Contacts of the helix formed by residues 378 - 390 (chain A) in PDB entry 6J8H
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 TYR 378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A LEU* 3.9 29.4 - - + -
267A PHE* 3.8 28.5 - + + -
270A ASN* 5.8 0.9 - - - -
371A LEU* 4.0 6.7 - - + -
374A ALA* 3.7 36.6 - - + -
375A GLY 3.4 9.5 + - - +
376A LYS 3.0 1.2 - - - -
377A THR* 1.3 82.8 - - + +
379A MET* 1.3 60.4 + - - +
380A ILE* 2.9 6.5 - - - +
381A PHE* 3.0 23.0 + - + +
382A PHE* 3.8 7.3 - - - -
1607A THR* 3.5 11.4 - - + +
1610A ARG* 2.1 39.0 + - - -
1611A VAL* 5.1 4.5 - - + +
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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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367A TYR* 3.7 27.4 - - + +
371A LEU* 3.8 20.0 - - + +
376A LYS 3.0 17.4 + - - +
377A THR 3.1 0.6 - - - +
378A TYR* 1.3 77.8 - - - +
380A ILE* 1.3 83.4 + - + +
382A PHE* 3.2 7.5 + - - +
383A VAL* 3.1 34.8 + - + +
1688A MET* 5.5 2.5 - - - +
1689A ILE* 4.3 22.4 - - + -
1692A PHE* 5.0 6.3 - - + -
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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
----------------------------------------------------------
377A THR* 3.6 18.2 - - + +
378A TYR* 2.9 0.6 - - - -
379A MET* 1.3 92.7 - - + +
381A PHE* 1.3 64.9 + - - +
383A VAL* 3.3 9.5 + - + +
384A VAL* 3.2 26.2 + - + +
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Residues in contact with PHE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 4.4 7.0 - + - -
262A ILE* 4.1 27.4 - - + -
263A GLY* 4.1 19.7 - - - -
266A LEU* 4.5 9.6 - - + -
267A PHE* 3.4 34.1 - + + -
344A PHE* 4.8 7.4 - + - -
354A LEU* 4.3 15.5 - - + -
357A LEU* 5.0 2.5 - - + -
378A TYR* 3.0 14.5 + - + +
380A ILE* 1.3 77.7 - - - +
382A PHE* 1.3 81.7 + + - +
384A VAL* 2.9 26.4 - - + +
385A VAL* 3.0 41.4 + - + +
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PHE* 4.7 4.0 - + - -
344A PHE* 5.5 1.8 - + - -
357A LEU* 4.0 38.1 - - + -
363A TRP* 4.7 0.7 - + + -
366A LEU* 4.4 4.5 - - + -
367A TYR* 3.6 47.1 - + + -
370A THR* 2.9 42.4 - - + -
371A LEU* 3.8 12.6 - - + -
378A TYR 3.8 13.7 - - - -
379A MET 3.2 6.6 + - - +
381A PHE* 1.3 94.6 - + - +
383A VAL* 1.3 60.2 + - - +
385A VAL* 4.4 3.1 - - - +
386A ILE* 2.8 38.4 + - + +
1692A PHE* 4.4 5.2 - - + -
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A MET* 3.1 32.9 + - + +
380A ILE* 3.3 12.1 + - + +
382A PHE* 1.3 75.4 - - - +
384A VAL* 1.3 59.8 + - + +
387A PHE* 2.9 54.1 + - + +
1692A PHE* 3.6 34.7 - - + -
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Residues in contact with VAL 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 4.8 13.4 - - + -
380A ILE* 3.2 16.9 + - + +
381A PHE* 2.9 31.4 - - + +
383A VAL* 1.3 82.1 - - - +
385A VAL* 1.3 59.5 + - + +
387A PHE* 4.7 2.2 - - - -
388A LEU* 2.9 36.8 + - + +
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Residues in contact with VAL 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A PHE* 3.9 26.2 - - + -
354A LEU* 4.1 21.5 - - + +
357A LEU* 4.4 23.6 - - + -
358A MET* 5.9 0.9 - - - +
381A PHE* 3.0 49.6 + - + +
382A PHE* 4.0 5.6 - - - +
383A VAL 3.4 0.2 - - - -
384A VAL* 1.3 77.8 - - + +
386A ILE* 1.3 59.3 + - + +
389A GLY* 2.7 36.9 + - - +
390A SER* 3.2 2.2 + - - +
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Residues in contact with ILE 386 (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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357A LEU* 3.5 45.8 - - + +
360A GLN* 4.3 16.2 - - + +
363A TRP* 3.7 35.2 - - + -
382A PHE* 2.8 24.7 + - - +
385A VAL* 1.3 71.3 - - + +
387A PHE* 1.3 61.4 + - + +
390A SER* 3.2 6.0 + - - -
391A PHE* 3.0 34.6 + - + +
1692A PHE* 4.2 16.8 - - + -
1696A THR* 4.4 16.6 - - + -
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Residues in contact with PHE 387 (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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383A VAL* 2.9 37.1 + - + +
384A VAL* 4.2 2.5 - - - +
386A ILE* 1.3 82.6 - - + +
388A LEU* 1.3 58.9 + - - +
391A PHE* 3.4 49.4 - + - +
392A TYR* 3.8 5.0 + - - +
1648A GLY* 6.1 4.5 - - - -
1651A LEU* 3.9 28.5 - - + -
1655A MET* 5.9 3.8 - - + -
1692A PHE* 4.9 15.0 - + - -
1695A THR* 5.8 4.0 - - + -
1751A VAL* 6.3 0.4 - - + -
1754A MET* 5.0 6.8 - - - +
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Residues in contact with LEU 388 (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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255A CYS* 4.6 13.2 - - - -
259A PHE* 4.2 20.0 - - + -
384A VAL* 2.9 22.9 + - + +
387A PHE* 1.3 77.5 - - + +
389A GLY* 1.3 71.3 + - - +
390A SER 3.5 0.2 - - - -
392A TYR* 2.9 44.3 - - + +
393A LEU* 3.6 2.4 + - + +
1637A LEU* 4.1 32.5 - - + -
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Residues in contact with GLY 389 (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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256A LEU* 6.2 1.8 - - - -
259A PHE* 4.3 13.9 - - - -
358A MET* 3.9 9.0 - - - +
384A VAL 3.9 0.2 + - - -
385A VAL* 2.7 23.6 + - - +
388A LEU* 1.3 84.3 - - - +
390A SER* 1.3 56.2 + - - -
393A LEU* 2.9 36.1 - - - +
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Residues in contact with SER 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A LEU 3.9 11.2 - - - -
358A MET* 3.1 25.3 + - - +
360A GLN* 2.0 37.2 + - - -
385A VAL 3.2 5.0 + - - -
386A ILE* 3.2 15.0 + - - -
389A GLY* 1.3 76.5 - - - +
391A PHE* 1.3 69.9 + - - +
392A TYR 3.3 0.9 - - - -
394A ILE* 3.3 28.2 + - - +
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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