Contacts of the helix formed by residues 395 - 406 (chain A) in PDB entry 1JZ3
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 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ARG* 3.4 33.1 - - + +
211A ASP* 3.7 27.0 + - - -
358A GLU* 2.9 18.9 + - - +
367A MET* 4.1 24.4 + - + -
368A ASP* 5.8 1.0 - - - -
369A GLU 6.4 0.2 - - - -
372A MET* 3.5 20.6 - - + +
394A ASN* 1.4 73.7 - - - +
396A PRO* 1.3 80.6 - - + +
397A LEU* 2.9 48.2 + - + +
398A TRP* 3.0 17.7 + - - +
399A TYR* 3.6 2.6 - - - -
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Residues in contact with PRO 396 (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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32A PRO* 5.3 13.2 - - + -
144A ASP* 3.9 34.1 - - + +
210A ARG* 4.9 1.6 - - - -
211A ASP* 5.6 0.7 - - - +
394A ASN 3.4 3.8 - - - +
395A HIS* 1.3 98.5 - - + +
397A LEU* 1.3 62.7 + - - +
398A TRP 3.2 0.9 + - - -
399A TYR* 3.4 23.2 + - + +
400A THR* 3.8 9.8 + - - -
446A ARG* 4.3 18.2 - - - +
450A HIS* 4.7 3.8 + - - +
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Residues in contact with LEU 397 (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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369A GLU* 3.7 49.4 - - + +
372A MET* 4.1 8.7 - - - -
395A HIS* 2.9 25.1 + - + +
396A PRO* 1.3 79.7 - - - +
398A TRP* 1.3 63.4 + - - +
400A THR* 3.2 24.3 + - + +
401A LEU* 3.0 33.2 + - + +
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Residues in contact with TRP 398 (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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356A ARG* 3.5 51.1 - - - +
372A MET* 3.8 37.8 - - + -
375A ASP* 4.6 0.7 - - + -
376A ILE* 3.5 33.4 - - + -
379A MET* 4.4 6.7 - - - -
387A VAL* 3.9 27.0 - - + +
389A CYS* 4.2 12.4 - - - -
394A ASN* 3.3 31.3 + - + +
395A HIS 3.0 15.3 + - - +
397A LEU* 1.3 78.6 - - - +
399A TYR* 1.3 64.6 + + - +
401A LEU* 3.2 5.4 + - + +
402A CYS* 2.9 49.6 + - - -
407A LEU* 4.8 2.5 - - + -
409A VAL* 4.9 1.3 - - + +
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Residues in contact with TYR 399 (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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389A CYS* 4.1 5.1 - - - -
393A PRO* 3.4 0.2 - - - +
394A ASN* 2.7 40.4 + - + +
395A HIS 3.6 5.6 - - - -
396A PRO* 3.6 14.8 - - + +
397A LEU 3.2 0.2 - - - -
398A TRP* 1.3 78.3 - + - +
400A THR* 1.3 55.7 + - - +
402A CYS* 3.2 2.4 + - - +
403A ASP* 2.8 39.8 + - - +
409A VAL* 4.4 13.7 - - + -
411A ASP* 2.6 38.8 + - - -
446A ARG* 3.2 23.9 + - - -
447A ASP* 3.4 11.0 - - - -
450A HIS* 3.4 32.8 - + + +
452A SER* 3.4 6.6 + - - +
453A VAL* 3.7 21.5 - - + -
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Residues in contact with THR 400 (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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45A ASP* 5.4 0.7 - - - +
329A ASP* 4.7 2.7 - - - +
396A PRO 3.8 9.4 + - - -
397A LEU* 3.2 26.4 + - + +
399A TYR* 1.3 76.1 - - - +
401A LEU* 1.3 66.6 + - + +
403A ASP* 3.2 13.0 + - - +
404A ARG* 3.0 59.6 + - - +
450A HIS* 3.8 10.4 - - - -
8404A DMS 5.6 1.6 + - - -
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Residues in contact with LEU 401 (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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369A GLU* 5.4 3.6 - - + +
372A MET* 3.5 37.7 - - + -
373A VAL* 3.8 20.2 - - + -
376A ILE* 3.3 21.3 - - + -
397A LEU* 3.0 36.3 + - + +
398A TRP* 3.6 5.2 - - - +
400A THR* 1.3 78.4 - - + +
402A CYS* 1.3 60.5 + - - +
404A ARG* 4.7 5.2 - - + -
405A TYR* 2.8 57.7 + - + +
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Residues in contact with CYS 402 (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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301A TRP* 3.9 1.2 - - - -
376A ILE* 4.5 3.8 - - - -
387A VAL* 4.3 0.4 - - - -
398A TRP* 2.9 59.6 + - - +
399A TYR* 3.8 0.7 - - - +
401A LEU* 1.3 73.0 - - - +
403A ASP* 1.3 64.1 + - - +
405A TYR* 5.1 0.7 - - - -
406A GLY* 2.9 23.9 + - - +
407A LEU* 3.3 27.2 + - + +
409A VAL* 3.7 16.6 - - + -
452A SER* 3.5 24.1 - - - +
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Residues in contact with ASP 403 (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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301A TRP* 2.9 27.7 + - - +
306A PRO* 3.6 3.6 - - - +
308A LEU* 3.6 15.2 - - + +
329A ASP* 4.5 12.0 - - - +
399A TYR 2.8 16.2 + - - +
400A THR* 3.3 10.4 - - - +
402A CYS* 1.3 78.9 - - - +
404A ARG* 1.3 61.3 + - + +
450A HIS* 2.7 27.4 + - - +
451A PRO* 3.4 23.3 - - + +
452A SER* 2.6 43.4 + - - -
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Residues in contact with ARG 404 (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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45A ASP* 2.7 35.5 + - - +
306A PRO* 3.4 17.5 - - - +
308A LEU* 3.7 20.6 - - + +
310A ARG* 4.0 1.6 - - - +
329A ASP* 2.9 32.0 + - - +
400A THR* 3.0 38.1 + - - +
401A LEU* 4.1 6.7 - - + +
403A ASP* 1.3 76.1 - - - +
405A TYR* 1.3 68.5 - - + +
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Residues in contact with TYR 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PRO* 3.6 10.7 - - - +
373A VAL* 3.8 26.3 - - + +
376A ILE* 3.7 31.0 - - + -
377A LEU* 4.0 10.8 - - + +
380A LYS* 3.0 26.0 + - + -
401A LEU* 2.8 53.7 + - + +
402A CYS* 5.1 0.4 - - - -
404A ARG* 1.3 78.9 - - + +
406A GLY* 1.3 60.6 + - - +
707A ALA* 3.6 36.5 + - + -
708A TRP* 4.3 17.6 - + + -
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Residues in contact with GLY 406 (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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301A TRP* 4.2 3.8 - - - -
303A ALA* 3.5 22.3 - - - +
306A PRO* 3.8 16.8 - - - -
380A LYS* 2.8 24.6 + - - -
402A CYS 2.9 13.1 + - - -
404A ARG 3.4 1.8 - - - -
405A TYR* 1.3 77.8 - - - +
407A LEU* 1.3 65.6 + - - +
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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