Contacts of the helix formed by residues 452 - 466 (chain D) in PDB entry 5ZR1
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 LEU 452 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412D TYR* 3.3 6.7 - - - +
450D LEU* 4.7 12.1 - - + +
451D TRP* 1.3 79.7 - - - +
453D LYS* 1.3 67.1 + - - +
454D LYS* 3.3 23.8 - - + +
455D ASP* 3.3 21.2 + - - +
456D VAL* 3.2 24.4 + - - +
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Residues in contact with LYS 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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408D PHE* 3.6 46.1 - - + -
409D ASN* 3.7 20.5 - - - +
412D TYR* 3.5 40.4 + - + -
452D LEU* 1.3 78.0 - - - +
454D LYS* 1.3 60.8 + - - +
455D ASP 3.5 0.5 + - - -
457D LYS* 3.9 6.1 + - - +
500D ASP* 5.5 0.4 + - + -
375E TYR* 6.1 1.4 - - - -
457E GLU* 3.1 29.0 + - + +
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Residues in contact with LYS 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LYS* 6.4 1.6 - - - -
253C GLN* 4.2 12.1 + - - -
452D LEU* 4.2 19.1 - - + +
453D LYS* 1.3 79.0 - - - +
455D ASP* 1.3 80.7 + - - +
457D LYS* 3.8 16.7 - - - +
458D ASN 4.8 0.3 + - - -
250E TYR* 5.1 1.7 + - - -
294E SER* 6.1 0.7 - - - +
295E THR* 5.9 0.4 - - - +
296E ASP* 5.9 1.0 + - - -
298E ASN* 4.1 25.2 - - - +
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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
----------------------------------------------------------
386D LEU* 5.0 0.6 - - - +
451D TRP* 3.7 34.0 - - + -
452D LEU* 3.3 28.2 + - - +
453D LYS 3.3 0.8 - - - -
454D LYS* 1.3 96.3 - - - +
456D VAL* 1.3 64.8 + - - +
457D LYS 3.2 2.3 + - - -
458D ASN* 3.6 5.1 + - - +
459D VAL* 4.1 4.0 + - - +
250E TYR* 3.2 30.6 - - + -
294E SER* 6.0 1.2 - - - -
295E THR* 3.3 26.5 + - - +
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Residues in contact with VAL 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D LEU* 4.2 12.8 - - + -
390D ILE* 3.7 35.0 - - + -
408D PHE* 3.6 25.1 - - + -
412D TYR* 3.7 20.4 - - + -
415D TYR* 4.6 1.6 - - + -
451D TRP* 3.8 21.1 - - + -
452D LEU 3.2 16.2 + - - +
453D LYS 3.9 0.4 + - - -
455D ASP* 1.3 73.4 - - - +
457D LYS* 1.3 53.8 + - - +
458D ASN 3.2 1.1 - - - -
459D VAL* 3.0 9.0 + - + -
460D TRP* 2.7 33.4 + - - +
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Residues in contact with LYS 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C GLU 4.2 10.6 + - - +
249C LYS* 4.1 23.8 - - + +
251C LEU 3.1 20.7 + - - -
252C ARG 4.1 0.2 - - - -
253C GLN* 3.8 23.3 - - - +
256C ILE* 5.2 0.4 - - - +
408D PHE* 3.9 7.1 - - + -
453D LYS 3.9 10.3 + - - +
454D LYS* 3.8 15.7 - - - +
455D ASP 3.2 0.6 - - - -
456D VAL* 1.3 77.3 - - - +
458D ASN* 1.3 61.4 + - - +
460D TRP* 3.4 7.1 + - - +
461D GLU* 2.5 54.8 + - - +
499D PHE* 3.6 34.4 - - + -
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Residues in contact with ASN 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C GLN* 3.9 18.0 - - + +
254C SER* 5.2 1.4 + - - -
257C ARG* 3.1 38.3 + - - +
454D LYS 4.8 0.4 + - - -
455D ASP 3.6 2.2 + - - -
456D VAL 3.2 0.6 - - - -
457D LYS* 1.3 75.6 - - - +
459D VAL* 1.3 64.1 + - - +
461D GLU* 3.4 5.5 + - - +
462D ASN* 3.0 37.3 + - - +
250E TYR* 3.5 47.6 + - + +
251E THR* 4.5 6.1 - - - +
254E ASP* 5.3 0.9 + - - +
257E ALA* 4.9 2.6 - - - +
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Residues in contact with VAL 459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386D LEU* 3.7 32.3 - - + +
387D GLU* 3.7 36.5 - - + +
390D ILE* 4.1 17.9 - - + -
455D ASP 4.4 5.2 - - - +
456D VAL* 3.0 10.9 + - - +
458D ASN* 1.3 75.3 - - - +
460D TRP* 1.3 63.2 + - - +
