Contacts of the helix formed by residues 324 - 328 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B ASP* 2.9 18.6 + - - +
289B LYS* 2.8 40.7 + - - -
323B GLN* 1.3 72.2 - - - +
325B ARG* 1.3 54.9 + - - +
326B PHE 3.2 2.0 - - - -
327B TYR* 2.6 38.5 + - - +
328B ARG 3.2 6.6 + - - -
7C PRO 3.7 14.4 - - - -
8C GLY 3.8 6.5 - - - -
9C THR* 3.3 12.5 + - - -
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PTR 2.6 40.8 + - - +
323B GLN 3.6 2.2 + - - -
324B SER* 1.3 71.8 - - - +
326B PHE* 1.3 63.3 + - + +
327B TYR 3.2 0.9 + - - -
328B ARG* 3.4 37.6 + - - +
363B GLY 3.1 27.5 + - - -
364B ALA* 3.4 20.7 + - - +
365B ASN* 3.8 22.7 - - - +
366B GLU* 5.4 0.2 - - - -
369B GLN* 3.0 35.7 + - + +
7C PRO* 3.4 38.6 + - + +
8C GLY 4.8 3.0 + - - -
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Residues in contact with PHE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B SER* 3.0 1.0 + - - -
325B ARG* 1.3 78.1 - - + +
327B TYR* 1.3 90.4 + + + +
328B ARG 3.5 0.6 - - - +
345B TRP* 5.2 0.3 + - - -
349B CYS* 4.1 13.3 - - - +
359B PRO* 3.3 39.5 - - + -
361B PHE* 3.5 22.1 + - - +
362B SER* 3.8 15.3 - - - -
363B GLY 3.5 24.7 - - - -
369B GLN* 3.5 11.0 + - - +
5C ALA* 4.1 18.8 - - + -
6C ARG* 4.2 7.9 - - - -
7C PRO* 3.6 34.7 + - + -
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Residues in contact with TYR 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B LEU 3.4 20.2 - - - +
289B LYS* 3.5 21.8 - - + -
290B PRO* 3.3 13.6 - - + +
323B GLN* 3.4 6.5 + - + +
324B SER* 2.6 26.7 + - - +
326B PHE* 1.3 95.8 - + + +
328B ARG* 1.3 57.8 + - - -
345B TRP* 3.8 4.9 - - - -
346B SER* 2.8 33.5 + - - +
349B CYS* 4.0 19.1 - - + -
350B ILE* 3.9 22.7 - - + -
353B GLU* 2.5 30.6 + - - -
359B PRO* 5.5 0.9 - - + -
360B LEU 6.1 0.7 - - - -
6C ARG* 2.7 32.1 + - - -
7C PRO 4.7 7.6 - - - -
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Residues in contact with ARG 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B PTR 2.8 57.2 + - - -
322B ILE 2.8 23.0 + - - +
323B GLN* 2.7 31.0 + - + +
324B SER 3.2 2.0 + - - +
325B ARG* 3.4 40.7 + - - +
326B PHE 3.5 0.6 - - - -
327B TYR* 1.3 76.8 - - - +
329B SER* 1.3 69.1 + - - +
332B VAL* 3.7 22.2 - - + +
333B LEU* 4.0 27.4 - - + +
345B TRP* 3.4 11.9 + - - -
366B GLU* 3.8 16.3 + - - +
369B GLN* 5.0 1.2 + - - -
373B ILE* 4.3 4.5 - - - +
10C PRO* 3.7 8.3 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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