Contacts of the helix formed by residues 451 - 464 (chain A) in PDB entry 2Z5K
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 LYS 451 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A TRP* 3.6 55.6 - - + +
449A ASP* 2.8 14.3 + - - +
450A LYS* 1.3 105.1 + - + +
452A ALA* 1.3 66.2 + - - +
453A LEU 3.3 0.9 - - - +
454A VAL* 3.1 24.4 + - + +
455A ARG* 3.3 14.4 + - - +
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Residues in contact with ALA 452 (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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319A LYS* 5.3 6.5 - - + -
450A LYS 3.4 4.4 + - - -
451A LYS* 1.3 72.0 - - - +
453A LEU* 1.3 60.1 + - + +
455A ARG* 3.1 26.0 + - - +
456A SER* 2.9 24.7 + - - -
493A ASN* 3.6 33.4 - - + +
496A VAL* 3.4 9.7 - - + +
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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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310A TYR* 3.8 38.1 + - + +
315A ILE* 4.9 11.2 - - + +
318A LEU* 3.9 22.2 - - + -
319A LYS* 4.0 35.4 - - + +
411A TRP* 4.1 29.2 - - + -
415A GLU* 3.7 4.5 - - + +
451A LYS* 3.3 1.8 - - - +
452A ALA* 1.3 78.6 - - + +
454A VAL* 1.3 61.2 + - - +
456A SER* 3.3 25.8 - - - +
457A ILE* 3.4 15.6 - - - +
495A ARG* 4.7 5.4 - - + +
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Residues in contact with VAL 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A TRP* 4.2 31.4 - - + +
414A LYS* 4.6 8.3 - - + -
415A GLU* 4.5 9.6 - - + +
418A ILE* 4.0 13.2 - - + -
446A CYS* 4.0 7.2 - - + +
449A ASP* 3.7 35.0 - - + +
451A LYS* 3.1 19.6 + - + +
453A LEU* 1.3 76.4 - - - +
455A ARG* 1.3 61.3 + - - +
457A ILE* 3.2 13.5 - - - +
458A THR* 2.4 34.7 + - - +
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Residues in contact with ARG 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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446A CYS 4.0 11.2 - - - +
447A LEU* 3.2 29.2 - - - +
448A SER* 4.4 2.5 - - - +
449A ASP 3.1 26.6 + - - +
450A LYS* 3.2 27.1 + - - +
451A LYS 3.6 2.7 - - - +
452A ALA* 3.1 29.3 + - - +
454A VAL* 1.3 74.5 - - - +
456A SER* 1.3 67.0 + - - +
458A THR* 3.4 4.1 + - - -
459A CYS* 3.2 25.7 + - - -
488A ARG* 4.0 7.3 - - - +
491A ASP* 2.7 44.4 + - - -
492A SER* 4.7 4.9 + - - -
493A ASN* 4.3 2.2 - - - +
496A VAL* 4.0 11.3 - - + +
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Residues in contact with SER 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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310A TYR* 5.9 1.1 - - - -
452A ALA 2.9 13.2 + - - -
453A LEU* 3.3 21.6 - - - +
454A VAL 3.2 0.4 - - - -
455A ARG* 1.3 80.8 - - - +
457A ILE* 1.3 64.0 + - - -
459A CYS* 3.1 16.8 + - - +
460A TRP* 3.5 2.8 + - - +
495A ARG* 3.4 39.2 + - - +
496A VAL* 3.9 6.3 + - - +
499A ALA* 3.6 16.0 - - - +
72B TYR* 5.2 7.4 - - - -
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Residues in contact with ILE 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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310A TYR* 6.0 0.2 - - - +
376A ARG* 4.5 1.1 - - - +
415A GLU* 2.8 41.1 - - + +
418A ILE* 3.8 29.2 - - + -
419A LEU* 4.1 21.3 - - + +
453A LEU 3.4 9.2 - - - +
454A VAL* 3.2 28.3 - - - +
456A SER* 1.3 75.9 - - - +
458A THR* 1.3 54.4 + - - +
460A TRP* 3.0 26.8 + - + +
461A THR* 2.6 37.8 + - - +
72B TYR* 4.8 7.0 - - - +
74B PRO* 4.4 11.0 - - + -
