Contacts of the helix formed by residues 453 - 467 (chain A) in PDB entry 5Z66
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 TRP 453 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438A THR* 3.4 21.5 + - - -
446A GLN* 3.0 62.6 + - + -
447A TRP* 3.4 48.6 - + + +
451A ASN* 3.8 5.6 - - + +
452A GLY* 1.3 74.9 - - - -
454A ALA* 1.3 65.7 + - - +
455A PRO* 3.9 5.2 - - + -
456A LEU* 2.9 20.2 + - + +
457A GLN* 3.0 18.4 + - - +
496A GLU* 3.6 37.7 - - + -
497A LYS* 3.5 23.1 - - + +
512A TYR* 4.6 0.4 - - - -
520A TRP* 3.4 29.6 - + - -
609A VDM 4.8 3.1 - - - -
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Residues in contact with ALA 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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453A TRP* 1.3 69.8 - - - +
455A PRO* 1.3 70.9 - - + +
457A GLN* 3.1 12.7 + - - +
458A TRP 3.0 17.8 + - - -
480A PHE* 3.8 18.0 - - + -
496A GLU 5.1 2.4 + - - -
497A LYS* 5.7 0.4 - - - +
498A TYR* 5.7 0.4 - - - -
520A TRP* 3.4 31.2 - - + +
521A SER* 3.7 18.4 + - - +
524A VAL* 3.7 14.8 - - + +
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Residues in contact with PRO 455 (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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160A TRP* 4.4 11.4 - - + -
164A PHE* 3.5 43.2 - - + -
447A TRP* 4.3 5.8 - - + -
453A TRP* 3.4 10.8 - - + -
454A ALA* 1.3 92.5 - - + +
456A LEU* 1.3 58.7 + - + +
458A TRP* 3.3 2.4 + - - +
459A VAL* 2.9 34.9 + - + +
520A TRP* 3.5 43.5 - - + -
524A VAL* 4.5 0.4 - - - -
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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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160A TRP* 4.9 6.5 - - + -
311A TRP* 3.7 36.6 - - + +
403A ALA* 3.9 23.0 - - + +
407A PHE* 4.0 26.2 - - + -
436A ILE* 4.0 5.4 - - + +
438A THR* 3.8 23.8 - - + +
447A TRP* 3.7 25.4 - - + -
453A TRP* 2.9 12.3 + - + +
455A PRO* 1.3 76.9 - - + +
457A GLN* 1.3 64.2 + - - +
459A VAL* 4.0 2.8 - - + +
460A ALA* 2.9 31.4 + - - +
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Residues in contact with GLN 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A GLY* 3.4 8.9 - - - -
436A ILE* 2.9 57.1 + - - +
452A GLY* 3.7 5.1 - - - -
453A TRP 3.0 33.9 + - - +
454A ALA 3.1 5.8 + - - +
456A LEU* 1.3 79.4 - - - +
458A TRP* 1.3 57.3 + - - +
460A ALA* 3.7 1.7 - - - +
461A ALA* 3.0 30.5 + - - +
476A VAL* 3.7 6.7 - - + +
480A PHE* 3.5 39.2 - - + +
524A VAL* 4.8 0.2 - - + -
528A MET* 3.7 18.5 - - + +
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Residues in contact with TRP 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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163A TYR* 4.7 1.6 + - - -
164A PHE* 3.9 14.1 - + + -
167A LEU* 3.4 32.6 - - + +
410A TYR* 4.0 17.0 + + - -
454A ALA 3.0 12.0 + - - +
455A PRO 3.7 6.3 - - - +
456A LEU 3.2 0.2 - - - -
457A GLN* 1.3 75.4 - - - +
459A VAL* 1.3 65.7 + - - +
461A ALA* 3.4 1.9 + - + -
462A GLU* 2.9 62.4 + - + +
524A VAL* 3.8 17.3 - - + -
527A LYS* 3.6 47.3 - - + -
528A MET* 4.0 24.8 - - + +
531A ARG* 3.3 34.5 - - - -
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Residues in contact with VAL 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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164A PHE* 4.3 13.0 - - + -
211A PHE* 5.1 0.2 - - + -
403A ALA 5.2 0.9 - - - +
406A LEU* 4.3 8.7 - - + +
407A PHE* 3.6 49.4 - - + -
410A TYR* 3.6 47.7 - - + +
455A PRO 2.9 22.5 + - - +
456A LEU* 4.0 4.9 - - + +
458A TRP* 1.3 73.7 - - - +
460A ALA* 1.3 58.3 + - - +
463A GLY* 2.9 28.2 + - - -
