Contacts of the helix formed by residues 370 - 383 (chain A) in PDB entry 3O8C
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 SER 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A TYR* 4.3 0.4 + - - -
368A CYS* 3.3 0.4 - - - +
369A HIS* 1.3 97.8 + - - +
371A LYS* 1.3 62.6 + - - +
372A LYS* 3.8 18.2 + - - +
373A LYS* 3.3 29.3 + - - +
374A CYS* 3.4 24.6 + - - -
411A THR* 4.0 3.8 - - - -
432A VAL* 5.6 0.7 - - - -
3C U 3.4 20.9 - - - -
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Residues in contact with LYS 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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370A SER* 1.3 69.4 - - - +
372A LYS* 1.3 68.4 + - + +
374A CYS* 2.9 6.4 + - - +
375A ASP* 2.9 27.3 + - - +
392A TYR* 3.5 44.4 - - + +
393A ARG* 3.8 18.8 - - - -
411A THR* 4.5 1.3 - - + -
3C U 2.8 45.5 + - - +
4C 5BU 2.9 35.5 + - - +
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Residues in contact with LYS 372 (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 SER* 3.9 20.1 - - - +
371A LYS* 1.3 76.5 - - + +
373A LYS* 1.3 64.5 + - + +
375A ASP* 3.0 11.1 + - - +
376A GLU* 2.9 40.4 + - - +
3C U 4.4 13.7 + - - +
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Residues in contact with LYS 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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350A TYR* 3.3 60.8 - - + +
368A CYS* 3.7 15.3 - - + -
369A HIS* 3.9 8.6 - - + -
370A SER* 3.3 15.5 + - - +
371A LYS 3.2 0.6 - - - -
372A LYS* 1.3 78.3 - - + +
374A CYS* 1.3 58.2 + - - +
376A GLU* 3.1 17.9 + - + +
377A LEU* 2.8 34.7 + - + +
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Residues in contact with CYS 374 (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 CYS* 3.8 10.7 - - - +
370A SER 3.4 14.3 + - - +
371A LYS 2.9 9.7 + - - +
373A LYS* 1.3 80.0 - - - +
375A ASP* 1.3 61.4 + - - +
378A ALA* 3.1 25.3 + - - +
390A ALA* 3.8 3.9 - - + +
392A TYR* 3.9 16.2 - - + -
409A VAL* 3.5 20.2 - - - +
410A ALA* 3.4 42.0 - - - -
411A THR* 3.6 8.5 - - - -
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Residues in contact with ASP 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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371A LYS* 2.9 19.1 + - - +
372A LYS* 3.5 9.6 - - - +
374A CYS* 1.3 74.9 - - - +
376A GLU* 1.3 62.1 + - + +
378A ALA* 3.4 5.2 + - - +
379A ALA* 2.9 30.2 + - - +
390A ALA* 4.2 8.5 - - - +
392A TYR* 3.0 32.5 + - - -
395A LEU* 5.8 0.2 - - - +
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Residues in contact with GLU 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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372A LYS* 2.9 32.6 + - - +
373A LYS* 3.8 21.7 - - + +
375A ASP* 1.3 81.5 - - + +
377A LEU* 1.3 57.9 + - - +
379A ALA* 3.5 6.7 + - - +
380A LYS* 3.1 27.5 + - - +
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Residues in contact with LEU 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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347A ILE* 3.6 28.7 - - + -
348A PRO 4.6 7.0 - - - +
349A PHE* 3.9 20.0 - - + -
354A ILE* 4.7 2.0 - - + -
366A ILE* 3.8 39.5 - - + -
368A CYS* 4.4 2.9 - - - -
373A LYS 2.8 20.5 + - - +
376A GLU* 1.3 70.9 - - - +
378A ALA* 1.3 66.0 + - - +
380A LYS* 3.5 10.3 + - + +
381A LEU* 3.0 43.3 + - + +
409A VAL* 4.0 12.1 - - + -
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Residues in contact with ALA 378 (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 CYS 3.1 20.2 + - - +
375A ASP* 3.6 3.8 - - - +
377A LEU* 1.3 76.6 - - - +
379A ALA* 1.3 63.3 + - - +
381A LEU* 3.4 1.0 + - - +
382A SER* 3.0 28.4 + - - -
388A ALA* 3.8 16.3 - - + +
389A VAL 4.5 2.2 - - - -
390A ALA* 3.9 26.5 - - + +
409A VAL* 4.1 8.8 - - + +
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Residues in contact with ALA 379 (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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375A ASP 2.9 18.1 + - - +
376A GLU* 3.6 8.3 - - - +
378A ALA* 1.3 77.4 - - - +
380A LYS* 1.3 59.3 + - - +
382A SER* 2.9 19.0 + - - -
383A GLY* 3.3 8.7 + - - -
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Residues in contact with LYS 380 (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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346A GLU 3.9 11.9 + - - -
347A ILE* 4.4 18.6 - - + +
348A PRO* 3.7 31.1 - - + +
376A GLU 3.1 17.3 + - - +
377A LEU* 3.9 9.6 - - + +
378A ALA 3.3 0.2 - - - -
379A ALA* 1.3 76.4 - - - +
381A LEU* 1.3 64.1 + - - +
383A GLY* 3.1 8.0 + - - -
384A LEU* 3.0 42.0 - - + +
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Residues in contact with LEU 381 (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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347A ILE* 3.3 44.2 - - + -
356A ILE* 5.0 3.6 - - + -
359A ILE* 3.9 11.0 - - + -
366A ILE* 4.3 6.7 - - + -
377A LEU* 3.0 39.9 + - + +
380A LYS* 1.3 76.8 - - + +
382A SER* 1.3 62.9 + - - +
384A LEU* 3.0 17.4 + - + +
386A ILE* 3.1 25.4 + - + +
388A ALA* 3.5 14.4 - - + -
407A VAL* 3.7 29.6 - - + -
409A VAL* 4.1 9.4 - - + -
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Residues in contact with SER 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ALA 3.0 14.6 + - - -
379A ALA* 2.9 21.0 + - - -
381A LEU* 1.3 70.1 - - - +
383A GLY* 1.3 58.0 + - - +
384A LEU 2.9 10.3 + - - -
385A GLY* 3.0 15.1 + - - -
386A ILE 3.1 16.4 + - - +
387A ASN* 5.9 0.2 - - - -
388A ALA* 4.1 11.0 - - - +
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Residues in contact with GLY 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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379A ALA 3.3 5.9 + - - -
380A LYS* 3.1 12.7 + - - -
382A SER* 1.3 80.7 + - - +
384A LEU* 1.3 65.7 + - - +
385A GLY 3.6 0.7 - - - -
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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