Contacts of the helix formed by residues 328 - 335 (chain A) in PDB entry 3DF0
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 PHE 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A PRO* 5.9 0.4 - - + -
222A PRO 6.1 0.2 - - - -
224A LEU* 3.8 26.2 - - + -
225A PHE* 3.3 48.7 - + + -
228A ILE* 4.5 10.8 - - + -
280A LYS* 3.1 38.1 + - + +
282A ILE* 4.6 8.7 - - + +
326A MET 3.6 1.2 + - - -
327A SER* 1.3 73.2 - - - +
329A SER* 1.3 56.2 + - - +
331A PHE* 3.5 33.6 - + - +
332A LEU* 2.8 66.4 + - + +
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Residues in contact with SER 329 (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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280A LYS* 4.0 20.1 + - - +
327A SER* 3.4 8.8 + - - -
328A PHE* 1.3 75.8 - - - +
330A ASP* 1.3 61.8 + - - +
332A LEU* 3.3 9.8 + - - +
333A ARG* 2.9 38.0 + - - +
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Residues in contact with ASP 330 (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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293A TRP* 3.7 28.9 - - + -
296A LYS* 3.9 18.5 - - - +
297A TRP* 5.5 0.9 - - - -
326A MET* 4.4 3.4 - - + -
327A SER* 2.7 24.9 + - - +
329A SER* 1.3 70.9 - - - +
331A PHE* 1.3 55.2 + - - +
333A ARG* 3.7 19.3 + - - -
334A HIS* 2.6 63.1 + - - +
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Residues in contact with PHE 331 (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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217A LEU* 3.7 31.9 - - + +
228A ILE* 5.4 0.4 - - + -
240A CYS* 4.0 22.0 - - + -
266A VAL* 4.3 5.8 - - + -
282A ILE* 4.0 20.4 - - + -
284A ILE* 3.8 31.0 - - + -
326A MET* 3.6 19.4 - - - -
327A SER 3.0 20.1 + - - +
328A PHE* 3.5 35.4 - + - +
330A ASP* 1.3 77.5 - - - +
332A LEU* 1.3 59.8 + - + +
335A TYR* 3.1 37.6 + + - +
338A LEU* 4.5 11.9 - - + -
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Residues in contact with LEU 332 (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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217A LEU* 3.5 50.2 - - + +
220A PRO* 4.7 15.9 - - + -
224A LEU* 4.2 5.2 - - + -
328A PHE* 2.8 67.7 + - + +
329A SER* 3.6 7.6 - - - +
331A PHE* 1.3 78.3 - - + +
333A ARG* 1.3 61.2 + - - +
334A HIS 3.5 0.2 + - - -
335A TYR 3.7 8.0 - - - +
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Residues in contact with ARG 333 (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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329A SER* 2.9 28.8 + - - +
330A ASP* 3.1 27.5 + - - +
332A LEU* 1.3 78.8 - - - +
334A HIS* 1.3 76.2 + - + +
335A TYR 4.9 0.2 - - - +
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Residues in contact with HIS 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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242A ILE* 3.2 27.3 - - + +
254A THR* 5.9 1.1 - - - -
256A GLN* 4.1 18.8 + - + -
258A LEU* 4.3 24.2 - - + -
293A TRP* 3.6 21.3 - + - -
326A MET* 4.9 1.9 - - + +
330A ASP* 2.6 55.9 + - - +
333A ARG* 1.3 91.3 - - + +
335A TYR* 1.3 70.9 + - + +
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Residues in contact with TYR 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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217A LEU* 3.2 34.5 - - + +
240A CYS* 4.0 13.2 - - + -
241A SER* 3.5 29.6 - - - +
242A ILE* 3.6 11.9 - - + -
258A LEU* 3.2 34.2 - - + +
264A TYR* 3.3 46.7 - + - -
284A ILE* 4.3 5.5 - - + +
324A PHE* 4.2 4.5 - - - -
326A MET* 4.0 21.1 - - + -
331A PHE* 3.1 32.3 + + + +
332A LEU 3.7 7.1 - - - +
333A ARG 4.9 0.5 - - - +
334A HIS* 1.3 81.4 - - + +
336A SER* 1.3 58.8 + - - +
337A ARG 4.6 1.6 - - - +
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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