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Residues in contact with ALA 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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403A ALA* 6.3 0.2 - - + -
406A LEU* 3.8 19.7 - - + +
436A ILE* 3.6 32.5 - - + -
456A LEU 2.9 19.2 + - - +
457A GLN 3.7 3.1 - - - +
459A VAL* 1.3 75.2 - - - +
461A ALA* 1.3 67.0 + - - +
463A GLY* 3.8 0.3 - - - -
464A LEU* 2.9 35.3 + - + +
476A VAL* 4.3 5.6 - - + -
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Residues in contact with ALA 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 GLN 3.0 18.7 + - - +
458A TRP* 3.9 4.7 - - + +
460A ALA* 1.3 75.5 - - - +
462A GLU* 1.3 61.0 + - + +
464A LEU* 4.6 0.7 - - - -
465A GLN* 3.0 19.1 + - - +
473A SER* 2.8 36.2 + - - +
476A VAL* 4.5 4.4 - - + +
477A THR* 3.5 24.0 - - - +
528A MET* 4.2 8.1 - - + -
531A ARG* 4.8 7.6 - - - +
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Residues in contact with GLU 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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410A TYR* 3.7 19.1 - - + -
458A TRP* 2.9 61.2 + - + +
461A ALA* 1.3 74.9 - - - +
463A GLY* 1.3 60.5 + - - +
465A GLN* 3.2 14.0 + - - +
466A ASN* 2.8 40.8 + - - +
531A ARG* 2.8 36.4 + - - -
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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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406A LEU* 4.7 1.8 - - - -
409A LEU* 3.6 12.8 - - - +
410A TYR* 3.6 30.2 - - - +
459A VAL 2.9 16.2 + - - -
460A ALA* 3.8 0.4 - - - -
462A GLU* 1.3 75.3 - - - +
464A LEU* 1.3 62.3 + - - +
466A ASN* 3.2 15.5 + - - +
467A TYR* 3.4 14.6 - - - -
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Residues in contact with LEU 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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406A LEU* 3.9 21.1 - - + +
409A LEU* 4.2 9.4 - - + -
423A ALA* 3.8 35.9 - - + -
426A THR* 4.4 5.6 - - + +
460A ALA* 2.9 27.6 + - + +
463A GLY* 1.3 74.5 - - - +
465A GLN* 1.3 62.4 + - - +
467A TYR* 3.1 8.0 + - - -
469A GLN* 2.9 43.7 + - + +
472A VAL* 3.6 27.6 - - + +
473A SER* 3.8 14.1 - - - +
476A VAL* 4.2 9.4 - - + -
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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
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461A ALA 3.0 19.0 + - - +
462A GLU* 3.5 23.2 + - - +
464A LEU* 1.3 76.2 - - - +
466A ASN* 1.3 68.6 + - - +
467A TYR 3.1 0.9 + - - -
468A GLY* 3.2 12.7 + - - +
469A GLN 4.7 1.3 - - - +
470A GLU* 3.3 36.1 - - - +
473A SER* 3.8 6.0 + - - +
474A MET* 5.0 0.3 - - - +
531A ARG* 3.3 29.1 + - - +
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Residues in contact with ASN 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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409A LEU 3.2 9.2 + - - +
410A TYR* 3.0 28.7 + - - +
412A LYS* 3.6 30.5 - - + +
462A GLU* 2.8 30.3 + - - +
463A GLY 3.2 9.1 + - - +
465A GLN* 1.3 81.9 + - - +
467A TYR* 1.3 73.5 + - + +
468A GLY 3.5 0.6 + - - -
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Residues in contact with TYR 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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409A LEU* 3.3 35.2 - - + -
412A LYS* 3.3 19.7 + - + +
414A ALA* 2.6 46.9 + - + -
416A GLN* 3.1 47.9 + - + +
419A ALA* 3.4 27.8 - - + -
420A ASP* 4.3 0.2 - - - +
463A GLY 3.4 14.6 - - - +
464A LEU 3.1 6.2 + - - +
465A GLN 3.1 1.0 - - - -
466A ASN* 1.3 86.1 - - + +
468A GLY* 1.3 61.8 + - - +
469A GLN* 3.2 13.2 + - + +
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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