Contacts of the helix formed by residues 419 - 425 (chain O) in PDB entry 2GLJ
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 ILE 419 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103O GLY* 5.5 1.1 - - - -
104O ALA* 4.8 9.0 - - - +
105O HIS* 4.7 20.4 - - + +
292O VAL* 4.3 24.0 - - + -
295O GLU* 3.5 20.6 - - + +
299O SER* 3.2 29.4 - - - +
338O MET* 4.9 3.5 - - - +
340O SER* 3.8 14.4 + - - +
341O SER 6.0 1.6 - - - +
342O ASP* 6.6 0.2 - - + -
417O GLY 5.7 0.2 - - - +
418O THR* 1.3 71.0 - - - +
420O ALA* 1.3 63.0 + - - +
421O TYR 3.4 1.6 - - - -
422O ILE* 3.5 35.4 + - + +
423O LEU* 4.1 4.7 + - - +
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Residues in contact with ALA 420 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338O MET* 4.0 2.6 - - - +
340O SER* 3.7 19.4 + - - +
382O ASN* 4.0 11.4 - - + +
418O THR* 2.9 18.6 - - - +
419O ILE* 1.3 77.0 - - - +
421O TYR* 1.3 64.6 + - - +
422O ILE 3.4 0.3 + - - -
423O LEU 3.6 2.1 + - - -
424O ALA* 3.4 19.2 + - - +
430O VAL* 3.8 26.1 - - + +
431O ILE 5.3 0.2 - - - -
432O ASP* 3.7 14.1 - - - +
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Residues in contact with TYR 421 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300N ILE* 4.1 36.3 - - + -
301N GLY* 4.1 9.8 - - - +
305N MET* 6.5 0.9 - - - -
298O GLY 5.4 2.8 + - - -
305O MET* 4.0 18.7 - - + +
380O GLY 5.6 3.1 - - - -
381O CYS* 4.8 9.0 - - - -
382O ASN* 3.6 25.8 - - + +
417O GLY* 5.6 3.1 - - - -
418O THR 3.2 27.3 + - - -
420O ALA* 1.3 77.1 - - - +
422O ILE* 1.3 89.0 + - + +
423O LEU 3.2 0.2 - - - -
424O ALA* 3.8 6.2 - - - +
425O GLU* 3.2 26.4 + - - +
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Residues in contact with ILE 422 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299O SER* 3.9 14.6 - - - -
304O GLY 5.1 4.3 - - - +
305O MET* 3.8 49.4 - - + +
419O ILE* 3.5 39.7 - - + +
420O ALA 3.2 0.4 - - - -
421O TYR* 1.3 108.2 - - + +
423O LEU* 1.3 67.1 + - + +
425O GLU* 3.6 19.5 - - - +
426O TYR* 4.9 3.5 - - - -
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Residues in contact with LEU 423 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101O ILE* 5.0 0.4 - - + -
290O ILE* 3.7 23.3 - - + -
309O PHE* 3.9 23.6 - - + -
338O MET* 3.3 41.5 - - + -
419O ILE 4.1 3.3 + - - +
420O ALA 3.6 2.4 + - - -
421O TYR 3.2 0.2 - - - -
422O ILE* 1.3 83.6 - - + +
424O ALA* 1.3 63.1 + - - +
425O GLU 2.9 7.3 + - - -
426O TYR* 3.1 47.5 + - + +
428O MET* 3.5 18.5 - - - +
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Residues in contact with ALA 424 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302N ALA* 3.0 28.6 + - + +
382O ASN* 3.3 30.1 - - - +
420O ALA 3.4 11.7 + - - +
421O TYR* 3.3 5.7 + - - +
423O LEU* 1.3 73.5 - - - +
425O GLU* 1.3 53.4 + - - +
426O TYR 2.9 5.8 - - - -
427O GLY* 2.7 22.9 + - - -
428O MET 4.3 10.3 - - - +
430O VAL* 3.8 16.1 - - + +
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Residues in contact with GLU 425 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301N GLY* 3.9 6.6 + - - -
302N ALA 3.8 9.2 - - - +
305N MET* 3.7 41.8 - - + +
306N GLN* 3.2 5.9 - - - +
307N SER* 3.0 35.8 + - - +
305O MET* 6.1 1.4 - - - +
421O TYR* 3.2 14.1 + - - +
422O ILE* 3.6 22.1 - - - +
423O LEU 2.9 0.4 - - - -
424O ALA* 1.3 76.8 - - - +
426O TYR* 1.3 61.2 + - + +
427O GLY 3.4 0.2 - - - -
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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