Contacts of the helix formed by residues 453 - 466 (chain A) in PDB entry 5JZU
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 ASP 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420A LYS* 3.0 29.7 + - - +
450A PHE* 3.2 20.5 + - + +
452A ASN* 1.3 75.9 - - - +
454A THR* 1.3 62.3 + - - +
455A SER* 2.5 34.4 + - - -
456A LEU* 3.1 27.2 + - + +
457A LYS* 3.5 23.2 + - - +
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Residues in contact with THR 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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452A ASN 3.2 8.5 + - - -
453A ASP* 1.3 68.6 + - - +
455A SER* 1.3 66.6 - - - +
456A LEU 3.1 2.5 - - - -
457A LYS* 2.9 23.4 + - + +
458A ASN* 3.0 13.3 + - - +
480A VAL* 3.7 29.6 - - + -
483A VAL* 5.4 3.5 - - - +
484A THR* 3.7 20.8 + - + +
487A ASP* 3.9 19.7 - - - +
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Residues in contact with SER 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A LYS* 5.2 7.8 + - - -
453A ASP* 2.5 29.5 + - - -
454A THR* 1.3 76.3 - - - +
456A LEU* 1.3 59.1 + - - +
458A ASN* 3.5 12.4 + - - +
459A ASP* 3.0 36.8 + - - +
487A ASP* 6.0 0.2 - - - -
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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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420A LYS* 4.3 5.2 - - + -
424A LYS* 3.9 37.7 - - + -
443A LEU* 5.0 3.5 - - + +
446A LEU* 3.7 39.5 - - + +
447A VAL* 3.7 15.3 - - + +
450A PHE* 3.8 19.3 - - + +
453A ASP* 3.1 37.0 + - + +
454A THR 3.1 0.6 - - - -
455A SER* 1.3 81.1 + - - +
457A LYS* 1.3 59.5 + - - +
459A ASP* 3.2 10.8 + - + +
460A LEU* 2.8 28.8 + - - +
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Residues in contact with LYS 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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447A VAL* 4.0 28.7 - - + -
451A PRO* 3.4 29.2 + - - -
452A ASN* 5.3 1.4 - - - +
453A ASP 3.5 13.6 + - - +
454A THR* 2.9 12.4 + - - +
456A LEU* 1.3 76.8 - - - +
458A ASN* 1.3 58.9 + - - +
460A LEU* 3.2 4.2 + - + +
461A GLY 2.9 23.0 + - - -
476A VAL* 3.0 18.4 - - + +
479A GLU* 4.5 33.3 + - + +
480A VAL* 3.5 26.0 - - + +
483A VAL* 5.2 12.5 - - - +
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Residues in contact with ASN 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 THR* 3.0 16.3 + - - +
455A SER* 3.5 14.6 - - - +
456A LEU 3.2 0.2 - - - -
457A LYS* 1.3 77.0 - - - +
459A ASP* 1.3 59.5 + - - +
461A GLY 2.9 15.1 + - - -
462A VAL* 3.1 4.7 + - - +
477A TYR* 2.9 38.0 + - - -
480A VAL* 3.7 17.2 - - - +
487A ASP* 3.1 32.7 + - - -
489A PHE* 3.4 33.3 - - + +
490A ALA* 3.7 1.2 - - - +
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Residues in contact with ASP 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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424A LYS* 4.3 14.4 + - - +
431A GLN* 5.1 0.7 + - - -
443A LEU* 3.5 24.3 - - + +
455A SER* 3.0 21.7 + - - +
456A LEU* 3.2 18.3 + - + +
458A ASN* 1.3 75.3 - - - +
460A LEU* 1.3 65.5 + - - +
462A VAL* 3.2 11.8 + - - +
463A GLY 3.0 17.5 + - - -
489A PHE* 5.0 7.3 - - - -
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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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440A LEU* 3.6 24.5 - - + -
