Contacts of the helix formed by residues 369 - 385 (chain A) in PDB entry 1O69
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 369 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A LYS* 4.9 0.9 - - - +
258A TRP* 3.9 5.2 - - - -
367A ALA 3.6 2.5 + - - -
368A MET* 1.3 77.0 - - - +
370A LYS* 1.3 64.5 + - - +
371A ASP* 3.3 13.2 + - - +
372A ASP* 3.1 39.4 + - - +
373A VAL* 3.2 13.7 + - - +
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Residues in contact with LYS 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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258A TRP* 3.4 61.1 - - + +
261A GLU* 4.8 10.5 + - - -
262A PHE* 3.9 25.6 - - + -
369A SER* 1.3 74.0 - - - +
371A ASP* 1.3 58.6 + - - +
373A VAL* 3.3 2.6 + - - +
374A TYR* 2.8 28.4 + - + +
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Residues in contact with ASP 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369A SER* 3.2 10.9 + - - +
370A LYS* 1.3 77.4 - - - +
372A ASP* 1.3 57.2 + - - +
374A TYR* 3.2 9.2 + - - +
375A GLU* 2.7 36.4 + - - +
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Residues in contact with ASP 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ALA 4.4 1.9 - - - +
368A MET* 3.5 27.8 - - + +
369A SER* 3.1 34.0 + - - +
371A ASP* 1.3 75.9 - - - +
373A VAL* 1.3 62.9 + - - +
375A GLU* 3.3 6.5 + - - +
376A ILE* 3.0 29.9 + - + +
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Residues in contact with VAL 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A ILE* 4.1 17.3 - - + -
258A TRP* 3.8 41.3 - - + -
259A TYR* 3.7 32.3 - - + +
262A PHE* 4.0 4.9 - - + -
368A MET* 4.0 23.1 - - + -
369A SER 3.2 12.1 + - - +
370A LYS 3.8 5.6 - - - +
372A ASP* 1.3 78.6 - - - +
374A TYR* 1.3 58.0 + - - +
376A ILE* 3.5 4.1 + - - +
377A SER* 2.9 33.1 + - - -
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Residues in contact with TYR 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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262A PHE* 3.7 46.3 - + + -
370A LYS 2.8 18.0 + - - +
371A ASP* 3.5 11.4 - - - +
373A VAL* 1.3 77.4 - - - +
375A GLU* 1.3 58.1 + - - +
377A SER* 3.3 2.2 + - - -
378A LYS* 3.0 39.5 + - + +
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Residues in contact with GLU 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 ASP 2.7 20.0 + - - +
372A ASP* 3.7 7.6 - - - +
374A TYR* 1.3 72.8 - - - +
376A ILE* 1.3 66.6 + - + +
378A LYS* 3.4 6.9 + - - +
379A LEU* 3.1 31.5 + - + +
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Residues in contact with ILE 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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259A TYR* 3.7 22.0 - - + +
321A LEU* 4.4 1.9 - - + +
326A ILE* 4.3 30.3 - - + -
363A PRO* 4.0 22.7 - - + -
368A MET* 3.0 37.0 - - + -
372A ASP* 3.0 15.7 + - + +
373A VAL* 3.7 3.6 - - - +
375A GLU* 1.3 74.6 - - + +
377A SER* 1.3 64.2 + - - +
379A LEU* 3.2 9.2 + - - +
380A ILE* 3.0 40.5 + - + +
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Residues in contact with SER 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A TYR* 3.5 21.0 - - - -
262A PHE* 3.6 32.8 - - - +
263A LEU* 3.6 15.8 - - - +
373A VAL 2.9 23.6 + - - -
374A TYR* 3.7 5.2 - - - -
375A GLU 3.3 0.2 - - - -
376A ILE* 1.3 77.3 - - - +
378A LYS* 1.3 56.0 + - - +
380A ILE* 3.2 7.9 + - - +
381A LEU* 2.9 34.3 + - - +
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Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A TYR* 3.0 30.2 + - + +
375A GLU* 3.8 6.7 - - - +
377A SER* 1.3 72.9 - - - +
379A LEU* 1.3 61.9 + - + +
381A LEU* 3.3 10.3 + - - +
382A LYS* 2.9 30.0 + - - +
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Residues in contact with LEU 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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320A ASP* 5.7 0.3 - - - +
321A LEU* 3.8 14.0 - - + +
324A LYS* 4.4 15.3 - - + -
326A ILE* 3.5 30.5 - - + -
375A GLU* 3.1 17.3 + - + +
376A ILE 3.2 8.0 + - - +
378A LYS* 1.3 77.8 - - - +
380A ILE* 1.3 57.0 + - - +
382A LYS* 3.4 16.8 + - + +
383A SER* 2.9 30.0 + - - -
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Residues in contact with ILE 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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259A TYR* 4.9 0.2 - - + -
263A LEU* 3.9 18.2 - - + -
267A PHE* 3.6 36.6 - - + -
317A LEU* 3.4 28.7 - - + -
321A LEU* 3.5 12.1 - - + -
362A LEU* 3.5 33.0 - - + -
376A ILE* 3.0 31.4 + - + +
377A SER* 3.2 7.6 + - - +
379A LEU* 1.3 75.0 - - - +
381A LEU* 1.3 57.7 + - - +
383A SER* 3.2 2.3 + - - -
384A ILE* 2.9 30.8 + - + +
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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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262A PHE* 3.7 21.5 - - + +
263A LEU* 4.0 16.4 - - + -
266A TYR* 3.4 41.7 - - + -
267A PHE* 5.2 0.7 - - + -
377A SER* 2.9 23.2 + - - +
378A LYS* 3.3 7.8 + - - +
380A ILE* 1.3 75.2 - - - +
382A LYS* 1.3 59.1 + - - +
384A ILE* 3.5 9.8 + - + +
385A LYS* 3.0 41.3 + - - +
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Residues in contact with LYS 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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316A LYS* 4.9 0.5 + - - -
378A LYS 2.9 17.2 + - - +
379A LEU* 3.7 17.7 - - + +
381A LEU* 1.3 75.2 - - - +
383A SER* 1.3 65.0 + - - +
385A LYS* 3.3 23.0 - - - +
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Residues in contact with SER 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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313A LYS 5.1 0.2 + - - -
316A LYS* 2.8 28.3 + - - +
317A LEU* 3.4 27.8 + - - +
320A ASP* 2.5 41.9 + - - +
321A LEU* 6.0 0.2 - - - -
379A LEU 2.9 17.6 + - - -
380A ILE 3.5 5.2 - - - -
382A LYS* 1.3 77.8 - - - +
384A ILE* 1.3 61.1 + - - +
385A LYS 3.1 6.1 + - - +
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Residues in contact with ILE 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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266A TYR* 3.6 45.5 - - + -
267A PHE* 4.1 20.2 - - + -
287A ILE* 3.9 26.5 - - + -
313A LYS* 4.4 43.2 + - + +
316A LYS* 5.9 0.4 - - - -
317A LEU* 4.7 7.2 - - + -
380A ILE* 2.9 25.9 + - + +
381A LEU* 3.5 16.6 - - + +
382A LYS 3.4 0.2 - - - -
383A SER* 1.3 74.4 - - - +
385A LYS* 1.3 62.4 + - + +
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Residues in contact with LYS 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A TYR* 3.4 46.6 + - + +
316A LYS* 4.3 7.1 + - - -
381A LEU* 3.0 33.0 + - - +
382A LYS* 3.3 16.8 - - - +
383A SER 3.1 10.9 - - - +
384A ILE* 1.3 83.7 - - + +
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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