Contacts of the helix formed by residues 383 - 390 (chain A) in PDB entry 2MYS
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 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A LEU* 3.9 17.8 - - + +
379A GLY 4.6 3.9 + - - +
380A THR* 4.5 9.2 - - - -
381A GLU 3.5 0.6 - - - +
382A VAL* 1.3 79.2 - - - +
384A ASP* 1.3 54.3 + - - +
386A ALA* 3.1 3.1 + - - +
387A ALA* 2.6 38.5 + - - +
394A SER* 3.6 8.3 - - - +
397A LEU* 4.6 3.1 - - + +
398A LEU* 3.6 42.6 - - + -
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Residues in contact with ASP 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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380A THR* 2.4 33.4 + - - +
381A GLU* 3.4 12.5 - - - +
383A ALA* 1.3 81.2 - - - +
385A MLY 1.3 58.7 + - + +
387A ALA* 3.6 1.9 - - - +
388A TYR* 3.0 29.6 + - - +
394A SER* 2.3 38.4 + - - -
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Residues in contact with MLY 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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304A LEU* 4.1 47.3 - - + -
360A HIS* 4.1 27.1 - - + +
381A GLU* 2.9 55.8 - - - +
382A VAL* 3.0 12.5 + - + +
384A ASP* 1.3 77.2 + - + -
386A ALA* 1.3 66.5 + - - +
387A ALA 3.1 0.2 - - - -
388A TYR* 3.8 2.1 - - - +
389A LEU* 2.9 31.6 + - - +
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Residues in contact with ALA 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 ALA* 4.5 4.3 - - - +
360A HIS* 4.2 13.6 - - + +
361A TYR* 3.6 35.0 - - + -
364A LEU* 4.6 4.7 - - + -
382A VAL 2.9 15.2 + - - +
383A ALA* 3.6 6.3 - - - +
385A MLY 1.3 78.3 + - - +
387A ALA* 1.3 64.0 + - - +
389A LEU* 3.7 4.0 - - - +
390A MET* 3.1 27.7 + - - +
397A LEU* 5.1 4.3 - - + -
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Residues in contact with ALA 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 ALA 2.6 22.1 + - - +
384A ASP 3.6 4.5 - - - +
386A ALA* 1.3 74.8 - - - +
388A TYR* 1.3 57.9 + - - +
391A GLY 3.1 3.1 + - - -
392A LEU* 2.6 50.6 + - + +
393A ASN 3.9 2.5 - - - +
394A SER* 3.5 34.1 - - - +
397A LEU* 4.6 6.2 - - + +
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Residues in contact with TYR 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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302A MET 4.8 3.8 - - - -
304A LEU* 3.9 19.5 - - + -
353A MLY 3.1 40.4 - - - -
384A ASP 3.0 18.4 + - - +
385A MLY 3.8 2.2 - - - +
387A ALA* 1.3 75.1 - - - +
389A LEU* 1.3 89.5 + - + +
391A GLY* 3.1 13.0 + - - +
392A LEU 4.6 3.8 - - - +
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Residues in contact with LEU 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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302A MET 3.6 23.1 - - - +
303A LEU* 3.1 26.5 - - - +
304A LEU* 4.0 4.3 - - + -
353A MLY 3.4 63.7 - - + +
354A LEU* 4.4 4.3 - - - +
356A GLY 4.7 0.9 - - - -
357A ALA* 4.4 10.5 - - + +
360A HIS* 3.9 17.9 - - + +
385A MLY 2.9 18.9 + - - +
386A ALA 3.7 3.4 - - - +
388A TYR* 1.3 98.4 - - + +
390A MET* 1.3 58.6 + - - +
616A VAL* 4.4 2.8 - - - +
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Residues in contact with MET 390 (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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354A LEU* 4.1 16.6 - - + +
357A ALA* 3.7 24.9 - - + -
358A VAL* 5.3 3.6 - - + -
361A TYR* 2.8 43.1 - - + +
386A ALA 3.1 15.6 + - - +
387A ALA 4.1 0.2 - - - +
388A TYR 3.1 0.4 - - - -
389A LEU* 1.3 77.9 - - - +
391A GLY* 1.3 50.1 + - - +
392A LEU* 4.1 14.1 - - + +
433A VAL* 4.2 26.2 - - + -
611A TYR* 4.2 19.1 - - + +
614A SER* 2.4 28.9 + - - -
616A VAL* 3.4 11.3 - - - +
619A LEU* 3.6 19.0 - - + +
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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