Contacts of the strand formed by residues 383 - 386 (chain G) in PDB entry 2JG7
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 THR 383 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325G TYR* 4.1 3.3 + - - -
352G TYR* 3.0 13.7 + - - -
356G ILE* 3.7 20.0 - - + -
366G LEU* 4.2 4.7 - - + -
368G CYS 3.3 13.0 - - - +
370G GLY* 2.7 27.0 + - - +
381G GLU 3.1 0.3 + - - -
382G PRO* 1.3 71.3 - - - +
384G ILE* 1.3 61.4 + - - +
385G ILE* 3.8 21.3 - - + -
402G PRO 2.9 14.1 + - - +
403G ILE* 3.5 11.2 - - + -
404G LEU* 2.8 33.5 + - - +
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Residues in contact with ILE 384 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318G VAL* 4.9 5.6 - - + +
321G ILE* 3.7 18.4 - - + -
322G ALA* 4.2 10.8 - - - +
325G TYR* 3.7 37.9 - - + +
366G LEU* 3.7 1.0 - - - -
367G VAL* 2.8 48.4 + - + -
368G CYS* 3.3 28.3 + - - +
383G THR* 1.3 77.3 - - - +
385G ILE* 1.3 69.5 + - - +
386G THR* 4.7 0.7 - - + -
404G LEU* 3.6 10.8 - - + +
406G VAL* 3.8 24.9 - - + -
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Residues in contact with ILE 385 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356G ILE* 4.4 7.4 - - + -
359G ALA* 3.6 24.9 - - + -
364G GLY* 3.8 12.6 - - - -
365G THR 3.4 9.4 - - - +
366G LEU* 3.8 20.6 - - + -
383G THR* 3.8 12.8 - - + -
384G ILE* 1.3 79.2 - - - +
386G THR* 1.3 69.2 + - - +
388G LEU* 3.8 23.0 + - + +
403G ILE* 3.7 23.3 - - + -
404G LEU 2.9 13.2 + - - +
405G TYR* 3.6 7.7 - - + +
406G VAL* 2.8 32.7 + - - +
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Residues in contact with THR 386 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G HIS* 4.5 13.5 - - + -
318G VAL* 4.1 19.1 - - + -
364G GLY* 3.6 2.1 - - - -
365G THR* 2.8 45.1 + - - +
367G VAL* 3.6 26.0 - - + +
384G ILE* 4.3 0.6 - - + -
385G ILE* 1.3 76.7 - - - +
387G GLY* 1.3 61.1 + - - +
388G LEU 3.4 4.9 + - - -
406G VAL* 3.9 23.6 - - + -
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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