Contacts of the strand formed by residues 382 - 392 (chain A) in PDB entry 1Z3S
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 GLU 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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374A HIS* 2.8 31.4 + - + +
375A LEU 3.1 8.5 - - - +
376A LYS* 3.2 33.0 - - + +
380A GLY 4.2 5.8 + - - +
381A ASN* 1.3 80.3 - - - +
383A ALA* 1.3 63.5 + - - +
409A THR* 4.8 1.2 + - - -
477A TRP* 3.8 5.5 - - - -
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Residues in contact with ALA 383 (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 HIS* 3.6 6.6 - - - -
375A LEU* 2.8 32.0 + - - +
382A GLU* 1.3 76.9 - - - +
384A TYR* 1.3 66.0 + - - +
409A THR* 3.5 23.3 - - - +
410A ALA* 4.1 6.5 - - + -
477A TRP* 3.4 36.5 - - + +
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Residues in contact with TYR 384 (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 LYS* 4.1 26.5 - - - -
373A ILE 3.1 15.3 - - - +
374A HIS* 4.4 9.2 - + + -
383A ALA* 1.3 80.2 - - - +
385A SER* 1.3 69.7 + - - +
386A LEU* 3.9 24.5 - - + +
407A THR* 4.9 1.3 + - - -
408A GLY* 3.4 24.4 + - - -
409A THR* 3.0 38.0 + - + +
410A ALA* 2.9 25.7 + - - -
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Residues in contact with SER 385 (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 LEU 4.0 0.6 - - - +
372A LYS* 3.5 2.4 - - - -
373A ILE* 2.9 34.7 + - - +
375A LEU* 6.1 0.2 - - - -
384A TYR* 1.3 75.0 - - - +
386A LEU* 1.3 63.6 + - - +
387A TYR* 4.3 6.3 - - - -
406A LEU* 4.0 16.2 - - - +
407A THR 3.6 6.2 + - - -
410A ALA* 3.0 33.4 + - - +
411A GLY 5.0 0.3 + - - -
474A TRP* 3.3 26.8 + - - -
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Residues in contact with LEU 386 (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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322A TRP* 4.6 2.9 - - + -
370A VAL* 3.3 33.4 - - + -
371A LEU 3.4 9.2 - - - +
372A LYS* 3.6 24.5 - - + -
384A TYR* 3.9 19.1 - - + +
385A SER* 1.3 77.0 - - - +
387A TYR* 1.3 65.7 + - - +
388A GLU* 5.9 0.2 - - - -
405A GLY 3.4 1.7 - - - +
406A LEU* 3.4 5.2 - - - +
407A THR* 2.9 48.9 + - - +
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Residues in contact with TYR 387 (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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370A VAL* 3.2 22.7 - - - +
371A LEU* 2.9 31.5 + - + +
373A ILE* 4.7 13.5 - - + -
385A SER* 4.3 12.6 - - - -
386A LEU* 1.3 78.8 - - - +
388A GLU* 1.3 65.4 + - - +
389A HIS 3.3 7.1 + - - +
403A LEU* 3.4 55.5 - - + +
404A LYS 3.7 11.7 - - - +
405A GLY 3.3 3.6 - - - -
406A LEU* 3.5 34.0 - - + +
414A SER* 2.8 31.3 + - - -
416A ILE* 4.3 0.6 - - + +
418A GLN* 5.2 2.0 - - - -
474A TRP* 4.0 15.5 - + - -
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Residues in contact with GLU 388 (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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368A ARG* 5.9 0.9 - - - +
369A TYR 3.7 1.4 - - - +
370A VAL* 3.0 24.2 - - - +
386A LEU* 5.9 0.4 - - - -
387A TYR* 1.3 71.4 - - - +
389A HIS* 1.3 63.2 + - + +
404A LYS* 2.9 15.3 + - + +
405A GLY* 3.0 31.7 + - - +
407A THR* 5.4 7.7 - - + +
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Residues in contact with HIS 389 (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 THR 4.8 1.6 - - - -
367A GLN 4.7 1.8 - - - -
368A ARG* 3.2 61.9 + - + +
369A TYR 3.1 18.9 + - - -
387A TYR* 3.2 4.0 - - - +
388A GLU* 1.3 83.9 + - + +
390A PHE* 1.3 71.2 + - - +
391A TYR* 3.5 31.8 - + + -
402A HIS 3.7 3.7 - - - +
403A LEU* 3.7 1.0 - - - -
404A LYS* 3.2 55.0 + - + +
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Residues in contact with PHE 390 (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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325A ILE* 4.3 13.2 - - + -
360A VAL* 3.9 11.9 - - + -
364A THR* 3.7 30.2 - - + +
369A TYR* 2.7 25.0 + - + +
371A LEU* 3.4 38.6 - - + +
389A HIS* 1.3 77.9 + - - +
391A TYR* 1.3 69.1 + - - +
392A LEU* 3.5 33.0 - - + -
401A ILE* 3.6 16.6 - - + -
402A HIS 3.4 5.6 - - - -
403A LEU* 3.8 14.8 - - + -
446A TRP* 4.8 5.6 - + - -
491A ILE* 3.8 28.0 - - + -
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Residues in contact with TYR 391 (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 THR* 3.3 32.1 - - - +
365A ASN* 3.8 22.9 - - - -
389A HIS* 3.5 31.6 - + + -
390A PHE* 1.3 79.9 - - - +
392A LEU* 1.3 69.2 + - - +
393A SER* 4.5 4.3 - - - -
402A HIS* 3.0 79.5 + + + -
404A LYS* 5.7 2.9 - - - -
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Residues in contact with LEU 392 (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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325A ILE* 6.2 0.2 - - + -
354A TRP* 6.1 0.2 - - + -
357A ASN* 4.1 23.1 - - - +
360A VAL* 3.5 31.6 - - + -
361A SER* 3.1 21.9 + - - +
364A THR* 3.2 5.9 + - - -
365A ASN* 2.7 28.6 - - - +
390A PHE* 3.5 30.1 - - + -
391A TYR* 1.3 79.8 - - - +
393A SER* 1.3 64.1 + - - +
399A TYR* 3.8 15.7 - - + +
400A ARG 3.2 2.5 - - - -
401A ILE* 3.9 14.8 - - - -
446A TRP* 3.9 16.2 - - + +
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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