Contacts of the helix formed by residues 357 - 365 (chain A) in PDB entry 1YA8
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 TRP 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LEU* 4.7 6.7 - - + -
355A PHE 3.4 2.2 - - - -
356A GLY* 1.3 77.6 - - - +
358A LEU* 1.3 78.3 + - + +
359A ILE 3.3 2.2 - - - -
360A PRO* 3.2 6.7 - - - +
361A MET* 2.8 80.3 + - + +
457A SER* 3.9 28.7 - - - -
459A MET* 3.3 39.1 + - + -
460A LYS* 3.8 23.3 - - + -
461A PRO* 3.6 19.7 - - + +
464A VAL* 4.4 11.7 - - + -
467A ASP* 2.9 20.6 + - - +
2011A MVB 3.6 33.7 + - + +
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Residues in contact with LEU 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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97A LEU* 5.0 0.7 - - + -
100A LEU* 3.6 38.6 - - + -
101A PHE* 3.3 31.6 - - + -
357A TRP* 1.3 89.3 - - + +
359A ILE* 1.3 67.8 + - + +
361A MET* 3.6 6.3 - - + +
363A LEU* 3.2 39.9 + - + +
467A ASP* 3.0 22.4 + - - +
468A HIS* 3.3 33.9 - - + +
4001A SMB 4.6 3.4 - - - +
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Residues in contact with ILE 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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354A GLU 3.5 19.7 + - - +
355A PHE* 3.2 28.0 - - + -
357A TRP 4.8 0.2 - - - +
358A LEU* 1.3 72.1 - - + +
360A PRO* 1.3 75.4 - - + +
363A LEU* 2.8 18.3 + - - +
364A MET* 2.9 34.1 + - + +
425A MET* 4.9 2.2 - - + -
426A PHE* 3.9 21.5 - - + -
467A ASP* 5.1 0.2 + - - -
468A HIS* 3.8 33.8 - - + +
4001A SMB 4.7 18.4 - - + +
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Residues in contact with PRO 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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355A PHE* 3.2 54.3 - - + +
356A GLY 4.9 0.2 - - - -
357A TRP* 3.2 13.9 - - - +
359A ILE* 1.3 95.2 - - + +
361A MET* 1.3 59.3 + - - +
364A MET* 4.5 2.0 - - + +
365A SER* 3.1 4.3 + - - -
366A TYR* 3.0 44.9 + - + +
368A LEU* 5.1 1.8 - - + -
418A LEU* 4.8 2.9 - - + -
2011A MVB 3.6 22.7 + - + +
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Residues in contact with MET 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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96A LEU* 5.1 6.1 - - + -
100A LEU* 4.1 9.6 - - + -
357A TRP* 2.8 71.7 + - + +
358A LEU* 3.6 11.2 - - + +
360A PRO* 1.3 73.1 - - - +
363A LEU* 1.3 92.7 + - + +
365A SER* 3.6 12.2 + - - +
459A MET* 6.2 5.2 - - + +
2011A MVB 3.9 8.0 + - + +
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Residues in contact with LEU 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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96A LEU* 3.7 28.7 - - + -
97A LEU* 4.4 14.8 - - + +
100A LEU* 4.2 1.8 - - + -
304A LEU* 5.5 4.3 - - - +
305A SER* 4.8 6.1 + - - -
358A LEU* 3.2 35.4 + - + +
359A ILE* 2.8 6.3 + - - +
361A MET* 1.3 99.2 - - + +
364A MET* 1.3 59.6 + - + +
365A SER* 3.2 8.6 + - - -
4001A SMB 4.4 31.9 - - + +
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Residues in contact with MET 364 (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 4.0 24.2 - - - +
305A SER* 4.4 5.9 + - - +
306A LEU* 3.9 30.4 + - + +
355A PHE* 4.4 4.7 - - + -
359A ILE* 2.9 38.9 + - + +
360A PRO* 3.3 5.4 + - + +
363A LEU* 1.3 79.0 - - + +
365A SER* 1.3 72.2 + - - +
366A TYR* 4.3 9.0 - - + +
388A LEU* 3.4 48.2 - - + -
425A MET* 5.3 1.6 - - + -
4001A SMB 5.3 14.8 - - + -
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Residues in contact with SER 365 (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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305A SER* 4.8 8.1 + - - -
306A LEU 5.7 0.5 - - - +
308A LEU* 5.5 2.3 - - - +
360A PRO 3.1 5.0 + - - -
361A MET 3.6 9.1 + - - -
363A LEU 3.2 5.6 + - - -
364A MET* 1.3 82.3 - - - +
366A TYR* 1.3 67.1 + - - +
367A PRO* 3.4 9.7 - - - +
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Residues in contact with TYR 366 (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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306A LEU* 4.0 29.2 - - + -
355A PHE* 4.2 22.2 - + - -
360A PRO* 3.0 29.1 + - + +
364A MET* 3.2 8.2 - - + -
365A SER* 1.3 76.4 - - - +
367A PRO* 1.3 66.2 - - + +
368A LEU* 3.0 40.8 + - + +
381A LEU* 3.6 23.0 - - + +
385A SER* 2.8 22.0 + - - -
388A LEU* 4.6 7.2 - - + -
417A PHE* 3.5 23.2 - + - -
418A LEU* 5.7 0.7 - - + -
421A ILE* 3.1 24.8 - - + +
2011A MVB 4.7 4.7 + - - +
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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