Contacts of the helix formed by residues 332 - 335 (chain A) in PDB entry 1ADI
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 LEU 332 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ALA* 3.7 13.2 - - + -
329A LEU* 4.4 15.0 - - + -
330A THR 3.4 1.4 + - - -
331A LYS* 1.3 72.4 - - - +
333A ASP* 1.3 68.8 + - - +
334A VAL 3.1 2.0 - - - -
335A LEU* 2.8 24.1 + - + +
336A ASP* 3.7 2.3 - - - +
378A TRP* 3.8 18.4 - - + -
382A THR* 4.2 20.2 - - + +
391A LEU* 4.3 11.2 - - + -
395A ALA* 4.2 20.4 - - + -
398A TYR* 3.4 39.3 - - + -
399A ILE* 5.0 11.4 - - + -
413A ILE* 5.5 10.3 - - + -
414A SER 5.3 1.6 + - - -
415A THR* 6.4 0.4 - - + +
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLN* 4.7 2.5 + - - -
331A LYS* 3.4 14.0 - - - +
332A LEU* 1.3 74.7 - - - +
334A VAL* 1.3 74.3 + - - +
336A ASP* 2.4 51.9 + - - +
382A THR* 4.1 7.3 - - + +
383A PHE* 2.9 55.8 - - + +
415A THR 3.8 8.7 - - - +
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Residues in contact with VAL 334 (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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269A TYR* 3.6 26.7 - - + -
289A PHE* 3.8 4.3 - - - -
290A LEU* 3.9 20.9 - - + +
293A GLN* 2.6 40.8 + - + +
294A GLY* 3.9 27.4 - - - +
331A LYS* 3.4 34.5 - - + +
333A ASP* 1.3 94.0 + - - +
335A LEU* 1.3 57.9 + - - +
336A ASP 3.2 1.2 + - - +
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Residues in contact with LEU 335 (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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268A ALA* 3.7 15.7 - - + +
269A TYR* 4.5 12.8 - - + -
290A LEU* 3.9 20.4 - - + -
309A TRP* 3.4 33.9 - - + -
332A LEU 2.8 14.5 + - - +
333A ASP 2.8 2.2 + - - -
334A VAL* 1.3 69.0 - - - +
336A ASP* 1.3 66.9 + - - +
338A LEU* 3.6 24.6 + - + +
341A VAL* 4.4 8.3 - - + +
378A TRP* 3.7 21.6 + - + +
398A TYR* 3.4 43.7 - - + +
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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