Contacts of the helix formed by residues 371 - 385 (chain A) in PDB entry 6YBO
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 ALA 371 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329A ALA* 6.0 0.3 - - - +
332A ALA* 4.5 20.0 - - + +
333A SER* 3.3 12.4 + - - +
369A GLY* 3.4 4.8 - - - +
370A MET* 1.3 78.9 - - - +
372A PHE* 1.3 63.6 + - - +
373A GLU 3.4 3.1 - - - +
374A ARG* 3.7 12.2 + - + +
375A LEU* 3.4 15.4 + - - +
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Residues in contact with PHE 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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333A SER* 3.8 28.5 - - - -
335A LEU* 4.8 7.0 - - + -
370A MET* 3.5 46.8 - - + +
371A ALA* 1.3 76.5 - - - +
373A GLU* 1.3 65.1 + - + +
374A ARG 3.4 0.2 - - - -
375A LEU* 3.4 12.3 + - + +
376A ASP* 2.9 29.1 + - - +
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Residues in contact with GLU 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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371A ALA* 3.4 0.8 - - - +
372A PHE* 1.3 81.3 - - + +
374A ARG* 1.3 58.9 + - - +
376A ASP* 3.3 13.3 + - - +
377A GLN* 2.9 30.5 + - - +
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Residues in contact with ARG 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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325A GLU* 2.6 38.6 + - - +
328A GLU* 5.0 9.3 + - - +
329A ALA* 3.9 25.4 - - + +
371A ALA* 3.7 14.6 + - + +
372A PHE 3.4 0.4 - - - -
373A GLU* 1.3 78.3 - - - +
375A LEU* 1.3 63.9 + - - +
377A GLN* 3.2 6.6 + - - +
378A LEU* 3.0 31.8 + - + +
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Residues in contact with LEU 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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270A TRP* 6.3 1.8 - - + -
320A PHE* 4.2 18.1 - - + -
326A VAL* 4.5 4.7 - - + -
329A ALA* 4.0 24.1 - - + +
330A LEU* 3.9 34.3 - - + -
333A SER* 4.1 16.8 - - - +
335A LEU* 4.4 11.0 - - + -
371A ALA 3.4 11.9 + - - +
372A PHE* 3.6 15.0 - - + +
373A GLU 3.3 0.4 - - - -
374A ARG* 1.3 78.7 - - - +
376A ASP* 1.3 62.1 + - - +
378A LEU* 3.2 12.5 + - + +
379A ALA* 3.0 19.2 + - - +
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Residues in contact with ASP 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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266A ARG* 2.7 40.0 + - - -
270A TRP* 4.1 14.5 + - - -
372A PHE 2.9 17.4 + - - +
373A GLU* 3.3 15.0 + - - +
375A LEU* 1.3 78.0 - - - +
377A GLN* 1.3 58.3 + - - +
379A ALA* 3.2 3.5 + - - +
380A MET* 2.9 27.7 + - - +
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Residues in contact with GLN 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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373A GLU 2.9 17.1 + - - +
374A ARG* 3.2 6.7 + - - +
376A ASP* 1.3 76.0 - - - +
378A LEU* 1.3 58.6 + - - +
380A MET* 3.8 22.7 - - - +
381A ASP* 2.9 57.3 + - - +
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Residues in contact with LEU 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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320A PHE* 4.2 2.5 - - + -
325A GLU* 4.1 24.7 - - + +
326A VAL* 4.1 19.1 - - + -
329A ALA* 3.8 28.3 - - + -
374A ARG* 3.0 32.8 + - + +
375A LEU* 3.5 7.6 - - + +
377A GLN* 1.3 76.4 - - - +
379A ALA* 1.3 57.2 + - - +
381A ASP* 3.4 7.8 + - - +
382A HIS* 3.0 34.0 + - - -
387A ARG* 3.6 37.5 - - - +
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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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266A ARG* 4.3 4.3 - - - +
269A PHE* 4.4 8.5 - - + -
270A TRP* 3.7 31.4 - - + -
320A PHE* 3.6 26.8 - - + -
375A LEU 3.0 11.3 + - - +
376A ASP* 3.4 10.3 - - - +
377A GLN 3.2 0.2 - - - -
378A LEU* 1.3 76.6 - - - +
380A MET* 1.3 57.1 + - - +
382A HIS* 3.4 2.3 + - - +
383A LEU* 3.0 29.3 + - - +
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Residues in contact with MET 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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266A ARG* 3.6 45.0 - - + +
376A ASP* 2.9 14.6 + - - +
377A GLN* 3.3 30.9 + - - +
379A ALA* 1.3 73.5 - - - +
381A ASP* 1.3 65.3 + - - +
383A LEU* 3.2 8.0 + - - +
384A LEU* 3.0 49.2 + - + +
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Residues in contact with ASP 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A GLN* 2.9 47.8 + - - +
378A LEU* 3.7 9.9 - - - +
379A ALA 3.3 0.2 - - - -
380A MET* 1.3 75.7 - - - +
382A HIS* 1.3 58.6 + - - +
384A LEU* 3.4 1.8 + - - +
385A GLY 3.0 6.9 + - - -
386A ALA* 2.8 50.5 + - - +
387A ARG* 3.7 26.6 + - + -
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Residues in contact with HIS 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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269A PHE* 5.3 0.9 - - + -
316A ARG* 3.4 22.2 - - - +
319A ALA* 3.5 31.1 - - + +
320A PHE* 3.7 37.3 + + + -
323A ASP* 2.7 33.6 + - + +
326A VAL* 4.1 4.9 - - + -
378A LEU* 3.0 25.4 + - + +
379A ALA 3.8 4.0 - - - +
380A MET 3.2 0.2 - - - -
381A ASP* 1.3 73.5 - - - +
383A LEU* 1.3 67.1 + - - +
385A GLY* 3.2 11.0 + - - +
387A ARG* 3.5 26.6 + - + +
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Residues in contact with LEU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LEU* 4.6 17.7 - - + -
266A ARG* 3.6 39.3 - - + -
269A PHE* 3.8 25.9 - - + -
312A ILE* 5.9 0.2 - - - +
313A LEU* 3.5 31.9 - - + -
316A ARG* 2.9 30.3 + - + +
379A ALA 3.0 17.2 + - - +
380A MET* 3.2 10.3 + - - +
382A HIS* 1.3 76.2 - - - +
384A LEU* 1.3 67.1 + - + +
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Residues in contact with LEU 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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265A LEU* 5.9 6.1 - - + -
316A ARG* 3.7 4.5 + - - +
380A MET* 3.0 43.8 + - + +
381A ASP* 4.2 3.4 - - - +
383A LEU* 1.3 87.7 - - + +
385A GLY* 1.3 62.7 + - - +
386A ALA* 3.5 10.5 + - + +
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Residues in contact with GLY 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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316A ARG* 3.5 16.1 - - - +
381A ASP 3.0 5.1 + - - -
382A HIS* 3.2 10.0 + - - -
383A LEU 3.2 1.2 + - - -
384A LEU* 1.3 79.9 - - - +
386A ALA* 1.3 57.2 + - - +
387A ARG* 3.5 9.3 + - - +
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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