Contacts of the helix formed by residues 419 - 425 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103H GLY* 5.5 0.9 - - - -
104H ALA* 4.8 8.3 - - - +
105H HIS* 4.7 19.3 - - + +
292H VAL* 4.3 24.2 - - + -
295H GLU* 3.5 20.4 - - + +
299H SER* 3.1 29.4 - - - +
338H MET* 4.9 3.1 - - - +
340H SER* 3.9 15.7 + - - +
341H SER 6.0 1.3 - - - +
342H ASP* 6.6 0.2 - - + -
417H GLY 5.6 0.7 - - - +
418H THR* 1.3 71.1 - - - +
420H ALA* 1.3 61.7 + - - +
421H TYR 3.4 1.6 - - - -
422H ILE* 3.5 36.2 + - + +
423H LEU* 4.2 4.2 + - - +
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Residues in contact with ALA 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338H MET* 4.0 2.2 - - - +
340H SER* 3.7 19.2 + - - +
382H ASN* 4.0 11.9 - - + +
418H THR* 2.9 18.8 + - - +
419H ILE* 1.3 76.8 - - - +
421H TYR* 1.3 64.7 + - - +
422H ILE 3.4 0.3 + - - -
423H LEU 3.6 1.7 + - - -
424H ALA* 3.4 18.5 + - - +
430H VAL* 3.8 26.2 - - + +
431H ILE 5.3 0.4 - - - -
432H ASP* 3.7 14.4 - - - +
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Residues in contact with TYR 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300G ILE* 4.1 33.2 - - + -
301G GLY* 4.1 11.6 - - - +
305G MET* 6.4 1.8 - - - -
298H GLY 5.5 2.4 + - - -
305H MET* 4.0 18.3 - - + +
380H GLY 5.5 3.6 - - - -
381H CYS* 4.8 9.6 - - - -
382H ASN* 3.6 26.1 - - + +
417H GLY* 5.6 2.7 - - - -
418H THR 3.3 27.6 + - - -
420H ALA* 1.3 76.3 - - - +
422H ILE* 1.3 88.5 + - + +
423H LEU 3.2 0.2 - - - -
424H ALA* 3.7 6.7 - - - +
425H GLU* 3.2 27.3 + - - +
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Residues in contact with ILE 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H SER* 3.9 13.9 - - - -
304H GLY 5.1 3.8 - - - +
305H MET* 3.7 48.9 - - + +
419H ILE* 3.5 39.9 - - + +
420H ALA 3.2 0.6 - - - -
421H TYR* 1.3 108.9 - - + +
423H LEU* 1.3 67.1 + - + +
425H GLU* 3.6 19.5 - - - +
426H TYR* 4.9 3.5 - - - -
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Residues in contact with LEU 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ILE* 5.0 0.2 - - + -
290H ILE* 3.8 23.1 - - + -
309H PHE* 3.9 23.1 - - + -
338H MET* 3.2 43.3 - - + -
419H ILE 4.2 3.2 + - - +
420H ALA 3.6 2.0 + - - -
421H TYR 3.2 0.2 - - - -
422H ILE* 1.3 83.4 - - + +
424H ALA* 1.3 63.1 + - - +
425H GLU 2.8 6.4 + - - -
426H TYR* 3.1 48.8 + - + +
428H MET* 3.6 16.7 - - - +
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Residues in contact with ALA 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G ALA* 3.1 26.7 + - + +
382H ASN* 3.3 30.3 - - - +
420H ALA 3.4 10.8 + - - +
421H TYR* 3.2 6.4 + - - +
423H LEU* 1.3 73.7 - - - +
425H GLU* 1.3 53.9 + - - +
426H TYR 2.9 6.1 - - - -
427H GLY* 2.7 22.4 + - - -
428H MET 3.9 9.8 + - - +
430H VAL* 3.8 17.1 - - + +
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Residues in contact with GLU 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301G GLY* 4.0 5.3 - - - -
302G ALA 4.0 8.5 - - - +
305G MET* 3.6 41.1 - - + +
306G GLN* 3.2 4.6 - - - +
307G SER* 2.9 36.8 + - - +
305H MET* 6.1 1.7 - - - +
421H TYR* 3.2 15.7 + - - +
422H ILE* 3.6 21.4 - - - +
423H LEU 2.8 0.2 - - - -
424H ALA* 1.3 76.8 - - - +
426H TYR* 1.3 61.6 + - + +
427H 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