Contacts of the strand formed by residues 420 - 427 (chain A) in PDB entry 1JEH
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 ILE 420 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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411A ILE* 4.3 8.7 - - + -
413A ILE* 3.8 9.6 - - + -
419A ARG* 1.3 72.3 - - - +
421A LEU* 1.3 63.0 + - - +
422A GLY 3.8 22.7 - - - +
423A ALA* 4.9 6.7 - - + -
437A ALA* 5.3 2.5 - - + +
440A ALA* 3.8 28.0 - - + +
441A LEU* 3.1 30.8 - - + +
444A GLY* 5.9 1.9 - - - -
445A ALA* 3.0 21.4 + - + +
446A SER 4.0 8.3 - - - +
447A ALA* 4.0 9.4 - - - +
450A VAL* 4.0 6.3 - - + -
464A PHE* 5.0 5.8 - - + -
468A ASN* 3.6 25.4 - - - +
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Residues in contact with LEU 421 (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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373A GLY* 3.3 7.4 - - - -
374A LYS* 3.0 38.3 + - + +
379A LEU* 3.8 38.4 - - + -
384A ILE* 3.8 19.5 - - + -
386A TYR* 4.6 1.6 - - + -
412A LEU 2.9 10.8 + - - +
413A ILE 4.0 4.7 - - - +
414A ASP* 3.8 26.9 - - + +
419A ARG* 3.8 16.8 - - + +
420A ILE* 1.3 76.4 - - - +
422A GLY* 1.3 58.7 + - - +
441A LEU* 4.2 7.8 - - - +
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Residues in contact with GLY 422 (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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372A VAL* 3.4 12.1 - - - -
373A GLY* 4.1 0.4 - - - -
374A LYS 3.6 17.2 + - - -
411A ILE* 3.7 2.9 - - - -
412A LEU* 3.1 29.5 + - - +
420A ILE* 3.7 9.3 - - - +
421A LEU* 1.3 80.8 - - - +
423A ALA* 1.3 61.5 + - - +
424A HIS* 3.9 5.2 - - - -
441A LEU* 5.3 1.3 - - - -
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Residues in contact with ALA 423 (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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371A TRP* 3.2 6.4 - - - +
372A VAL* 3.0 35.1 + - + -
410A LYS 3.4 4.9 - - - -
411A ILE* 3.9 16.4 - - + -
420A ILE* 4.9 4.3 - - + -
422A GLY* 1.3 74.2 - - - +
424A HIS* 1.3 62.9 + - - +
425A ILE* 4.0 2.2 - - + -
434A ILE* 3.3 7.0 - - + +
437A ALA* 3.6 31.2 - - + -
464A PHE* 4.4 2.7 - - + -
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Residues in contact with HIS 424 (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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223A ASP* 3.5 23.3 - - + -
226A VAL* 3.7 23.3 - - + -
370A ALA 3.7 4.0 - - - -
371A TRP* 3.4 31.0 - + + +
372A VAL 4.0 3.2 + - - -
373A GLY 4.4 0.4 + - - -
374A LYS 3.1 26.5 + - - -
375A THR* 3.5 23.8 + - - +
408A PHE* 3.7 7.3 - - - +
410A LYS* 3.0 37.8 + - + +
412A LEU* 3.5 18.7 - - + +
422A GLY* 3.9 2.5 - - - -
423A ALA* 1.3 85.8 + - - +
425A ILE* 1.3 61.8 + - - +
426A ILE 4.0 0.7 + - - -
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Residues in contact with ILE 425 (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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226A VAL* 5.5 0.6 - - - +
368A GLU 3.4 4.5 - - - +
369A VAL* 3.5 1.0 - - - -
370A ALA 3.0 37.2 + - - +
393A PHE* 4.1 5.2 - - + -
408A PHE 3.5 2.2 - - - -
409A VAL* 3.7 36.8 - - + -
423A ALA* 4.6 1.3 - - + -
424A HIS* 1.3 76.8 - - - +
426A ILE* 1.3 68.7 + - - +
427A GLY* 4.4 0.4 - - - +
430A ALA* 3.5 20.6 - - + +
433A MET* 3.5 41.1 - - + -
434A ILE* 3.9 23.6 - - + +
464A PHE* 4.1 10.8 - - + -
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Residues in contact with ILE 426 (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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226A VAL* 3.4 45.3 - - + +
229A ALA* 3.7 21.5 - - + +
230A THR* 3.7 9.0 - - - +
233A PHE* 3.6 25.1 - - + -
367A PRO* 3.7 13.5 - - + -
368A GLU 3.5 3.4 - - - -
369A VAL* 4.2 9.0 - - + +
393A PHE* 3.3 4.7 - - - -
406A GLU* 5.5 0.7 - - - +
407A GLY* 3.2 14.3 - - - -
408A PHE* 2.8 48.7 + - + +
424A HIS 4.0 1.0 + - - -
425A ILE* 1.3 73.3 - - - +
427A GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 427 (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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367A PRO* 3.6 7.8 - - - +
368A GLU 2.9 26.8 + - - +
393A PHE* 3.8 10.1 - - - -
406A GLU 3.5 9.0 - - - -
425A ILE 3.9 0.4 - - - -
426A ILE* 1.3 76.7 - - - +
428A PRO* 1.3 78.1 - - - +
430A ALA* 3.3 9.0 + - - +
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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