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Residues in contact with THR 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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418A ILE* 3.6 22.5 - - - +
443A LEU* 3.1 49.4 - - + +
446A CYS* 3.8 10.4 - - + +
447A LEU* 3.9 12.8 - - + -
454A VAL 2.4 25.5 + - - -
455A ARG* 3.6 7.6 - - - -
456A SER 3.1 0.6 + - - -
457A ILE* 1.3 74.8 - - - +
459A CYS* 1.3 64.9 + - - +
461A THR* 3.9 0.6 - - - -
462A LEU* 2.9 26.5 + - + +
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Residues in contact with CYS 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 3.7 19.4 - - - +
455A ARG 3.2 17.4 + - - -
456A SER 3.1 9.3 + - - +
458A THR* 1.3 76.8 - - - +
460A TRP* 1.3 63.6 + - - +
462A LEU* 3.5 3.7 + - - +
463A SER 3.0 17.3 + - - -
485A LEU* 3.9 9.4 - - - -
488A ARG* 4.2 10.1 - - - -
496A VAL* 4.7 2.0 - - - -
499A ALA* 3.7 20.4 - - - +
500A ALA* 3.7 28.5 - - - -
503A ALA* 3.4 18.3 - - + +
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Residues in contact with TRP 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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419A LEU* 3.9 13.2 - - + -
422A GLY* 3.6 25.6 - - - -
456A SER 3.5 1.6 + - - +
457A ILE* 3.0 20.7 + - + +
459A CYS* 1.3 79.9 - - - +
461A THR* 1.3 80.1 + - - +
463A SER* 2.7 30.4 + - - -
464A ARG* 3.0 39.5 + - - +
499A ALA* 5.0 1.8 - - - +
502A SER* 6.3 1.1 - - - -
503A ALA* 5.0 1.8 - - - +
72B TYR* 3.7 33.4 + + + -
73B ASN* 3.4 22.6 + - + -
74B PRO* 3.2 32.8 - - + +
75B TYR* 3.4 30.5 - + - -
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Residues in contact with THR 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ILE* 2.8 32.9 + - + +
419A LEU* 4.3 0.3 + - - -
421A LEU* 3.6 25.6 - - + -
422A GLY* 3.6 23.9 - - - +
443A LEU* 3.9 10.1 - - + -
457A ILE 2.6 20.8 + - - -
458A THR 4.0 1.6 - - - -
460A TRP* 1.3 87.7 - - - +
462A LEU* 1.3 62.5 + - - +
464A ARG* 3.1 11.6 + - - +
465A TYR* 3.3 15.8 - - + -
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Residues in contact with LEU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A ILE* 3.8 39.9 - - + +
443A LEU* 3.8 31.0 - - + -
444A ILE* 4.1 4.7 - - + +
447A LEU* 3.8 28.0 - - + -
458A THR* 2.9 21.1 + - + +
459A CYS* 3.7 4.3 - - - +
461A THR* 1.3 76.4 - - - +
463A SER* 1.3 58.0 + - - +
465A TYR* 2.9 22.1 + - - +
466A ALA* 3.1 10.6 + - - +
469A VAL* 5.1 1.3 - - + +
481A LEU* 3.6 39.6 - - + +
485A LEU* 5.4 1.1 - - + -
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Residues in contact with SER 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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459A CYS 3.0 13.1 + - - -
460A TRP* 2.7 25.8 + - - -
462A LEU* 1.3 77.3 - - - +
464A ARG* 1.3 63.5 + - - +
465A TYR 3.1 0.6 + - - -
466A ALA* 3.4 22.8 + - - +
481A LEU* 6.2 0.2 - - - -
503A ALA* 3.7 27.7 - - - +
506A THR* 3.4 26.4 + - - +
507A LEU* 6.1 0.9 - - - -
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Residues in contact with ARG 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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384A ASP* 3.6 23.7 + - - -
422A GLY* 2.7 35.3 + - - +
423A ALA 3.7 6.5 + - - -
425A ALA* 3.8 20.1 - - + +
426A GLU* 3.3 45.7 + - - +
429A MET* 4.3 7.6 - - - +
460A TRP* 3.0 44.9 + - + +
461A THR* 3.5 10.3 - - - +
462A LEU 3.0 1.0 - - - -
463A SER* 1.3 84.4 + - - +
465A TYR* 1.3 62.9 + - - +
466A ALA 3.6 0.2 - - - -
73B ASN* 5.7 0.4 + - - -
75B TYR* 4.0 4.3 + - - -
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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