Contacts of the helix formed by residues 442 - 451 (chain A) in PDB entry 3ZRH
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 ASP 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A ALA 5.4 0.3 - - - +
441A GLY* 1.3 73.7 - - - +
443A CYS* 1.3 60.6 + - - +
444A LEU* 3.1 4.7 - - - +
445A LEU* 3.0 27.0 + - + +
446A ASP* 2.9 35.5 + - - +
457A ASP* 5.0 2.2 - - + +
460A SER* 5.9 1.1 - - - -
463A ARG* 2.6 41.8 + - - +
517A PRO* 4.8 1.0 - - - +
518A GLY* 3.2 25.5 + - - -
519A ALA 4.7 6.4 + - - -
521A LEU* 5.6 2.0 - - - -
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Residues in contact with CYS 443 (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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437A ASN* 3.9 9.5 + - - +
438A ARG 5.0 3.6 - - - +
439A THR* 5.6 0.4 - - - -
441A GLY* 3.1 9.7 - - - +
442A ASP* 1.3 78.4 - - - +
444A LEU* 1.3 63.6 + - - +
446A ASP* 4.4 4.5 - - - -
447A SER* 2.8 35.6 + - - -
584A GLY 4.3 6.5 - - - -
585A HIS* 3.4 36.3 - - + +
586A PHE* 3.4 34.8 - - - +
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Residues in contact with LEU 444 (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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442A ASP* 3.1 0.8 - - - -
443A CYS* 1.3 84.4 - - - +
445A LEU* 1.3 58.0 + - + +
447A SER* 3.6 0.9 - - - -
448A VAL* 3.1 26.2 + - + +
521A LEU* 4.0 39.7 - - + +
522A GLU 5.0 0.4 - - - +
525A HIS* 4.1 11.2 - - + -
526A ILE* 4.3 17.3 - - + -
529A LEU* 3.4 32.5 - - + -
579A LEU* 3.9 26.2 - - + -
586A PHE* 3.9 31.6 - - + -
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Residues in contact with LEU 445 (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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442A ASP* 3.0 31.4 + - + +
444A LEU* 1.3 73.8 - - + +
446A ASP* 1.3 67.9 + - - +
448A VAL* 3.4 3.6 + - - +
449A LEU* 3.1 27.5 + - - +
457A ASP* 4.0 15.0 - - + +
462A LEU* 3.4 28.1 - - + +
463A ARG* 3.6 48.2 - - + +
466A LEU* 4.2 14.1 - - + -
521A LEU* 3.9 15.9 - - + -
529A LEU* 4.3 9.0 - - + -
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Residues in contact with ASP 446 (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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437A ASN* 4.3 18.4 - - + +
438A ARG* 4.6 21.1 - - - +
441A GLY 4.7 3.1 - - - +
442A ASP* 2.9 24.1 + - - +
443A CYS* 4.0 4.3 - - - +
445A LEU* 1.3 76.9 - - - +
447A SER* 1.3 56.9 + - - +
449A LEU* 3.4 0.9 + - - -
450A GLN* 2.9 36.6 + - - +
455A ILE 3.8 1.4 - - - +
456A TYR* 3.5 20.1 - - + +
457A ASP* 2.8 31.6 + - - +
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Residues in contact with SER 447 (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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437A ASN* 3.0 8.3 + - - -
443A CYS 2.8 22.4 + - - -
444A LEU 3.6 4.3 - - - -
446A ASP* 1.3 75.6 - - - +
448A VAL* 1.3 60.3 - - - +
450A GLN* 3.3 7.9 + - - -
451A ALA* 2.9 25.6 + - - +
579A LEU* 4.0 11.0 - - - -
586A PHE* 3.0 25.6 + - - -
587A SER* 3.2 11.0 - - - -
588A ALA* 3.2 19.7 + - - +
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Residues in contact with VAL 448 (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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444A LEU* 3.1 32.1 + - + +
445A LEU 3.9 4.0 - - - +
447A SER* 1.3 75.0 - - - +
449A LEU* 1.3 59.9 + - + +
451A ALA* 3.3 6.6 + - - +
452A THR* 2.9 27.4 - - + +
462A LEU* 4.1 17.0 - - + -
529A LEU* 4.1 18.2 - - + -
533A LEU* 3.7 37.5 - - + -
537A ILE* 4.9 3.8 - - + -
577A ILE* 4.3 14.2 - - + +
579A LEU* 4.1 13.5 - - + -
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Residues in contact with LEU 449 (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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359A ILE* 4.1 20.0 - - + -
375A LEU* 6.2 3.4 - - + -
445A LEU 3.1 15.6 + - - +
446A ASP 3.9 0.9 - - - +
448A VAL* 1.3 74.9 - - + +
450A GLN* 1.3 61.2 + - - +
452A THR* 3.4 15.7 - - + -
453A TRP* 2.9 41.4 + - + -
454A GLY 2.9 6.8 + - - -
455A ILE* 3.1 21.0 + - + +
456A TYR 3.6 7.6 - - - +
457A ASP* 3.5 43.1 - - + +
461A VAL* 5.6 3.8 - - + -
462A LEU* 4.0 22.9 - - + +
533A LEU* 6.2 1.1 - - + -
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Residues in contact with GLN 450 (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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343A ILE* 4.0 22.4 - - + +
381A PHE* 3.4 17.3 - - - +
435A LEU* 4.0 24.4 - - + +
436A TRP 2.9 26.0 + - - +
437A ASN* 3.5 27.7 + - - +
446A ASP* 2.9 22.8 + - - +
447A SER* 3.8 6.5 - - - +
449A LEU* 1.3 71.8 - - - +
451A ALA* 1.3 61.3 + - - +
452A THR 3.0 6.1 + - - -
454A GLY* 3.6 17.4 - - - +
455A ILE* 3.1 16.5 + - - +
456A TYR* 4.7 4.8 - - - +
588A ALA* 4.1 9.5 - - + +
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Residues in contact with ALA 451 (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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380A THR* 3.8 3.5 - - - -
381A PHE* 2.9 24.4 + - - +
447A SER 2.9 16.6 + - - +
448A VAL 3.7 6.1 - - - +
449A LEU 3.3 0.6 - - - -
450A GLN* 1.3 75.8 - - - +
452A THR* 1.3 57.3 + - - +
577A ILE* 4.1 33.5 - - + +
578A ALA 4.7 7.4 - - - +
579A LEU* 4.7 0.7 - - + -
588A ALA* 3.9 14.6 - - + +
589A LEU 5.4 0.4 - - - +
590A VAL* 4.2 12.8 - - + +
665A GLN* 5.9 0.3 + - - -
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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