Contacts of the helix formed by residues 340 - 347 (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 LEU 340 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LEU 5.2 0.9 - - - +
276A LEU* 3.8 4.0 - - + +
277A ALA* 3.5 40.2 - - + +
282A SER* 3.9 15.9 - - - +
283A ILE 3.7 22.0 - - - +
284A ILE* 3.5 24.0 - - + -
314A LEU* 3.7 25.1 - - + -
339A ASP* 1.3 77.3 + - + +
341A ALA* 1.3 63.4 + - - +
342A ILE 3.0 1.6 + - - -
343A ASP* 3.1 21.6 + - - +
344A MET* 3.8 2.8 + - - +
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Residues in contact with ALA 341 (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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331A GLU* 4.4 0.4 - - - +
339A ASP* 3.0 16.3 + - - +
340A LEU* 1.3 79.0 - - - +
342A ILE* 1.3 59.6 + - - +
344A MET* 3.1 19.7 + - - +
345A TRP 3.1 6.1 + - - -
464A PRO* 4.0 24.2 - - + +
467A ARG* 2.9 36.9 + - + +
468A ILE 6.2 0.2 - - - +
469A GLN* 6.3 3.4 - - + +
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Residues in contact with ILE 342 (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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284A ILE* 3.6 24.0 - - + -
286A CYS* 4.1 6.3 - - - -
322A ILE* 3.9 13.5 - - + -
323A GLN* 3.2 37.4 + - + +
329A SER* 3.5 21.3 - - - +
331A GLU* 3.6 9.9 - - - +
332A VAL* 4.2 0.9 - - + -
338A TYR* 3.5 39.3 - - + -
339A ASP 3.4 15.0 - - - +
340A LEU 3.0 1.4 + - - -
341A ALA* 1.3 78.0 - - - +
343A ASP* 1.3 67.5 + - - +
345A TRP* 3.4 4.0 + - - +
346A SER 3.2 15.6 + - - -
467A ARG* 4.0 4.9 - - - +
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Residues in contact with ASP 343 (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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273A LEU* 4.1 18.8 - - + +
276A LEU* 4.5 1.7 - - - +
283A ILE 4.3 3.1 - - - +
284A ILE* 3.6 13.4 - - - +
285A HIS* 2.8 34.3 + - - +
286A CYS* 3.1 25.3 + - - -
287A ASP 4.6 0.2 + - - -
288A LEU* 3.7 19.5 + - + +
323A GLN* 4.7 1.6 + - - -
340A LEU* 3.1 11.5 + - + +
342A ILE* 1.3 80.3 - - - +
344A MET* 1.3 55.9 + - - +
346A SER* 3.1 8.8 + - - -
347A LEU* 2.9 27.9 + - - +
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Residues in contact with MET 344 (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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270A CYS* 4.8 2.5 - - - -
273A LEU* 4.0 14.9 - - + +
340A LEU 3.8 2.7 + - - +
341A ALA* 3.1 15.0 + - - +
343A ASP* 1.3 76.7 - - - +
345A TRP* 1.3 65.2 + - - +
347A LEU* 3.1 11.1 + - - +
348A GLY 3.0 18.7 + - - -
459A MET* 3.8 51.7 - - + +
467A ARG* 4.2 4.7 - - - -
468A ILE* 3.3 29.6 - - - +
469A GLN 3.9 1.6 - - - -
470A PRO* 3.6 39.7 - - + -
473A ALA* 4.4 6.7 - - + -
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Residues in contact with TRP 345 (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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326A PHE 5.1 0.6 + - - -
327A TYR 3.5 20.7 + - - -
328A ARG 3.5 11.7 + - - -
329A SER* 3.6 13.2 - - - -
330A PRO* 3.6 34.3 - - + -
341A ALA 3.1 5.5 + - - -
342A ILE 3.5 8.5 - - - +
343A ASP 3.3 0.2 - - - -
344A MET* 1.3 76.8 - - - +
346A SER* 1.3 61.5 + - - +
348A GLY 3.2 8.8 + - - -
349A CYS* 3.2 24.9 + - - -
361A PHE* 3.9 14.5 - + - -
373A ILE* 3.8 26.2 - - + -
377A LEU* 3.6 22.9 - - + -
459A MET 3.7 10.2 + - - -
460A LEU* 3.5 48.3 - - + +
461A ASP 4.3 3.4 - - - -
462A TYR* 4.8 1.8 - + - -
467A ARG* 3.9 24.4 - - - +
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Residues in contact with SER 346 (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* 3.7 37.0 + - - +
323A GLN* 3.1 18.5 + - - +
327A TYR* 3.1 28.2 + - - +
342A ILE 3.2 2.2 + - - -
343A ASP* 3.1 11.2 + - - -
345A TRP* 1.3 77.8 - - - +
347A LEU* 1.3 58.4 + - - +
349A CYS* 3.2 6.0 + - - +
350A ILE* 2.9 31.2 + - - +
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Residues in contact with LEU 347 (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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266A ALA 4.6 0.4 - - - +
269A MET* 3.6 41.3 - - + -
270A CYS* 3.8 17.9 - - - -
273A LEU* 4.0 17.9 - - + -
288A LEU* 4.7 4.0 - - + +
343A ASP 2.9 12.9 + - - +
344A MET* 3.1 11.0 + - - +
346A SER* 1.3 78.0 - - - +
348A GLY* 1.3 57.8 + - - +
350A ILE* 3.2 14.7 + - + +
351A LEU* 2.9 53.8 + - + +
459A MET* 3.8 22.9 - - + -
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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