Contacts of the helix formed by residues 365 - 372 (chain A) in PDB entry 1J8V
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 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLN* 3.3 12.0 + - - -
136A ARG 5.2 2.6 + - - -
198A LYS* 4.3 25.3 + - + +
199A ASN* 5.4 0.9 + - - -
363A TYR 3.8 1.3 + - - +
364A ALA* 1.3 71.1 - - - +
366A PRO* 1.3 73.4 - - - +
367A ALA* 2.6 40.3 + - - +
368A MET* 2.9 36.3 + - + +
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Residues in contact with PRO 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LYS* 3.2 36.2 + - + +
71A GLN* 3.2 14.2 - - - +
364A ALA 3.5 8.7 - - - +
365A ASP* 1.3 87.1 - - - +
367A ALA* 1.3 61.2 + - + +
368A MET 3.1 1.1 + - - -
369A ALA* 3.3 7.8 + - - +
370A GLU* 5.9 0.3 - - - +
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Residues in contact with ALA 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365A ASP* 2.6 28.1 + - - +
366A PRO* 1.3 74.2 - - + +
368A MET* 1.3 61.8 + - - +
369A ALA 3.4 0.6 + - - -
370A GLU* 4.3 13.2 + - - +
371A GLN* 5.3 2.8 + - - +
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Residues in contact with MET 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.8 34.8 - - + +
136A ARG* 3.9 29.8 - - + +
137A ALA* 3.0 15.6 - - - +
198A LYS 5.7 0.9 - - - +
199A ASN* 3.1 32.8 - - + +
365A ASP* 2.9 36.1 + - + +
367A ALA* 1.3 78.0 - - - +
369A ALA* 1.3 59.9 + - - +
370A GLU 3.2 3.1 - - - -
371A GLN* 2.8 40.2 + - + +
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Residues in contact with ALA 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ALA* 3.7 17.2 - - + +
68A LYS* 3.5 26.7 - - + +
71A GLN* 3.6 8.0 - - - +
137A ALA 3.5 11.7 - - - -
366A PRO 3.3 16.1 + - - +
368A MET* 1.3 78.5 - - - +
370A GLU* 1.3 63.8 + - + +
371A GLN 3.1 1.0 + - - -
372A LEU* 3.3 20.8 + - - +
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Residues in contact with GLU 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ALA 4.3 10.1 + - - +
368A MET 3.1 0.8 + - - -
369A ALA* 1.3 77.5 - - + +
371A GLN* 1.3 68.7 + - - +
372A LEU 3.2 7.3 + - - +
374A LYS* 4.0 16.5 + - + +
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Residues in contact with GLN 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.3 48.9 - - + +
134A GLU* 3.1 17.4 - - - +
367A ALA 5.3 0.2 - - - +
368A MET* 2.8 45.9 + - + +
370A GLU* 1.3 81.6 - - - +
372A LEU* 1.3 61.0 + - - +
373A GLY 3.1 1.6 + - - -
374A LYS* 3.2 37.7 + - - +
377A HIS* 3.2 15.6 + - - -
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Residues in contact with LEU 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A THR* 5.2 0.9 - - - -
67A ALA* 4.0 24.0 - - + +
100A GLN* 4.5 0.7 - - + -
103A VAL* 3.5 27.6 - - + -
104A TYR 3.7 11.2 - - - +
105A GLY* 4.2 4.7 - - - +
106A ALA* 3.4 33.4 - - + +
134A GLU* 3.7 25.4 - - + +
137A ALA* 3.6 9.8 - - + +
138A THR* 4.3 3.4 - - + -
369A ALA 3.3 13.2 + - - +
370A GLU 3.2 6.5 - - - +
371A GLN* 1.3 76.2 - - - +
373A GLY* 1.3 61.9 + - - +
374A LYS 3.5 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