462D ASN* 3.4 8.7 + - - +
463D LEU* 3.3 25.2 + - + +
249E SER 4.0 4.5 - - - +
250E TYR 3.4 22.7 - - - +
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Residues in contact with TRP 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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390D ILE* 3.6 25.1 - - + -
394D ALA* 4.4 0.2 - - + -
406D PHE* 3.5 30.1 - + - -
407D ASN 3.4 23.8 - - - -
408D PHE* 3.4 34.1 - + + +
411D ALA* 3.6 19.7 - - + -
456D VAL* 2.7 19.2 + - - +
457D LYS* 3.6 6.7 - - - +
458D ASN 3.3 0.2 - - - -
459D VAL* 1.3 76.9 - - - +
461D GLU* 1.3 59.4 + - + +
463D LEU* 3.6 5.7 + - - +
464D VAL* 3.3 27.6 + - + +
469D PHE* 3.5 23.3 - + - -
499D PHE* 3.5 26.6 + + + -
504D TYR* 3.4 34.8 - + - -
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Residues in contact with GLU 461 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ARG* 3.6 27.6 - - + +
253C GLN* 2.9 30.4 + - - +
254C SER 4.5 0.9 + - - -
457D LYS* 2.5 48.1 + - - +
458D ASN* 4.0 5.3 - - - +
459D VAL 3.3 0.4 - - - -
460D TRP* 1.3 75.2 - - + +
462D ASN* 1.3 65.3 + - - +
463D LEU 3.4 0.2 - - - -
464D VAL* 3.6 10.7 + - + +
465D GLN* 3.3 23.6 + - - +
499D PHE* 3.6 22.3 - - + -
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Residues in contact with ASN 462 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387D GLU* 3.9 14.8 + - - +
458D ASN* 3.0 35.8 + - - +
459D VAL* 3.9 6.3 - - - +
460D TRP 3.3 0.4 - - - -
461D GLU* 1.3 79.2 - - - +
463D LEU* 1.3 60.3 + - + +
464D VAL 3.2 0.2 - - - -
465D GLN* 3.3 25.7 + - - +
466D LEU* 3.0 42.2 + - + +
191E ARG* 6.3 0.9 - - - +
250E TYR 4.7 0.4 + - - -
251E THR 3.6 22.6 + - - -
254E ASP* 4.1 12.2 + - - +
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Residues in contact with LEU 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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383D LEU* 4.2 19.3 - - + -
387D GLU* 3.8 29.6 - - + +
390D ILE* 4.0 17.7 - - + -
391D LEU* 4.1 11.7 - - + +
459D VAL* 3.3 19.4 + - + +
460D TRP* 3.9 1.1 - - - +
461D GLU 3.4 0.2 - - - -
462D ASN* 1.3 75.4 - - + +
464D VAL* 1.3 63.2 + - - +
466D LEU* 4.0 1.3 - - + -
467D ASP 3.9 0.7 + - - -
468D PHE* 3.0 52.0 + - + -
469D PHE* 3.2 42.4 + - + -
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Residues in contact with VAL 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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460D TRP* 3.3 21.2 + - + +
461D GLU* 3.6 12.1 - - + +
462D ASN 3.2 0.4 - - - -
463D LEU* 1.3 79.4 - - - +
465D GLN* 1.3 64.7 + - + +
467D ASP* 3.3 15.2 + - - +
469D PHE* 3.7 29.0 - - + +
470D THR* 6.1 0.2 - - - -
471D GLU 6.3 0.2 - - - +
504D TYR* 4.1 35.9 - - + +
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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 GLU 3.3 10.4 + - - +
462D ASN* 3.3 33.5 + - - +
464D VAL* 1.3 81.1 - - + +
466D LEU* 1.3 62.2 + - + +
467D ASP* 3.3 4.0 + - - -
38E TYR* 3.7 17.2 - - + -
39E SER* 5.4 11.5 - - - -
172E GLU* 5.5 2.8 - - - +
254E ASP* 5.3 5.5 + - - -
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Residues in contact with LEU 466 (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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379D ARG* 2.4 38.6 + - + +
383D LEU* 4.4 13.9 - - + -
387D GLU* 5.6 0.7 - - - +
462D ASN* 3.0 26.7 + - + +
463D LEU* 3.9 1.1 + - + -
464D VAL 3.3 0.6 - - - -
465D GLN* 1.3 83.1 - - + +
467D ASP* 1.3 61.7 + - - +
468D PHE* 3.4 29.9 + - + -
38E TYR* 3.7 33.9 - - + -
191E ARG* 3.7 44.6 - - - +
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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