Contacts of the helix formed by residues 415 - 421 (chain C) in PDB entry 5AO3
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 ASP 415 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243C HIS* 5.6 0.3 - - - -
401C GLY* 3.1 11.4 - - - -
402C ALA* 2.6 44.6 + - - +
407C TYR* 3.4 31.8 - - + +
412C ALA 2.8 20.4 + - - +
413C ILE 3.2 0.2 - - - -
414C ASP* 1.3 81.1 - - - +
416C MET* 1.3 64.5 + - - +
417C GLU* 3.5 6.9 + - - +
418C ALA* 3.1 4.4 + - + +
419C TYR 2.8 14.9 + - - -
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Residues in contact with MET 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C TRP* 4.6 6.7 - - + -
236C GLY 4.3 1.3 - - - +
239C MET* 3.6 53.6 - - + +
240C MET* 3.7 30.7 - - + +
243C HIS* 3.2 27.5 + - + +
413C ILE* 3.3 27.6 - - - +
415C ASP* 1.3 75.5 + - - +
417C GLU* 1.3 50.5 + - - +
419C TYR* 3.6 24.0 - - + +
420C THR* 2.7 36.2 + - - -
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Residues in contact with GLU 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243C HIS* 3.7 22.3 + - + +
400C THR 4.1 2.2 - - - +
401C GLY* 3.8 8.1 - - - +
402C ALA* 3.3 44.7 - - + +
403C GLY 4.9 0.2 + - - -
415C ASP* 3.1 4.1 + - - +
416C MET* 1.3 75.8 - - - +
418C ALA* 1.3 65.3 + - - +
420C THR* 3.6 15.8 + - - -
421C LYS* 3.9 14.6 + - - +
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Residues in contact with ALA 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C ILE* 3.3 28.6 - - + +
400C THR 3.8 10.3 - - - -
401C GLY* 3.7 15.7 - - - +
407C TYR* 3.9 19.3 - - + -
412C ALA* 4.1 12.8 - - + +
415C ASP* 3.1 12.7 + - - +
417C GLU* 1.3 78.7 - - - +
419C TYR* 1.3 65.5 + - - +
421C LYS* 2.9 12.8 + - - -
422C LEU* 3.4 3.6 + - - +
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Residues in contact with TYR 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C ARG* 3.2 31.6 + - - -
209C GLY* 2.7 37.7 + - - -
211C GLY* 3.2 17.6 + - - -
217C PHE* 3.9 21.8 - + - -
231C TRP* 3.7 21.2 + + - -
236C GLY* 5.2 0.4 - - - -
240C MET* 3.5 19.7 - - + -
412C ALA* 3.5 15.9 + - - +
413C ILE* 4.2 5.8 - - + -
415C ASP 2.8 14.7 + - - +
416C MET* 3.8 24.2 - - + +
417C GLU 3.3 0.2 - - - -
418C ALA* 1.3 77.5 - - - +
420C THR* 1.3 62.8 + - - +
422C LEU* 3.0 33.8 + - + +
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Residues in contact with THR 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A TYR* 4.4 4.5 + - + -
139C PRO* 4.2 27.4 - - + +
140C GLN* 3.8 34.4 + - - +
143C ARG* 3.3 26.7 + - - +
240C MET* 3.8 3.9 - - - +
243C HIS* 4.8 0.7 - - - -
416C MET 2.7 22.9 + - - -
417C GLU* 3.6 11.3 - - - -
418C ALA 3.1 0.2 - - - -
419C TYR* 1.3 77.7 - - - +
421C LYS* 1.3 60.9 + - + +
422C LEU 3.3 2.3 + - - -
423C THR* 4.2 4.0 - - - +
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Residues in contact with LYS 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431A LEU 5.5 1.3 - - - -
432A TYR* 3.6 67.9 + - + +
433A SER 4.8 1.2 + - - -
434A THR* 3.5 30.3 - - - +
399C ILE* 4.2 13.9 - - + +
400C THR* 3.6 31.8 + - - +
417C GLU* 4.0 15.5 - - - +
418C ALA 2.9 9.9 + - - +
420C THR* 1.3 79.1 - - + +
422C LEU* 1.3 57.9 + - - +
423C THR 3.7 1.5 + - - -
425C ASN* 5.3 1.0 + - - -
426C ILE* 6.1 0.3 - - - +
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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