Contacts of the helix formed by residues 324 - 328 (chain A) in PDB entry 2WO6
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 SER 324 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A ASP* 2.7 26.1 + - - -
289A LYS* 3.2 30.5 + - - -
321A PTR 5.7 0.4 - - - -
323A GLN* 1.3 71.4 - - - +
325A ARG* 1.3 56.5 + - - +
326A PHE 3.4 1.3 - - - -
327A TYR* 2.9 40.9 + - - +
328A ARG* 3.2 8.8 + - - +
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Residues in contact with ARG 325 (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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321A PTR 2.8 45.6 + - - +
323A GLN 3.6 1.2 + - - -
324A SER* 1.3 71.9 - - - +
326A PHE* 1.3 70.8 + - + +
327A TYR 3.0 1.4 + - - -
328A ARG* 3.1 33.8 + - - +
363A GLY 2.8 36.4 + - - +
364A ALA* 3.3 21.8 + - - +
365A ASN* 3.4 29.7 - - - +
366A GLU 4.8 0.2 - - - +
369A GLN* 3.1 29.4 - - + +
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Residues in contact with PHE 326 (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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324A SER* 3.3 0.6 + - - -
325A ARG* 1.3 85.5 - - + +
327A TYR* 1.3 86.6 + + + +
328A ARG 3.5 1.0 - - - +
345A TRP* 5.1 0.3 + - - -
349A CYS* 4.2 9.7 - - - +
359A PRO* 3.8 33.9 - - + -
361A PHE* 3.3 23.7 + - - +
362A SER* 3.7 10.5 - - - -
363A GLY 3.2 42.2 - - - -
369A GLN* 3.4 12.0 + - - -
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Residues in contact with TYR 327 (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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288A LEU 3.6 17.5 - - - +
289A LYS* 3.7 22.0 - - + -
290A PRO* 3.3 20.9 - - + +
291A GLU* 4.9 3.5 + - - -
323A GLN* 3.7 4.8 + - + -
324A SER* 2.9 22.8 + - - +
326A PHE* 1.3 105.2 - + + +
328A ARG* 1.3 62.1 + - - +
329A SER 3.6 1.0 + - - -
345A TRP* 3.5 12.1 - - - -
346A SER* 3.1 23.9 + - - +
349A CYS* 3.9 26.9 - - + -
350A ILE* 4.1 16.2 - - + -
353A GLU* 2.6 34.9 + - - -
359A PRO* 5.6 1.3 - - + -
360A LEU 6.2 0.7 - - - -
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Residues in contact with ARG 328 (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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321A PTR 2.7 49.2 + - - -
322A ILE 2.9 23.9 + - - +
323A GLN* 2.8 27.1 + - + +
324A SER* 3.2 4.8 + - - +
325A ARG* 3.1 30.4 + - - +
326A PHE 3.5 0.4 - - - -
327A TYR* 1.3 77.4 - - - +
329A SER* 1.3 73.5 + - - +
332A VAL* 3.8 17.0 - - + -
333A LEU* 3.7 24.5 - - + +
345A TRP* 3.5 9.4 + - - -
366A GLU* 2.8 44.7 + - - +
369A GLN* 4.9 1.4 + - - -
373A ILE* 4.0 5.4 - - - +
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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