Contacts of the helix formed by residues 357 - 367 (chain A) in PDB entry 1JSC
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 CYS 357 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A LEU 3.9 18.6 - - - +
350A ASP* 4.7 17.3 - - + -
351A MET* 3.0 8.8 + - - +
356A GLY* 1.3 71.7 - - - -
358A ALA* 1.3 65.7 + - - +
359A THR* 4.2 11.9 - - - +
360A ALA* 3.3 4.3 + - - +
361A ASN* 3.1 24.2 + - - -
458A TYR 5.6 2.0 - - - -
460A TYR* 4.1 30.0 - - - -
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Residues in contact with ALA 358 (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 3.7 1.8 + - - -
357A CYS* 1.3 72.7 - - - +
359A THR* 1.3 58.4 + - - +
361A ASN* 3.1 12.2 + - - +
362A LEU* 2.8 37.1 + - + +
458A TYR* 3.7 44.6 + - + +
460A TYR* 5.2 3.4 - - + +
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Residues in contact with THR 359 (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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349A LEU* 4.1 9.2 - - + -
357A CYS* 4.7 9.3 - - - +
358A ALA* 1.3 79.1 - - - +
360A ALA* 1.3 57.6 + - - +
362A LEU* 3.2 7.3 + - - +
363A ALA* 2.9 28.8 + - - +
451A ILE* 3.6 36.8 - - + +
454A TRP* 3.4 17.7 + - + -
455A LYS* 3.3 38.7 + - + +
458A TYR* 4.8 4.4 + - - +
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Residues in contact with ALA 360 (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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332A THR* 3.7 17.7 - - - +
349A LEU* 3.4 35.4 + - + +
351A MET 3.6 21.8 - - - +
352A LEU* 3.8 4.3 - - - -
357A CYS* 3.3 6.4 + - + +
358A ALA 3.3 0.6 - - - -
359A THR* 1.3 78.8 - - - +
361A ASN* 1.3 63.7 + - - +
363A ALA* 3.4 2.6 + - - +
364A VAL* 3.2 27.7 + - - +
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Residues in contact with ASN 361 (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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352A LEU* 3.2 10.9 - - - +
353A GLY* 2.9 48.1 + - - +
354A MET* 5.1 1.4 - - - +
356A GLY 3.9 3.2 + - - -
357A CYS 3.1 20.7 + - - -
358A ALA* 3.1 10.5 + - - +
360A ALA* 1.3 77.9 - - - +
362A LEU* 1.3 59.1 + - + +
364A VAL* 3.5 2.8 + - - +
365A GLN* 3.1 35.6 + - + +
381A VAL 4.8 1.9 - - - +
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Residues in contact with LEU 362 (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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358A ALA* 2.8 23.8 + - + +
359A THR 3.2 4.7 + - - +
361A ASN* 1.3 76.9 - - + +
363A ALA* 1.3 59.7 + - - +
365A GLN* 3.0 8.6 + - + +
366A ASN* 2.8 39.4 + - - +
454A TRP* 3.4 58.8 - - + +
458A TYR* 4.5 20.9 - - + +
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Residues in contact with ALA 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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303A VAL* 3.6 11.8 - - + +
349A LEU* 3.8 29.8 - - + -
359A THR 2.9 16.1 + - - +
360A ALA 3.4 4.2 + - - +
362A LEU* 1.3 76.1 - - - +
364A VAL* 1.3 58.4 + - - +
367A ALA* 2.8 33.1 + - - +
447A TRP* 3.6 12.6 - - + -
451A ILE* 4.6 4.3 - - + -
454A TRP* 3.7 12.5 - - + -
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Residues in contact with VAL 364 (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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303A VAL* 4.0 22.9 - - + -
305A TYR* 5.5 2.5 - - + -
332A THR* 4.4 3.4 - - + -
352A LEU* 3.6 28.0 - - + -
360A ALA 3.2 15.8 + - - +
361A ASN* 3.8 4.3 - - - +
362A LEU 3.1 0.8 - - - -
363A ALA* 1.3 79.3 - - - +
365A GLN* 1.3 64.5 + - - +
366A ASN 3.5 0.2 + - - -
367A ALA* 3.8 10.0 + - - +
370A ILE* 3.6 27.0 - - + +
388A PHE* 3.5 33.2 - - + -
389A ALA* 3.7 7.5 - - + +
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Residues in contact with GLN 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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361A ASN* 3.1 23.1 + - + +
362A LEU* 3.0 12.5 + - + +
364A VAL* 1.3 79.8 - - - +
366A ASN* 1.3 64.1 + - - +
382A THR 5.9 0.4 + - - -
387A LYS 3.1 24.0 + - - -
388A PHE* 3.7 10.1 - - - +
389A ALA* 2.6 28.1 + - - +
390A PRO* 3.5 29.5 - - + +
391A GLU* 3.5 13.5 + - - +
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Residues in contact with ASN 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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301A LYS* 3.6 29.3 + - - +
362A LEU* 2.8 23.4 + - - +
365A GLN* 1.3 83.4 - - - +
367A ALA* 1.3 65.8 + - - +
368A ASP* 4.7 0.2 - - - -
391A GLU* 3.4 17.7 - - - +
447A TRP* 4.0 12.5 - - + -
450A GLN* 6.0 0.6 - - - +
454A TRP* 3.7 29.1 - - + -
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Residues in contact with ALA 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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301A LYS 3.1 19.3 - - - +
303A VAL* 3.6 18.6 - - + -
363A ALA 2.8 18.5 + - - +
364A VAL 3.8 8.5 + - - +
365A GLN 3.6 1.4 - - - -
366A ASN* 1.3 78.1 - - - +
368A ASP* 1.3 58.9 + - - +
369A LEU 3.8 12.1 - - - +
370A ILE* 4.3 5.8 - - + -
391A GLU* 3.2 5.2 - - - +
392A ALA* 3.1 25.7 + - - +
447A TRP* 4.3 2.0 - - - -
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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