Contacts of the helix formed by residues 381 - 386 (chain A) in PDB entry 5JG8
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 ASN 381 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A VAL* 4.2 14.6 - - - +
327A PHE* 4.5 1.0 - - - -
342A TYR* 2.9 32.9 + - - -
364A GLY 3.1 16.2 + - - +
365A GLY 3.3 20.4 + - - +
366A PHE* 3.7 5.2 - - + +
380A LEU* 1.3 71.5 - - - +
382A MET* 1.3 60.2 + - - +
383A ASN* 3.0 34.1 + - - +
384A PHE* 3.8 15.5 + - + -
385A CYS 4.5 0.2 + - - -
402A GLN* 2.6 34.7 + - - +
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Residues in contact with MET 382 (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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316A VAL 4.6 4.4 + - - -
380A LEU* 3.5 30.2 + - + +
381A ASN* 1.3 72.2 + - - +
383A ASN* 1.3 58.4 + - - +
384A PHE 3.3 0.4 - - - -
385A CYS* 2.7 52.1 + - - +
386A SER 3.2 4.0 + - - -
424A GLY* 3.9 5.8 - - - -
425A HIS* 3.6 21.5 - - + +
426A ILE* 3.1 53.8 - - + +
428A PRO* 4.3 8.5 - - + -
431A CYS* 4.3 2.5 - - - -
435A TRP* 4.2 15.0 - - + -
439A TYR* 5.6 0.9 - - + -
455A PHE* 3.9 17.7 - - + -
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Residues in contact with ASN 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A VAL* 3.7 10.6 + - - +
317A GLY 3.1 20.2 + - - -
318A ASN* 3.3 28.2 + - - +
325A ASN* 5.0 1.4 - - - +
327A PHE* 3.3 45.1 - - + -
381A ASN* 3.0 21.6 + - - +
382A MET* 1.3 74.3 - - - +
384A PHE* 1.3 59.1 + - - +
385A CYS 2.9 4.0 - - - -
386A SER* 2.8 30.2 + - - -
389A ASN* 3.2 16.4 + - + +
392A LEU* 4.0 0.2 - - - +
425A HIS* 6.4 0.2 - - - -
426A ILE* 4.3 6.7 - - - +
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Residues in contact with PHE 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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327A PHE* 3.6 28.3 - - + -
328A PRO 4.1 2.7 - - - -
329A PRO* 3.8 23.1 - - + -
330A PRO* 4.3 4.7 - - + -
342A TYR* 3.7 16.6 - + - -
364A GLY* 3.4 27.6 - - - -
366A PHE* 4.5 2.0 - + - -
381A ASN* 3.8 13.4 + - + +
382A MET 3.3 0.4 - - - -
383A ASN* 1.3 78.2 - - + +
385A CYS* 1.3 57.7 + - - +
389A ASN* 4.3 2.0 - - - -
392A LEU* 3.6 13.2 - - + +
399A PRO* 3.4 41.6 - - + +
400A ALA* 3.6 26.9 - - + -
402A GLN* 3.9 22.2 - - - +
432A LEU* 5.0 1.7 - - - +
435A TRP* 3.6 11.8 - - - +
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Residues in contact with CYS 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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381A ASN 4.5 0.6 + - - -
382A MET* 2.7 30.5 + - - +
384A PHE* 1.3 77.4 - - - +
386A SER* 1.3 62.6 + - - +
392A LEU* 4.5 0.9 - - - -
431A CYS* 2.0 50.9 - - - +
432A LEU* 3.5 26.5 + - - +
435A TRP* 3.2 47.1 - - + +
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Residues in contact with SER 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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325A ASN* 4.2 5.9 + - - -
382A MET 3.2 2.6 + - - -
383A ASN* 2.8 24.3 + - - -
384A PHE 3.4 0.2 - - - -
385A CYS* 1.3 79.3 - - - +
387A ARG* 1.3 61.9 + - - +
388A GLU* 3.0 22.3 + - - +
389A ASN* 3.4 12.8 + - - +
392A LEU* 3.1 23.6 - - - +
426A ILE* 3.9 27.3 - - - +
430A HIS 5.7 0.4 - - - -
431A CYS* 5.3 2.0 - - - +
432A LEU* 3.8 3.9 - - - +
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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