Contacts of the helix formed by residues 419 - 425 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103F GLY* 5.5 0.9 - - - -
104F ALA* 4.8 9.0 - - - +
105F HIS* 4.7 19.5 - - + +
292F VAL* 4.3 23.8 - - + -
295F GLU* 3.5 20.6 - - + +
299F SER* 3.1 29.6 - - - +
304F GLY 6.1 0.4 - - - +
338F MET* 4.9 3.1 - - - +
340F SER* 3.8 15.0 + - - +
341F SER 6.0 0.7 - - - +
342F ASP* 6.6 0.2 - - + -
418F THR* 1.3 71.9 - - - +
420F ALA* 1.3 61.4 + - - +
421F TYR 3.4 1.3 - - - -
422F ILE* 3.5 36.3 + - + +
423F LEU* 4.2 4.3 + - - +
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Residues in contact with ALA 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F MET* 4.0 2.1 - - - +
340F SER* 3.7 20.6 + - - +
382F ASN* 4.0 13.0 - - + +
418F THR* 3.0 19.2 + - - +
419F ILE* 1.3 78.6 - - - +
421F TYR* 1.3 63.3 + - - +
422F ILE 3.4 0.3 + - - -
423F LEU 3.6 2.6 + - - -
424F ALA* 3.4 18.2 + - - +
430F VAL* 3.9 24.0 - - + +
431F ILE 5.3 0.2 - - - -
432F ASP* 3.7 14.4 - - - +
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Residues in contact with TYR 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F GLY 5.5 2.4 + - - -
305F MET* 4.0 18.4 - - + +
380F GLY 5.5 3.4 - - - -
381F CYS* 4.7 9.2 - - - -
382F ASN* 3.6 25.8 - - + +
417F GLY* 5.7 3.1 - - - -
418F THR 3.3 26.9 - - - -
419F ILE* 4.9 0.2 - - - -
420F ALA* 1.3 77.9 - - - +
422F ILE* 1.3 87.4 + - + +
424F ALA* 3.7 7.4 - - - +
425F GLU* 3.2 27.7 + - - +
300H ILE* 4.0 36.3 - - + -
301H GLY* 4.1 8.1 - - - +
305H MET* 6.5 1.3 - - - -
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Residues in contact with ILE 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F SER* 3.9 13.2 - - - +
304F GLY 5.2 4.0 - - - +
305F MET* 3.7 50.9 - - + +
419F ILE* 3.5 40.6 - - + +
420F ALA 3.2 0.4 - - - -
421F TYR* 1.3 107.9 - - + +
423F LEU* 1.3 66.9 + - + +
425F GLU* 3.6 19.6 - - - +
426F TYR* 4.9 3.8 - - - -
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Residues in contact with LEU 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F ILE* 5.0 0.4 - - + -
103F GLY* 6.3 0.2 - - - -
290F ILE* 3.7 24.2 - - + -
309F PHE* 3.9 23.3 - - + -
338F MET* 3.3 40.6 - - + -
419F ILE 4.2 3.0 + - - +
420F ALA 3.6 2.2 + - - -
421F TYR 3.2 0.2 - - - -
422F ILE* 1.3 84.1 - - + +
424F ALA* 1.3 62.5 + - - +
425F GLU 2.9 6.9 + - - -
426F TYR* 3.1 46.9 + - + +
428F MET* 3.5 17.2 - - - +
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Residues in contact with ALA 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F ASN* 3.3 30.1 - - - +
420F ALA 3.4 10.8 + - - +
421F TYR* 3.2 6.7 + - - +
423F LEU* 1.3 74.3 - - - +
425F GLU* 1.3 52.9 + - - +
426F TYR 2.9 6.3 - - - -
427F GLY* 2.7 23.1 + - - -
428F MET 4.3 9.6 - - - +
430F VAL* 3.8 17.0 - - + +
302H ALA* 3.0 28.1 + - + +
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Residues in contact with GLU 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305F MET* 6.1 1.4 - - - +
421F TYR* 3.2 14.5 + - - +
422F ILE* 3.6 21.7 - - - +
423F LEU 2.9 0.4 - - - -
424F ALA* 1.3 77.2 - - - +
426F TYR* 1.3 61.5 + - + +
301H GLY* 3.9 5.7 + - - -
302H ALA 3.8 9.6 - - - +
305H MET* 3.6 42.7 - - + +
306H GLN* 3.1 6.1 - - - +
307H SER* 2.9 35.7 + - - +
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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