Contacts of the helix formed by residues 374 - 385 (chain A) in PDB entry 1YA8
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 ASP 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373A LEU* 1.3 78.3 - - - +
375A GLN* 1.3 55.3 + - - +
376A LYS* 2.6 36.9 + - - +
377A THR* 2.7 34.3 + - - -
378A ALA* 2.8 21.5 + - - -
404A LEU* 5.5 0.4 - - - -
410A THR* 5.0 8.3 - - + -
413A LYS* 3.6 9.9 - - + -
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Residues in contact with GLN 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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374A ASP* 1.3 70.3 - - - +
376A LYS* 1.3 61.4 + - + +
378A ALA* 3.6 5.1 - - - +
379A MET* 3.1 42.0 + - + +
400A THR* 3.3 28.5 + - - +
401A GLU* 3.7 16.8 + - - +
404A LEU* 3.2 30.8 - - - +
405A GLY* 3.5 8.3 + - - -
413A LYS* 3.0 27.4 + - - +
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Residues in contact with LYS 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 ASP* 2.6 19.0 + - - +
375A GLN* 1.3 74.0 - - + +
377A THR* 1.3 67.6 + - - +
378A ALA 2.9 2.6 + - - -
379A MET* 2.9 20.1 + - + +
380A SER* 3.0 12.0 + - - -
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Residues in contact with THR 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A LEU* 3.3 28.9 - - + -
374A ASP* 2.7 27.3 + - - -
376A LYS* 1.3 76.6 - - - +
378A ALA* 1.3 56.1 + - - +
380A SER* 3.1 10.0 + - - -
381A LEU* 2.8 35.9 + - + +
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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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373A LEU* 3.7 19.2 - - + +
374A ASP 2.8 14.8 + - - +
375A GLN 3.6 7.4 - - - +
376A LYS 2.9 0.6 + - - -
377A THR* 1.3 76.3 - - - +
379A MET* 1.3 54.4 + - - +
381A LEU* 2.9 4.8 + - - +
382A LEU* 2.7 36.8 + - - +
400A THR* 3.7 4.5 - - + -
404A LEU* 3.2 34.8 - - + -
417A PHE* 4.1 5.8 - - + -
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Residues in contact with MET 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 GLN* 3.1 37.9 + - + +
376A LYS* 2.9 13.7 + - + +
378A ALA* 1.3 79.9 - - - +
380A SER* 1.3 61.2 + - - +
382A LEU* 4.0 0.9 - - - -
383A TRP* 3.3 22.5 + - - +
393A LYS* 4.7 4.2 + - - +
396A ILE* 3.4 18.9 - - + +
397A PRO* 3.6 37.0 - - + +
400A THR* 3.2 21.8 - - + +
401A GLU* 5.9 1.6 - - + +
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Residues in contact with SER 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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376A LYS 3.0 10.5 + - - -
377A THR* 3.2 16.6 - - - -
378A ALA 3.0 0.6 - - - -
379A MET* 1.3 78.7 - - - +
381A LEU* 1.3 63.5 + - - +
383A TRP* 3.3 7.7 + - - +
384A LYS* 3.1 48.4 + - - +
393A LYS* 5.7 2.0 - - - +
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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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306A LEU* 5.7 1.8 - - + -
308A LEU* 5.4 4.7 - - + -
366A TYR* 3.6 37.5 - - + +
367A PRO* 4.0 22.2 - - + +
368A LEU* 4.0 10.3 - - + -
373A LEU* 3.9 25.4 - - + -
377A THR* 2.8 14.3 + - + +
378A ALA 3.5 6.3 - - - +
380A SER* 1.3 77.2 - - - +
382A LEU* 1.3 51.4 + - - +
384A LYS* 2.9 16.7 + - + +
385A SER* 2.5 40.8 + - - +
417A PHE* 3.8 22.7 - - + -
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Residues in contact with LEU 382 (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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378A ALA 2.7 20.3 + - - +
381A LEU* 1.3 71.8 - - - +
383A TRP* 1.3 59.0 - - - +
385A SER* 3.7 14.0 + - - -
386A TYR* 3.9 4.7 + - - +
389A VAL* 3.9 28.5 - - + +
391A ILE* 3.9 10.1 - - + +
396A ILE* 3.5 33.8 - - + +
399A ALA* 4.6 3.1 - - + -
400A THR* 3.5 27.8 - - - +
417A PHE* 3.8 15.8 - - + -
420A LEU* 3.6 33.7 - - + -
421A ILE* 5.2 0.9 - - + -
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Residues in contact with TRP 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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311A ASP* 4.9 1.8 - - - -
312A PRO* 3.2 42.0 - - + +
313A ARG* 3.7 39.7 - - + -
379A MET 3.3 19.1 + - - +
380A SER* 3.3 6.4 + - - +
381A LEU 3.0 1.0 - - - -
382A LEU* 1.3 74.3 - - - +
384A LYS* 1.3 66.5 + - + +
385A SER 3.1 1.8 - - - -
386A TYR* 3.3 28.8 + + - +
391A ILE 3.8 13.9 - - - -
392A ALA* 4.1 0.7 - - - -
393A LYS* 3.3 77.0 - - + +
396A ILE* 4.1 6.9 - - + +
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Residues in contact with LYS 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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306A LEU* 4.0 11.6 - - + +
307A ASP 4.8 7.4 - - - +
308A LEU* 3.8 37.5 + - + +
312A PRO* 4.0 20.9 - - + +
315A SER* 6.0 0.3 - - - -
380A SER* 3.1 35.6 + - - +
381A LEU* 2.9 14.7 + - + +
383A TRP* 1.3 76.1 - - + +
385A SER* 1.3 58.4 + - - +
386A TYR 3.0 9.0 + - - -
387A PRO* 3.3 16.4 - - - +
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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
----------------------------------------------------------
306A LEU* 4.5 9.3 - - - +
366A TYR* 2.8 34.2 + - - -
381A LEU* 2.5 24.3 + - - +
382A LEU* 3.8 11.8 - - - -
383A TRP 3.1 0.6 - - - -
384A LYS* 1.3 76.4 - - - +
386A TYR* 1.3 52.7 + - - +
387A PRO* 3.2 4.3 - - - -
388A LEU* 2.7 33.2 + - - +
389A VAL* 3.1 21.6 + - - -
421A ILE* 5.3 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