Contacts of the helix formed by residues 438 - 449 (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 HIS 438 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156D ALA* 5.0 2.9 - - + -
157D GLY* 3.8 16.7 - - - -
265D ARG* 5.1 2.2 - - - -
322D LEU* 4.1 14.6 - - + -
425D PHE* 4.0 11.6 - + + -
436D TYR* 5.7 0.9 - - - -
437D LEU* 1.3 74.3 - - - +
439D ASP* 1.3 67.3 + - + +
440D LEU* 3.1 42.3 + - + +
441D GLN* 2.8 38.4 + - - +
442D VAL* 3.1 9.4 + - - +
903D ADP 2.9 60.0 + - - -
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Residues in contact with ASP 439 (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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189D LYS 5.7 0.2 + - - -
244D ASP* 3.9 12.5 - - - +
246D TRP* 4.8 5.5 + - - -
265D ARG* 3.4 28.8 + - - +
391D LYS* 3.4 46.6 + - + +
392D ASP* 3.8 17.5 + - - +
437D LEU 3.7 2.0 + - - +
438D HIS* 1.3 77.7 + - - +
440D LEU* 1.3 58.6 + - + +
442D VAL* 3.2 4.5 + - - +
443D ASP* 3.0 33.8 + - - +
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Residues in contact with LEU 440 (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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156D ALA* 4.2 25.4 - - + +
157D GLY* 4.4 4.9 - - - -
265D ARG* 5.3 1.8 - - - +
320D SER* 5.4 5.4 - - - +
322D LEU* 4.6 10.1 - - + -
352D ARG* 4.8 0.3 + - - -
359D TYR* 3.2 50.0 + - + -
364D LEU* 3.3 36.9 - - + +
438D HIS* 3.1 27.7 + - + +
439D ASP* 1.3 84.0 - - + +
441D GLN* 1.3 55.7 + - - +
443D ASP* 3.5 8.7 - - - +
444D PHE* 3.2 20.1 + - - +
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Residues in contact with GLN 441 (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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322D LEU* 4.0 21.4 - - + +
326D LEU* 4.3 0.2 - - - +
364D LEU* 5.1 0.4 - - + -
368D MET* 3.7 29.9 - - + -
422D SER 2.8 28.2 + - - -
423D LEU* 3.6 16.3 + - - +
425D PHE* 3.2 15.7 - - - -
437D LEU* 3.8 17.9 - - + +
438D HIS* 2.8 30.0 + - - +
440D LEU* 1.3 75.8 - - - +
442D VAL* 1.3 65.2 + - - +
443D ASP 3.3 0.2 - - - -
444D PHE* 3.3 6.9 + - - +
445D LEU* 3.1 31.2 + - - +
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Residues in contact with VAL 442 (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 5.5 1.5 - - - +
389D LEU 3.9 19.1 - - - +
390D GLN* 4.3 2.9 - - - +
391D LYS* 3.6 44.9 - - + +
437D LEU* 3.8 27.4 - - + +
438D HIS 3.1 13.3 + - - +
439D ASP* 3.2 8.0 + - - +
441D GLN* 1.3 77.0 - - - +
443D ASP* 1.3 57.3 + - - +
445D LEU* 3.3 3.6 + - - +
446D THR* 2.9 44.1 + - - +
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Residues in contact with ASP 443 (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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352D ARG* 3.5 12.5 + - - +
354D ARG* 4.4 15.2 + - - +
359D TYR* 2.8 40.2 + - - +
391D LYS* 2.7 34.8 + - - -
439D ASP* 3.0 16.1 + - - +
440D LEU* 3.5 7.7 - - - +
441D GLN 3.3 0.2 - - - -
442D VAL* 1.3 75.1 - - - +
444D PHE* 1.3 61.6 + - - +
446D THR* 3.9 6.5 - - - +
447D GLU* 3.1 25.1 + - - +
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Residues in contact with PHE 444 (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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350D PHE* 3.5 26.0 - + - -
352D ARG* 3.9 7.8 - - - +
364D LEU* 5.3 0.4 - - + -
365D ASP* 3.3 38.6 - - - +
368D MET* 3.6 36.1 - - + -
369D SER* 3.6 22.7 - - - -
372D VAL* 4.2 15.5 - - + -
440D LEU 3.2 11.2 + - - +
441D GLN* 3.6 9.4 - - - +
442D VAL 3.3 0.2 - - - -
443D ASP* 1.3 81.0 - - - +
445D LEU* 1.3 60.9 + - + +
447D GLU* 3.6 2.5 - - - +
448D LYS* 2.8 63.9 + - + +
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Residues in contact with LEU 445 (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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368D MET* 4.9 0.7 - - + -
372D VAL* 5.2 0.9 - - + -
383D TYR* 3.7 44.9 - - + +
384D THR* 5.2 0.4 - - - -
386D LEU* 4.3 1.6 - - + -
387D SER* 3.5 31.2 + - - +
437D LEU* 3.6 31.6 - - + -
441D GLN 3.1 17.8 + - - +
442D VAL* 3.9 3.6 - - - +
444D PHE* 1.3 89.8 - - + +
446D THR* 1.3 60.4 + - - +
448D LYS* 4.3 3.1 - - + -
449D ASN* 2.9 52.8 + - - +
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Residues in contact with THR 446 (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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354D ARG* 5.7 11.4 - - - +
387D SER 4.4 9.2 + - - -
442D VAL* 2.9 28.3 + - - +
443D ASP* 3.9 6.7 - - - +
445D LEU* 1.3 77.5 - - - +
447D GLU* 1.3 58.5 + - - +
450D CYS* 3.1 33.7 + - - +
453D LEU* 3.8 22.5 - - + +
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Residues in contact with GLU 447 (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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350D PHE* 4.0 20.2 - - + -
351D LYS 4.3 2.5 - - - +
352D ARG* 3.3 25.3 + - - +
353D ILE* 2.8 55.1 + - + +
354D ARG* 3.1 26.0 + - - +
443D ASP 3.1 18.7 + - - +
444D PHE* 3.6 3.6 - - - +
446D THR* 1.3 79.0 - - - +
448D LYS* 1.3 65.7 + - - +
449D ASN 3.4 0.5 + - - -
450D CYS* 3.6 14.1 + - - +
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Residues in contact with LYS 448 (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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350D PHE* 4.0 22.4 - - + -
369D SER* 5.9 3.6 - - - +
372D VAL* 4.2 22.4 - - + +
384D THR* 4.4 10.3 + - - -
444D PHE* 2.8 47.9 + - + +
445D LEU* 4.1 4.0 - - + +
447D GLU* 1.3 74.3 - - - +
449D ASN* 1.3 83.5 + - - +
450D CYS 3.8 0.3 + - - -
451D SER* 5.7 0.3 + - - -
452D GLN* 5.8 0.6 - - - +
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Residues in contact with ASN 449 (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* 3.8 24.3 + - + +
387D SER* 2.7 30.7 + - - +
445D LEU* 2.9 37.1 + - - +
446D THR 3.9 2.0 - - - -
448D LYS* 1.3 101.0 + - - +
450D CYS* 1.3 64.5 + - - +
451D SER* 3.2 4.0 - - - -
452D GLN* 3.0 35.8 + - + +
453D LEU* 3.3 13.2 + - + +
456D LEU* 4.8 0.4 - - + -
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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