443A LEU* 3.7 22.8 - - + +
444A GLN* 3.8 19.7 - - + +
447A VAL* 3.9 27.6 - - + -
456A LEU 2.8 13.2 + - - +
457A LYS* 3.3 10.1 - - + +
459A ASP* 1.3 77.6 - - - +
461A GLY* 1.3 62.7 + - - +
463A GLY* 3.0 12.0 + - - -
464A TYR* 3.1 35.0 + - + +
476A VAL* 4.1 13.7 - - + -
479A GLU* 6.1 0.7 - - - +
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Residues in contact with GLY 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 LYS 2.9 9.8 + - - -
458A ASN 2.9 9.5 + - - -
460A LEU* 1.3 75.9 - - - +
462A VAL* 1.3 60.9 + - - +
464A TYR* 3.2 9.6 + - - +
465A LEU* 3.1 23.4 + - - +
473A ALA* 3.6 2.7 - - - +
476A VAL* 4.0 12.6 - - - -
477A TYR* 3.4 24.7 - - - -
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Residues in contact with VAL 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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431A GLN* 4.9 6.3 - - - +
458A ASN 3.1 8.3 + - - +
459A ASP* 3.2 11.4 + - - +
461A GLY* 1.3 72.5 - - - +
463A GLY* 1.3 65.8 + - - +
465A LEU* 2.9 18.1 + - - +
466A LEU* 2.9 31.7 + - + +
477A TYR* 3.5 14.4 - - - +
489A PHE* 3.8 20.4 - - + -
493A HIS* 4.0 9.9 - - - +
108B TYR* 4.0 20.9 - - + +
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Residues in contact with GLY 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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431A GLN* 4.4 9.6 - - - +
436A MET* 5.1 2.3 - - - +
439A SER* 6.1 0.4 - - - -
440A LEU* 3.9 14.3 - - - +
443A LEU* 3.9 19.5 - - - +
459A ASP 3.0 7.5 + - - -
460A LEU 3.0 9.6 + - - -
462A VAL* 1.3 77.7 - - - +
464A TYR* 1.3 60.5 + - - +
466A LEU* 3.6 9.9 + - - +
467A ILE* 3.7 18.2 + - - +
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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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440A LEU* 3.9 27.1 - - + -
444A GLN* 3.2 26.4 + - - +
460A LEU* 3.1 45.3 + - + +
461A GLY 3.5 6.5 - - - +
462A VAL 3.1 0.6 - - - -
463A GLY* 1.3 73.7 - - - +
465A LEU* 1.3 61.9 + - - +
467A ILE* 3.1 11.2 - - - +
469A ASP* 2.8 54.1 + - + +
472A ASN* 3.4 35.4 + - + -
473A ALA* 3.7 6.7 - - + -
476A VAL* 3.7 23.8 - - + -
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Residues in contact with LEU 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 GLY 3.1 17.4 + - - +
462A VAL* 2.9 10.4 + - - +
464A TYR* 1.3 78.3 - - - +
466A LEU* 1.3 59.1 + - - +
467A ILE 3.2 0.9 - - - -
468A GLY* 3.2 13.2 + - - +
469A ASP 4.7 1.8 - - - +
470A ASN* 3.6 25.0 + - - +
473A ALA* 3.8 16.2 - - + -
477A TYR* 4.3 8.1 - - + +
493A HIS* 3.6 31.9 - - + +
496A PHE* 4.9 5.6 - - + -
497A ILE* 3.9 16.6 - - + -
108B TYR* 3.7 45.7 - - + +
109B THR* 5.1 1.2 + - - -
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Residues in contact with LEU 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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431A GLN* 3.7 37.7 - - + +
436A MET* 4.2 34.7 - - + +
462A VAL* 2.9 27.8 + - + +
463A GLY* 4.0 6.3 - - - +
464A TYR 3.2 0.4 - - - -
465A LEU* 1.3 76.3 - - - +
467A ILE* 1.3 61.9 + - - +
468A GLY 3.4 0.2 - - - -
108B TYR* 3.8 13.5 - - + -
109B THR* 3.6 39.9 + - + +
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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