Contacts of the strand formed by residues 366 - 377 (chain A) in PDB entry 4ZCH
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 ALA 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A TYR* 4.5 5.6 - - + -
364A THR* 3.8 8.0 - - - +
365A TYR* 1.3 106.9 - - + +
367A MET* 1.3 72.0 + - - +
392A ILE* 4.2 23.3 - - + -
393A GLN 3.3 9.6 - - - +
394A ASN* 4.0 7.9 - - - +
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Residues in contact with MET 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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360A TYR* 3.5 39.3 - - + -
362A ASP* 3.7 30.7 - - + +
364A THR* 3.9 11.4 - - - +
366A ALA* 1.3 82.0 - - - +
368A GLY* 1.3 59.0 + - - +
392A ILE* 3.5 5.1 - - - +
393A GLN* 2.8 37.5 + - - +
395A MET* 3.6 28.2 - - + +
422A ILE* 4.3 2.2 - - + -
424A ARG* 3.8 31.2 - - + -
427A ALA* 3.7 19.3 - - + -
428A GLN 4.7 0.2 - - - +
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Residues in contact with GLY 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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360A TYR* 2.9 26.2 + - - -
367A MET* 1.3 77.2 - - - +
369A HIS* 1.3 59.0 + - - -
391A CYS 3.1 15.7 - - - -
392A ILE* 4.3 1.8 - - - -
404A CYS* 4.6 1.3 - - - -
422A ILE* 3.4 18.4 - - - +
423A PRO* 3.5 11.9 - - - +
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Residues in contact with HIS 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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356A GLY 3.1 22.4 + - - -
358A VAL* 3.4 18.4 - - + +
360A TYR* 2.8 24.7 + - - +
368A GLY* 1.3 72.0 - - - +
370A LEU* 1.3 65.2 + - - +
371A ILE* 4.2 14.2 - - + +
390A ARG* 3.6 2.1 - - - -
391A CYS* 2.9 46.4 + - + +
404A CYS* 3.1 28.9 - - + -
406A SER 5.0 0.2 + - - -
420A LEU* 3.6 33.4 - - + +
421A ALA 3.3 12.3 - - - +
422A ILE* 3.8 2.5 - - + -
423A PRO* 4.3 1.3 - - - -
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Residues in contact with LEU 370 (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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133A HIS* 5.8 0.4 - - - +
322A TYR* 4.1 24.7 - - + +
369A HIS* 1.3 75.6 - - - +
371A ILE* 1.3 61.8 + - - +
372A GLN* 3.6 29.0 + - + +
387A THR* 3.9 20.0 - - + +
389A PHE 3.6 3.4 - - - -
390A ARG* 3.7 38.8 - - + +
419A GLN 3.4 4.5 - - - +
420A LEU* 3.4 3.3 - - - -
421A ALA* 2.8 36.4 + - - +
423A PRO* 4.3 17.5 - - + -
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Residues in contact with ILE 371 (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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354A ILE* 3.8 25.1 - - + -
355A TYR* 4.8 1.6 - - - -
356A GLY* 4.2 9.6 - - - +
369A HIS* 4.2 18.6 - - + +
370A LEU* 1.3 71.9 - - - +
372A GLN* 1.3 57.3 + - - +
387A THR* 3.7 2.3 - - - -
388A LEU* 2.7 43.6 + - + +
389A PHE* 2.8 43.9 + - + +
390A ARG 6.2 0.2 - - - -
406A SER* 4.1 23.1 - - - +
418A LEU* 4.7 2.0 - - + -
419A GLN 3.6 3.8 - - - +
420A LEU* 4.5 7.4 - - + -
438A PHE* 4.1 24.2 - - + -
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Residues in contact with GLN 372 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A TYR* 4.2 10.2 + - - -
370A LEU* 3.6 27.7 - - + +
371A ILE* 1.3 73.7 - - - +
373A ARG* 1.3 59.0 + - - +
374A LYS 4.0 0.2 + - - -
385A LEU* 3.5 37.0 - - + +
386A VAL 3.3 6.5 - - - +
387A THR* 3.6 20.1 + - - +
388A LEU* 4.5 0.7 - - - -
418A LEU* 3.3 12.6 - - - +
419A GLN* 2.7 62.5 + - + +
421A ALA* 3.3 21.5 - - - +
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Residues in contact with ARG 373 (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 GLN* 1.3 72.2 - - - +
374A LYS* 1.3 62.2 + - - +
375A LYS* 3.5 28.9 - - - +
384A SER* 3.7 4.0 + - - +
385A LEU* 3.4 5.0 - - - +
386A VAL* 2.8 66.8 + - - +
388A LEU* 4.1 30.4 - - + +
411A LYS 4.7 8.8 + - - -
412A LEU* 3.8 21.7 - - + +
416A ASP* 3.5 30.7 - - + +
417A GLU 3.5 6.7 - - - +
418A LEU* 4.4 2.0 - - + -
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Residues in contact with LYS 374 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319A LYS* 6.1 0.6 - - - +
343A LYS* 3.1 30.8 - - + +
372A GLN 4.0 0.6 - - - +
373A ARG* 1.3 73.2 - - - +
375A LYS* 1.3 62.7 + - - +
376A VAL* 3.6 28.6 + - + -
383A LEU* 3.8 20.6 - - + -
384A SER 3.4 4.0 - - - +
385A LEU* 3.8 12.8 - - + -
415A GLY 4.6 0.7 - - - +
416A ASP* 3.9 3.5 - - - +
417A GLU* 2.7 53.1 + - + +
419A GLN* 3.9 23.0 + - + +
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Residues in contact with LYS 375 (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 ARG* 3.5 28.2 - - - +
374A LYS* 1.3 74.3 - - - +
376A VAL* 1.3 64.6 + - - +
382A GLU 4.5 0.2 - - - -
383A LEU* 3.5 4.7 - - - -
384A SER* 3.0 50.2 + - - +
413A GLU* 4.8 18.0 - - - +
415A GLY 5.2 3.4 - - - -
416A ASP* 3.1 43.2 + - - +
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Residues in contact with VAL 376 (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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374A LYS* 3.6 36.5 + - + -
375A LYS* 1.3 80.2 - - - +
377A HIS* 1.3 62.1 + - - +
378A VAL* 4.0 22.0 + - + +
382A GLU 3.4 12.6 - - - +
383A LEU* 3.9 8.1 - - + -
415A GLY 5.2 6.2 + - - +
417A GLU* 4.2 12.0 + - - +
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Residues in contact with HIS 377 (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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376A VAL* 1.3 72.1 - - - +
378A VAL* 1.3 59.4 + - - +
379A PHE* 4.1 17.5 - + + +
380A GLY* 3.2 36.5 + - - -
381A ASP 3.0 8.7 + - - -
382A GLU* 2.9 63.3 + - + +
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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