Contacts of the helix formed by residues 438 - 449 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B ALA* 4.6 4.3 - - + -
157B GLY* 3.8 9.4 - - - -
265B ARG* 5.4 1.1 - - - -
322B LEU* 4.0 15.7 - - + -
425B PHE* 4.1 12.2 - + + -
436B TYR* 5.6 1.8 - - - -
437B LEU* 1.3 75.2 - - - +
439B ASP* 1.3 77.3 + - + +
440B LEU* 3.2 39.8 + - + +
441B GLN* 2.9 37.5 + - + +
442B VAL* 3.1 9.4 + - - +
901B ADP 2.6 59.2 + - - -
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Residues in contact with ASP 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B LYS* 5.8 0.3 + - - +
244B ASP* 4.0 10.5 - - - +
246B TRP* 4.5 7.1 + - - -
265B ARG* 3.2 28.6 + - - +
391B LYS* 3.6 38.6 + - + +
392B ASP* 3.6 22.4 + - - +
437B LEU 3.6 2.2 + - - +
438B HIS* 1.3 80.0 + - + +
440B LEU* 1.3 65.4 + - + +
442B VAL* 3.2 5.6 + - - +
443B ASP* 3.0 27.1 + - - +
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ALA* 4.2 17.0 - - + +
157B GLY* 4.4 4.5 - - - -
265B ARG* 5.5 3.6 - - - +
322B LEU* 4.7 8.5 - - + -
359B TYR* 3.3 61.2 - - + +
361B TYR* 4.2 10.5 - - + +
364B LEU* 3.2 27.6 - - + +
438B HIS* 3.2 27.0 + - + +
439B ASP* 1.3 82.1 - - + +
441B GLN* 1.3 57.5 + - - +
443B ASP* 3.5 12.7 - - - +
444B PHE* 3.1 21.1 + - - +
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Residues in contact with GLN 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B LEU* 3.8 20.4 - - + +
326B LEU* 4.2 0.6 - - - +
364B LEU* 5.1 1.3 - - + -
368B MET* 3.7 34.3 - - + -
422B SER 2.9 27.3 + - - -
423B LEU* 3.9 9.0 - - - +
425B PHE* 3.3 16.0 - - - -
437B LEU* 3.8 18.7 - - + +
438B HIS* 2.9 32.4 + - + +
440B LEU* 1.3 77.0 - - - +
442B VAL* 1.3 64.2 + - - +
443B ASP 3.3 0.2 - - - -
444B PHE* 3.3 7.9 + - - +
445B LEU* 3.0 31.1 + - - +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387B SER 5.6 1.5 - - - +
389B LEU 4.0 24.2 - - - +
390B GLN* 4.2 3.1 - - - +
391B LYS* 3.7 42.4 - - + +
437B LEU* 3.8 23.6 - - + +
438B HIS 3.1 12.3 + - - +
439B ASP* 3.2 7.8 + - - +
441B GLN* 1.3 76.1 - - - +
443B ASP* 1.3 57.4 + - - +
445B LEU* 3.3 4.0 + - - +
446B THR* 2.9 43.9 + - - +
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Residues in contact with ASP 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ARG* 3.4 9.6 + - - +
354B ARG* 4.1 14.9 + - - +
361B TYR* 2.7 38.7 + - + +
391B LYS* 2.8 31.1 + - - -
439B ASP* 3.0 18.2 + - - +
440B LEU* 3.5 15.5 - - - +
442B VAL* 1.3 75.9 - - - +
444B PHE* 1.3 62.4 + - - +
446B THR* 3.9 6.2 - - - +
447B GLU* 3.1 24.9 + - - +
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Residues in contact with PHE 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B PHE* 3.4 27.8 - + - -
352B ARG* 3.7 8.9 - - - +
364B LEU* 5.5 0.7 - - + -
365B ASP* 3.2 43.3 - - - +
368B MET* 3.7 37.7 - - + -
369B SER* 3.6 21.1 - - - -
372B VAL* 4.3 8.3 - - + -
440B LEU 3.1 11.8 + - - +
441B GLN* 3.3 9.8 + - - +
443B ASP* 1.3 78.7 - - - +
445B LEU* 1.3 60.5 + - + +
447B GLU* 3.3 2.6 + - - +
448B LYS* 2.7 64.3 + - + +
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Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B MET* 4.9 0.4 - - + -
372B VAL* 5.2 0.9 - - + -
383B TYR* 3.8 46.0 - - + +
384B THR* 5.3 0.7 - - - -
386B LEU* 4.2 2.5 - - + +
387B SER* 3.5 31.2 + - - +
437B LEU* 3.8 29.4 - - + -
441B GLN 3.0 16.5 + - - +
442B VAL* 3.9 4.0 - - - +
444B PHE* 1.3 91.6 - - + +
446B THR* 1.3 60.9 + - - +
448B LYS* 4.4 2.2 - - + -
449B ASN* 2.8 53.4 + - - +
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Residues in contact with THR 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B ARG* 5.7 10.3 - - - +
387B SER* 4.3 9.6 + - - -
442B VAL* 2.9 29.1 + - - +
443B ASP* 3.9 6.1 - - - +
445B LEU* 1.3 76.8 - - - +
447B GLU* 1.3 59.5 + - - +
450B CYS* 3.0 32.3 + - + +
453B LEU* 3.9 23.5 - - + +
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Residues in contact with GLU 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B PHE* 3.8 24.9 - - + -
351B LYS 3.3 8.1 - - - +
352B ARG* 3.6 22.1 + - - +
353B ILE* 2.8 47.6 + - - +
354B ARG* 3.4 21.8 + - - +
443B ASP 3.1 18.9 + - - +
444B PHE 3.5 3.1 - - - +
446B THR* 1.3 75.5 - - - +
448B LYS* 1.3 67.2 + - - +
449B ASN 3.3 0.5 + - - -
450B CYS* 3.5 13.2 + - - +
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Residues in contact with LYS 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B PHE* 4.1 21.1 - - + -
369B SER* 6.0 2.2 - - - +
372B VAL* 4.1 22.7 - - + +
384B THR* 4.5 9.5 + - - -
444B PHE* 2.7 49.2 + - + +
445B LEU* 4.1 3.8 - - + +
447B GLU* 1.3 75.6 - - - +
449B ASN* 1.3 82.8 + - - +
450B CYS 3.9 0.3 + - - -
452B GLN* 5.4 1.7 + - - +
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Residues in contact with ASN 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B THR* 3.8 18.2 + - + +
387B SER* 2.8 32.0 + - - +
445B LEU* 2.8 36.9 + - - +
446B THR 3.8 2.2 - - - -
448B LYS* 1.3 104.7 + - - +
450B CYS* 1.3 64.5 + - - +
451B SER* 3.2 3.4 - - - -
452B GLN* 2.9 40.3 + - + +
453B LEU* 3.3 12.8 + - + +
456B LEU* 5.0 0.7 - - + -
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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