 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457D HIS 3.6 12.8 - - - +
458D LYS 3.3 6.8 + - - +
459D LYS 3.3 0.2 - - - -
460D ILE* 1.3 78.6 - - + +
462D THR* 1.3 63.1 + - - +
464D PHE* 3.4 3.6 + - + +
465D GLN* 3.1 47.0 + - + +
483D TRP* 5.3 2.0 - - + -
487D LEU* 3.4 30.3 - - + -
490D HIS* 3.6 22.7 - - + -
491D MET* 3.7 36.3 - - + +
496D MET* 3.8 23.6 - - + -
499D GLU* 4.9 0.4 - - + -
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Residues in contact with THR 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D LYS* 2.5 35.4 + - - +
459D LYS* 3.5 8.4 - - - -
461D ILE* 1.3 77.4 - - - +
463D GLN* 1.3 65.6 + - - +
465D GLN* 3.5 17.3 + - - +
466D ARG* 3.3 40.0 + - - +
496D MET* 5.0 3.8 - - - +
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Residues in contact with GLN 463 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D ILE* 2.8 35.8 + - + +
403D LEU* 3.4 23.9 + - - +
405D ASP* 3.6 31.0 + - - +
459D LYS* 2.9 27.7 + - + +
460D ILE 3.9 3.4 - - - +
462D THR* 1.3 77.7 - - - +
464D PHE* 1.3 66.5 + - - +
466D ARG* 3.1 33.0 + - - +
467D TYR* 3.5 20.4 - - - -
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Residues in contact with PHE 464 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402D ILE* 3.7 10.0 - - - +
460D ILE 2.8 19.8 + - - +
461D ILE* 3.6 7.0 - - + +
463D GLN* 1.3 76.1 - - - +
465D GLN* 1.3 69.5 + - + +
466D ARG 3.1 1.6 + - - -
467D TYR* 3.1 2.0 + - - -
468D HIS* 2.9 66.4 + + + +
469D GLN 4.3 10.1 - - - -
470D PRO* 4.2 14.4 - - + -
473D LEU* 5.1 4.0 - - + -
483D TRP* 3.5 57.9 - + + -
487D LEU* 3.9 33.4 - - + -
491D MET* 5.8 1.6 - - + -
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Residues in contact with GLN 465 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D ILE* 3.1 35.0 + - + +
462D THR* 3.8 12.3 - - - +
463D GLN 3.2 0.4 - - - -
464D PHE* 1.3 86.5 - - + +
466D ARG* 1.3 60.0 + - - +
467D TYR 3.6 0.2 - - - -
468D HIS 3.7 14.6 - - - +
470D PRO* 6.3 1.6 - - + -
491D MET* 4.5 9.1 - - - +
496D MET* 5.2 2.4 - - - +
499D GLU* 3.8 22.3 - - - +
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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