Contacts of the strand formed by residues 362 - 369 (chain A) in PDB entry 1JRX
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A PHE* 4.0 23.3 - - + -
323A VAL* 3.8 18.2 - - + +
326A LEU* 3.6 31.0 - - + -
327A ASP* 4.2 13.6 + - + +
330A LEU* 3.4 30.7 - - + +
359A MET 3.6 12.6 - - - +
360A GLN 3.2 5.4 + - - +
361A TYR* 1.3 79.8 - - - +
363A GLN* 1.3 62.9 + - - +
364A ALA 3.7 2.4 + - - -
503A VAL* 3.8 20.6 - - + -
505A HIS 3.7 8.3 - - - +
506A THR* 4.1 8.7 - - + -
507A MET* 3.8 3.3 - - - +
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Residues in contact with GLN 363 (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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330A LEU* 5.1 0.2 - - - -
362A ILE* 1.3 73.1 - - - +
364A ALA* 1.3 68.1 + - - +
365A HIS 4.4 1.3 - - - +
402A ALA* 3.6 15.5 - - + +
403A ASP* 5.5 0.7 - - - +
503A VAL* 3.7 3.3 - - - +
504A HIS* 2.7 40.3 + - + +
505A HIS* 2.8 22.1 + - + +
507A MET* 3.5 19.3 - - + +
543A ASN* 3.1 20.8 + - - +
544A ARG* 2.8 63.7 + - - +
546A GLY* 6.2 0.2 - - - -
1806A FUM 4.5 1.2 - - - +
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Residues in contact with ALA 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 4.1 24.9 - - + +
333A PHE* 5.0 0.7 - - + -
362A ILE 3.7 4.2 + - - +
363A GLN* 1.3 81.8 - - - +
365A HIS* 1.3 58.8 + - - +
366A PRO* 3.5 3.8 - - - +
402A ALA* 3.8 6.1 - - - +
403A ASP* 4.8 1.1 + - - +
406A SER* 3.0 27.8 + - - +
410A LEU* 6.3 0.2 - - + -
501A PRO* 4.1 11.9 - - + -
502A GLY 3.1 14.1 - - - +
503A VAL* 4.3 1.3 - - - +
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Residues in contact with HIS 365 (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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336A THR* 4.2 8.1 - - + -
363A GLN* 4.9 0.4 - - - -
364A ALA* 1.3 72.1 - - - +
366A PRO* 1.3 68.3 - - + +
367A THR* 3.0 47.4 + - - -
368A LEU 4.4 0.9 + - - +
375A MET* 3.5 23.3 - - + +
376A VAL 3.2 11.9 - - - -
378A GLU* 3.8 5.6 + - - +
381A ARG* 3.7 12.5 + - - -
402A ALA* 4.8 2.0 - - - -
406A SER* 3.6 0.2 - - - -
500A THR 4.2 0.2 - - - +
501A PRO* 3.0 2.6 - - - +
502A GLY 2.8 33.1 + - - +
504A HIS* 3.6 37.0 - + + +
1806A FUM 2.5 31.6 + - + -
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Residues in contact with PRO 366 (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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364A ALA 3.6 6.3 - - - +
365A HIS* 1.3 94.1 - - + +
367A THR* 1.3 59.8 + - + -
378A GLU* 5.8 0.9 - - - +
381A ARG* 3.4 26.0 - - - +
402A ALA* 3.8 17.5 - - + +
405A ALA* 3.6 32.3 - - + -
406A SER* 3.1 20.0 - - - +
409A ILE* 3.3 17.8 - - + +
500A THR* 3.2 18.5 - - - -
501A PRO* 3.2 7.5 - - + -
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Residues in contact with THR 367 (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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365A HIS* 3.0 17.9 + - - -
366A PRO* 1.3 90.0 - - + +
368A LEU* 1.3 58.6 + - - +
376A VAL* 2.8 43.8 + - - +
377A THR 4.6 0.5 + - - -
381A ARG* 3.6 30.0 + - - +
387A LEU* 4.2 7.0 - - + -
409A ILE* 4.0 6.7 - - + -
419A LEU* 4.6 4.2 - - + +
499A VAL* 3.6 33.9 - - + -
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Residues in contact with LEU 368 (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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334A ILE* 3.7 36.6 - - + -
335A SER 4.0 14.4 - - - +
336A THR* 3.8 25.6 - - + -
365A HIS* 4.4 1.6 + - - -
366A PRO 3.8 0.2 - - - -
367A THR* 1.3 72.0 - - - +
369A SER* 1.3 78.7 + - - +
370A VAL* 5.4 1.3 - - - -
373A GLY* 3.9 18.8 - - - +
374A VAL* 3.5 11.4 - - - +
375A MET* 4.2 2.0 - - - +
499A VAL* 3.2 3.7 - - - -
500A THR* 2.8 54.9 + - + +
501A PRO 4.6 4.7 - - - +
502A GLY* 4.1 10.5 - - - +
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Residues in contact with SER 369 (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 THR 3.8 2.0 + - - -
368A LEU* 1.3 74.9 - - - +
370A VAL* 1.3 60.5 + - - +
371A LYS* 3.2 2.8 + - - +
372A GLY* 2.8 25.2 + - - -
373A GLY* 2.8 27.5 + - - -
374A VAL* 2.7 21.8 + - - -
376A VAL* 3.7 19.4 - - - +
440A VAL* 3.3 23.7 - - - +
497A ILE* 4.3 1.7 - - - +
498A GLU 3.4 9.8 + - - -
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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