Contacts of the helix formed by residues 357 - 368 (chain A) in PDB entry 4RYL
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 MET 357 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279A VAL* 3.3 30.5 - - + +
280A GLY* 3.6 20.4 - - - +
303A GLN* 5.8 4.9 - - - +
345A SER* 3.6 11.9 - - - +
346A GLU 3.7 17.5 - - - +
347A TRP* 2.8 19.9 + - + +
356A SER* 1.3 71.8 - - - +
358A LEU* 1.3 62.4 + - - +
359A ASP* 3.3 3.4 - - - -
360A SER* 3.1 31.8 + - - +
361A VAL* 3.2 12.1 + - - +
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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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347A TRP* 3.6 49.0 - - + +
353A LEU* 4.1 8.1 - - + -
356A SER* 3.1 17.6 + - - +
357A MET* 1.3 74.0 - - - +
359A ASP* 1.3 67.4 + - - +
361A VAL* 3.1 11.2 + - + -
362A LEU* 2.9 43.4 + - + +
439A ILE* 4.6 10.8 - - + -
441A CYS* 4.5 9.6 - - - -
444A THR* 5.6 0.4 - - + -
449A LEU* 3.6 40.2 - - + -
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Residues in contact with ASP 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLU* 4.8 1.8 - - - +
356A SER* 4.8 3.4 + - - +
357A MET 3.3 1.2 - - - -
358A LEU* 1.3 73.9 - - - +
360A SER* 1.3 58.1 + - - +
362A LEU* 3.4 3.3 + - - +
363A TYR* 3.0 27.5 + - - +
446A ILE* 3.7 27.7 - - + +
449A LEU* 3.5 22.9 - - - +
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Residues in contact with SER 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 4.3 7.2 - - - -
330A ILE* 3.6 20.8 - - - +
331A GLU* 3.2 22.3 + - - -
357A MET* 3.1 27.1 + - - +
359A ASP* 1.3 77.4 - - - +
361A VAL* 1.3 59.6 + - - +
363A TYR* 3.3 3.6 + - - +
364A ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A VAL* 4.1 10.3 - - + -
343A ILE* 4.5 9.3 - - + +
345A SER* 3.4 33.9 - - - +
347A TRP* 3.8 17.3 - - + +
357A MET* 3.2 11.8 + - + +
358A LEU* 3.1 19.4 + - + +
360A SER* 1.3 76.8 - - - +
362A LEU* 1.3 63.2 + - + +
364A ALA* 3.3 7.8 + - - +
365A LYS* 2.9 26.4 + - + +
375A VAL* 4.1 25.8 - - + -
441A CYS* 5.6 2.0 - - + -
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Residues in contact with LEU 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A LEU* 2.9 43.0 + - + +
359A ASP 3.7 4.0 - - - +
361A VAL* 1.3 76.2 - - + +
363A TYR* 1.3 64.9 - - - +
365A LYS* 3.3 17.4 + - + +
366A ASN* 3.0 36.4 + - - +
441A CYS* 3.9 14.1 - - + +
444A THR* 3.7 27.1 - - + +
445A SER* 3.8 31.9 - - - +
446A ILE* 3.8 17.5 - - + +
449A LEU* 4.4 5.4 - - + -
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Residues in contact with TYR 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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330A ILE* 3.7 27.4 - - + -
331A GLU* 3.7 42.6 + - + +
359A ASP 3.0 14.9 + - - +
360A SER* 3.4 11.7 - - - +
362A LEU* 1.3 77.9 - - - +
364A ALA* 1.3 60.2 + - - +
366A ASN* 3.8 4.8 - - - +
367A LYS* 2.9 61.1 + - + +
368A TYR* 4.7 1.1 - + - -
446A ILE* 5.9 0.4 - - - +
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Residues in contact with ALA 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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277A LEU* 3.9 26.0 - - + -
279A VAL* 4.0 12.3 - - + -
330A ILE* 4.1 7.9 - - + -
343A ILE* 3.7 6.7 - - + +
360A SER 2.9 13.6 + - - +
361A VAL 3.4 8.7 - - - +
363A TYR* 1.3 79.4 - - - +
365A LYS* 1.3 59.6 + - - +
368A TYR* 2.7 42.5 + - - +
369A LEU 3.5 1.4 + - - -
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Residues in contact with LYS 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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343A ILE* 3.5 13.2 - - + +
361A VAL* 2.9 14.6 + - + +
362A LEU* 3.5 24.0 - - + +
364A ALA* 1.3 73.9 - - - +
366A ASN* 1.3 83.3 + - - +
369A LEU* 3.1 49.4 + - + +
375A VAL* 4.6 10.1 - - + -
441A CYS 3.3 24.5 - - - +
442A HIS* 3.6 22.9 - - - +
444A THR 4.0 9.0 - - - -
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Residues in contact with ASN 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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339A LYS* 4.8 4.0 + - - -
362A LEU* 3.0 25.0 + - - +
363A TYR* 3.9 4.6 - - - +
365A LYS* 1.3 96.7 - - - +
367A LYS* 1.3 60.9 + - - +
369A LEU 5.2 1.0 + - - +
444A THR 5.4 2.4 + - - -
445A SER* 5.9 3.8 - - - +
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Residues in contact with LYS 367 (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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338A GLU 4.3 1.0 - - - +
339A LYS* 3.1 22.6 + - - -
363A TYR* 2.9 46.6 + - + +
366A ASN* 1.3 78.8 - - - +
368A TYR* 1.3 101.5 + - + +
369A LEU 3.9 0.4 - - - -
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Residues in contact with TYR 368 (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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277A LEU* 4.6 5.6 - - + -
330A ILE* 4.2 26.5 + - + -
333A VAL 3.7 19.2 + - - -
334A HIS* 5.2 0.2 - - - -
335A LEU* 3.7 43.3 + - + +
337A VAL 4.6 4.3 - - - -
338A GLU* 3.5 21.3 - - - +
339A LYS* 3.0 10.3 - - - -
340A VAL* 2.8 38.7 + - + -
363A TYR* 4.7 0.7 - + - -
364A ALA* 2.7 28.5 + - - +
367A LYS* 1.3 108.8 - - + +
369A LEU* 1.3 60.1 + - - +
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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