Contacts of the helix formed by residues 455 - 462 (chain A) in PDB entry 1ZJH
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 ASN 455 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432A LYS* 3.4 16.4 + - + +
433A SER* 5.6 0.6 - - - +
453A THR* 3.0 8.9 + - - +
454A ARG* 1.3 77.4 - - - +
456A PRO* 1.3 69.2 - - - +
457A GLN* 3.0 24.0 + - - +
458A THR* 3.1 26.4 + - - +
459A ALA* 3.1 16.8 + - - +
472A LEU* 4.0 1.1 - - - -
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Residues in contact with PRO 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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454A ARG 3.1 11.9 - - - +
455A ASN* 1.3 84.9 - - - +
457A GLN* 1.3 61.7 + - - +
459A ALA* 3.4 5.4 + - + +
460A ARG* 3.2 45.9 + - - +
472A LEU* 3.9 26.0 - - + -
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Residues in contact with GLN 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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235A ASP* 4.0 18.2 + - - -
236A VAL 4.3 12.9 + - - -
237A ASP* 3.6 9.2 + - - +
263A ASN* 3.1 33.0 - - - +
264A ILE* 4.5 8.3 - - - +
455A ASN* 3.0 11.1 + - - +
456A PRO* 1.3 76.8 - - - +
458A THR* 1.3 65.9 + - - +
460A ARG* 3.3 17.4 + - - +
461A GLN* 2.9 57.6 + - - +
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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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431A THR* 4.5 2.9 - - + -
432A LYS 2.7 23.9 + - - +
433A SER* 3.5 10.4 + - - +
434A GLY* 3.5 34.8 - - - +
438A HIS* 5.8 0.7 - - - +
453A THR* 4.0 13.7 - - + +
455A ASN* 3.1 22.0 + - - -
457A GLN* 1.3 76.4 - - - +
459A ALA* 1.3 65.0 + - - +
461A GLN* 3.3 9.3 + - - +
462A ALA* 3.0 26.7 + - + +
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Residues in contact with ALA 459 (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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106A PRO* 3.8 24.2 - - + +
453A THR* 3.9 13.6 - - + +
455A ASN 3.1 10.6 + - - +
456A PRO* 3.4 11.0 - - + +
458A THR* 1.3 80.0 - - - +
460A ARG* 1.3 62.0 + - - +
462A ALA* 3.5 2.8 - - - +
463A HIS* 4.2 0.2 - - - -
470A PRO* 3.2 35.6 - - + +
472A LEU* 4.4 16.8 - - + +
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Residues in contact with ARG 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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91A ARG* 6.0 3.9 - - - +
104A TYR* 6.0 0.6 + - - +
106A PRO* 4.1 14.8 - - + -
107A VAL 3.4 26.0 - - - +
108A ALA* 3.5 17.0 - - + +
109A VAL* 6.0 0.9 - - - -
235A ASP* 3.7 23.4 + - - -
237A ASP* 2.9 41.0 + - - +
238A MET* 4.7 0.7 - - - +
456A PRO* 3.2 35.6 + - - +
457A GLN* 3.6 22.8 - - - +
458A THR 3.2 0.2 - - - -
459A ALA* 1.3 75.7 - - - +
461A GLN* 1.3 61.2 + - - +
462A ALA 3.3 0.9 + - - -
463A HIS* 3.4 23.1 + - - +
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Residues in contact with GLN 461 (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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237A ASP* 3.0 36.8 + - + +
238A MET* 4.4 9.0 - - + -
263A ASN* 2.9 27.3 + - - +
265A LYS* 3.5 33.3 - - + +
433A SER 5.4 2.9 - - - +
438A HIS* 5.5 2.2 - - + +
457A GLN* 2.9 43.4 + - - +
458A THR* 4.0 6.0 - - - +
460A ARG* 1.3 74.1 - - - +
462A ALA* 1.3 64.2 + - - +
464A LEU* 3.1 25.8 + - + +
465A TYR* 4.3 5.1 - - + -
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Residues in contact with ALA 462 (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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434A GLY* 6.4 0.4 - - - -
437A ALA* 6.3 0.4 - - + -
438A HIS* 4.8 9.6 + - + +
451A ALA* 5.3 3.4 - - + -
458A THR* 3.0 19.6 + - + +
459A ALA 3.5 9.9 - - - +
460A ARG 3.2 0.2 - - - -
461A GLN* 1.3 77.9 - - - +
463A HIS* 1.3 56.0 + - - +
464A LEU 3.0 6.0 + - - -
465A TYR* 3.0 30.4 + - - +
468A ILE* 3.9 21.6 - - + +
470A PRO* 3.7 18.4 - - + -
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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