Contacts of the helix formed by residues 357 - 363 (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 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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353A MLY 3.1 13.4 + - - +
354A LEU 3.6 10.3 - - - +
356A GLY* 1.3 76.0 - - - +
358A VAL* 1.3 51.3 + - - +
360A HIS* 2.9 15.5 + - - +
361A TYR* 2.8 41.0 + - + -
386A ALA* 4.7 3.8 - - - +
389A LEU* 4.4 10.2 - - + +
390A MET* 3.7 39.3 - - + -
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Residues in contact with VAL 358 (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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275A VAL* 3.9 28.9 - - + +
288A PHE* 4.6 11.9 - - + -
314A TYR* 3.4 16.6 - - + -
354A LEU 3.4 17.7 - - - +
355A THR* 4.0 8.7 - - - +
357A ALA* 1.3 81.3 - - + +
359A MET* 1.3 62.9 + - - +
360A HIS 3.3 0.2 + - - -
361A TYR* 3.3 16.5 + - + +
390A MET* 5.3 3.1 - - + -
430A ALA* 4.0 28.3 - - + +
433A VAL* 4.7 14.6 - - + -
434A TYR* 4.8 9.9 - - + +
437A MET* 6.5 0.4 - - + -
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Residues in contact with MET 359 (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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288A PHE* 3.8 30.5 - - + +
291A ILE* 4.6 12.3 - - + -
292A MET* 4.2 25.6 - - + +
303A LEU* 5.2 0.2 - - + -
305A ILE* 3.8 31.0 - - + -
312A TYR* 3.6 44.1 - - + +
314A TYR* 4.5 8.9 - - - -
315A VAL* 4.7 6.3 - - + -
355A THR 3.5 13.9 - - - +
356A GLY* 3.0 19.6 + - - +
358A VAL* 1.3 78.9 - - - +
360A HIS* 1.3 62.8 - - - +
362A GLY* 3.4 10.7 + - - -
363A ASN* 3.8 5.9 + - - +
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Residues in contact with HIS 360 (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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303A LEU 3.2 27.1 - - - -
304A LEU* 3.1 21.7 + - + -
305A ILE* 3.9 14.6 - - + +
312A TYR* 4.2 12.6 + + - -
356A GLY 3.0 14.6 + - - -
357A ALA* 2.9 9.5 + - - +
359A MET* 1.3 78.9 - - - +
361A TYR* 1.3 60.7 + - - +
362A GLY 3.1 0.2 - - - -
363A ASN* 2.7 27.1 + - - +
364A LEU* 3.1 8.4 + - - +
382A VAL* 3.4 28.1 - - + +
385A MLY 4.1 20.7 - - + +
386A ALA* 4.2 10.9 + - + -
389A LEU* 3.9 13.6 - - + +
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Residues in contact with TYR 361 (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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314A TYR* 4.1 6.1 - - + -
357A ALA 2.8 26.9 + - - -
358A VAL* 3.5 13.2 - - + +
359A MET 3.3 0.2 - - - -
360A HIS* 1.3 73.3 - - - +
362A GLY* 1.3 59.2 + - - +
364A LEU* 2.7 41.5 + - + +
386A ALA* 3.6 26.0 - - + -
390A MET* 2.8 37.8 - - + -
392A LEU* 4.6 4.0 - - - +
397A LEU* 4.6 14.6 - - + +
401A LEU* 6.0 3.8 - - + -
426A VAL* 3.7 36.7 - - + +
429A LEU* 4.3 14.4 - - + -
430A ALA* 4.3 11.7 - - + -
433A VAL* 5.6 0.7 - - + -
607A VAL* 6.2 0.2 - - + -
611A TYR* 3.0 27.2 + - - -
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Residues in contact with GLY 362 (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 HIS* 4.1 20.2 - - - +
314A TYR* 3.1 45.2 - - - -
359A MET 3.4 5.7 + - - -
360A HIS 3.1 1.0 - - - -
361A TYR* 1.3 79.0 - - - +
363A ASN* 1.3 65.4 + - - +
364A LEU 3.4 2.1 - - - +
365A LYS* 4.2 10.4 + - - -
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Residues in contact with ASN 363 (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 2.6 30.5 + - - +
312A TYR* 3.8 15.7 - - - -
313A HIS* 4.0 13.9 + - - +
359A MET 3.8 4.9 + - - -
360A HIS* 2.7 16.4 + - - +
362A GLY* 1.3 83.0 - - - +
364A LEU* 1.3 67.3 + - - +
365A LYS* 3.1 18.1 + - - +
382A VAL* 4.1 23.7 - - + +
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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