Contacts of the helix formed by residues 419 - 425 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103R GLY* 5.5 1.3 - - - -
104R ALA* 4.8 9.0 - - - +
105R HIS* 4.7 18.8 - - + +
292R VAL* 4.3 24.5 - - + -
295R GLU* 3.6 19.7 - - + +
299R SER* 3.1 30.3 - - - +
304R GLY 6.1 0.2 - - - +
338R MET* 4.9 2.9 - - - +
340R SER* 3.9 15.1 + - - +
341R SER 6.0 1.6 - - - +
342R ASP* 6.6 0.2 - - + -
417R GLY 5.7 0.2 - - - +
418R THR* 1.3 72.2 - - - +
420R ALA* 1.3 62.0 + - - +
421R TYR 3.4 1.3 - - - -
422R ILE* 3.5 34.9 + - + +
423R LEU* 4.1 4.3 + - - +
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Residues in contact with ALA 420 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338R MET* 4.0 2.2 - - - +
340R SER* 3.7 23.3 + - - +
382R ASN* 4.0 12.3 - - + +
418R THR* 3.0 18.8 - - - +
419R ILE* 1.3 79.6 - - - +
421R TYR* 1.3 62.1 + - - +
422R ILE 3.4 0.2 + - - -
423R LEU 3.6 2.3 + - - -
424R ALA* 3.4 18.9 + - - +
430R VAL* 3.9 23.6 - - + +
431R ILE 5.3 0.2 - - - -
432R ASP* 3.7 14.4 - - - +
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Residues in contact with TYR 421 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298R GLY 5.5 2.4 + - - -
305R MET* 4.0 19.0 - - + +
380R GLY 5.6 2.9 - - - -
381R CYS* 4.8 8.7 - - - -
382R ASN* 3.6 26.5 - - + +
417R GLY* 5.6 3.4 - - - -
418R THR 3.2 28.0 + - - -
420R ALA* 1.3 77.5 - - - +
422R ILE* 1.3 88.8 + - + +
424R ALA* 3.7 6.3 - - - +
425R GLU* 3.2 26.6 + - - +
300T ILE* 4.1 33.0 - - + -
301T GLY* 4.0 12.6 - - - +
305T MET* 6.3 3.4 - - - -
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Residues in contact with ILE 422 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299R SER* 3.9 14.1 - - - -
304R GLY 5.1 3.8 - - - +
305R MET* 3.8 50.5 - - + +
419R ILE* 3.5 41.3 - - + +
420R ALA 3.2 0.8 - - - -
421R TYR* 1.3 108.6 - - + +
423R LEU* 1.3 67.6 + - + +
425R GLU* 3.6 20.2 - - - +
426R TYR* 4.9 2.9 - - - -
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Residues in contact with LEU 423 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101R ILE* 5.0 0.7 - - + -
290R ILE* 3.7 23.1 - - + -
309R PHE* 3.9 22.0 - - + -
338R MET* 3.3 42.4 - - + -
419R ILE 4.1 2.8 + - - +
420R ALA 3.6 2.2 + - - -
421R TYR 3.2 0.4 - - - -
422R ILE* 1.3 82.7 - - + +
424R ALA* 1.3 62.8 + - - +
425R GLU 2.9 6.9 + - - -
426R TYR* 3.1 48.4 + - + +
428R MET* 3.5 17.5 - - - +
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Residues in contact with ALA 424 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382R ASN* 3.3 29.6 - - - +
420R ALA 3.4 10.9 + - - +
421R TYR* 3.3 6.4 + - - +
423R LEU* 1.3 74.1 - - - +
425R GLU* 1.3 53.5 + - - +
426R TYR 2.9 6.3 - - - -
427R GLY* 2.7 22.4 + - - -
428R MET 4.3 9.0 - - - +
430R VAL* 3.8 17.4 - - + +
302T ALA* 3.1 29.8 + - + +
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Residues in contact with GLU 425 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305R MET* 6.1 1.4 - - - +
421R TYR* 3.2 15.9 + - - +
422R ILE* 3.6 22.1 - - - +
423R LEU 2.9 0.6 - - - -
424R ALA* 1.3 76.2 - - - +
426R TYR* 1.3 58.3 + - + +
427R GLY 3.4 0.4 - - - -
301T GLY* 4.1 4.0 - - - -
302T ALA 4.0 9.0 - - - +
305T MET* 3.5 42.1 - - + +
306T GLN* 3.1 3.5 - - - +
307T SER* 2.7 41.0 + - - +
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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