Contacts of the helix formed by residues 349 - 356 (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 CYS 349 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A PHE 4.2 9.2 - - - +
327A TYR* 3.9 19.5 - - + -
345A TRP* 3.2 41.6 + - - -
346A SER 3.2 8.2 + - - +
348A GLY* 1.3 76.1 - - - +
350A ILE* 1.3 61.8 + - - +
352A VAL* 3.6 2.8 + - - +
353A GLU* 3.2 21.8 + - - +
360A LEU* 4.4 19.5 + - + +
361A PHE* 3.8 28.3 - - - -
460A LEU* 4.0 4.7 - - - +
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Residues in contact with ILE 350 (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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245A LEU* 5.0 2.5 - - + -
288A LEU* 3.7 16.6 - - + +
289A LYS* 3.6 40.2 - - - +
290A PRO* 4.1 13.9 - - + -
293A ILE* 4.0 24.9 - - + -
327A TYR* 4.1 10.8 - - + -
346A SER 2.9 21.2 + - - +
347A LEU* 3.2 17.0 + - + +
349A CYS* 1.3 77.3 - - - +
351A LEU* 1.3 62.3 + - + +
353A GLU* 3.1 8.8 + - - +
354A MET* 2.9 42.2 + - + +
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Residues in contact with LEU 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A THR* 3.8 19.0 - - + +
265A PHE* 4.4 7.6 - - + -
266A ALA* 3.6 45.8 - - + +
269A MET* 5.6 0.4 - - + -
347A LEU* 2.9 44.8 + - + +
350A ILE* 1.3 77.0 - - + +
352A VAL* 1.3 68.7 + - - +
354A MET* 3.2 15.0 + - + +
355A HIS 3.3 7.8 + - - -
452A PHE* 3.8 13.7 - - + -
455A LEU* 5.4 1.8 - - + -
456A ILE* 4.0 14.4 - - + -
459A MET* 3.9 20.4 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A GLY 3.3 16.4 + - - +
349A CYS 4.0 4.3 - - - +
350A ILE 3.3 0.6 - - - -
351A LEU* 1.3 75.7 - - - +
353A GLU* 1.3 59.1 + - - +
355A HIS* 3.1 3.6 + - - +
356A THR* 2.8 46.9 + - + +
360A LEU* 4.3 24.7 - - + -
423A LEU* 4.0 19.7 - - + -
426A ILE* 4.5 3.1 - - + -
427A LEU* 4.1 13.2 - - + -
452A PHE* 4.4 7.4 - - + -
456A ILE* 3.7 30.5 - - + -
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Residues in contact with GLU 353 (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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246A TYR* 5.2 8.1 - - - -
249A LEU* 3.9 18.2 - - + +
254A PHE* 6.1 0.3 - - - -
290A PRO* 4.0 13.1 - - + +
327A TYR* 2.6 38.5 + - - -
349A CYS 3.2 9.0 + - - +
350A ILE 3.1 8.6 + - - +
352A VAL* 1.3 80.2 - - - +
354A MET* 1.3 55.0 + - - +
356A THR* 3.8 0.7 - - - -
357A GLY* 2.7 31.4 + - - +
358A GLU* 3.2 27.4 - - - +
359A PRO* 3.6 28.4 - - + +
360A LEU 4.6 0.8 + - - +
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Residues in contact with MET 354 (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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245A LEU* 3.8 49.8 - - + +
248A LEU* 4.1 10.8 - - + -
249A LEU* 3.7 29.5 - - + +
256A GLY* 3.3 6.1 - - - -
257A VAL* 2.9 39.7 + - + +
262A THR* 4.2 7.6 - - + +
265A PHE* 4.1 22.2 - - + -
290A PRO* 4.6 8.7 - - - -
350A ILE* 2.9 28.8 + - + +
351A LEU* 3.2 13.6 + - + +
353A GLU* 1.3 76.0 - - - +
355A HIS* 1.3 57.8 + - - +
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Residues in contact with HIS 355 (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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255A ARG 3.7 5.4 - - - +
256A GLY* 3.6 11.1 - - - -
257A VAL 2.9 23.7 + - - +
258A SER 3.7 4.8 - - - -
259A LEU* 3.7 15.8 + - + -
262A THR* 3.9 9.0 - - + +
351A LEU 3.3 6.4 + - - +
352A VAL 3.1 6.5 + - - +
354A MET* 1.3 81.7 - - - +
356A THR* 1.3 62.0 + - + +
357A GLY 3.4 0.2 - - - -
427A LEU* 4.7 7.6 - - + -
434A PRO* 3.4 30.6 - - + +
437A ARG* 3.9 0.2 + - - -
438A ARG* 4.1 12.9 + - + -
444A HIS* 3.7 23.8 - + - -
449A TYR* 2.7 41.7 + + - -
452A PHE* 4.5 9.6 - + + -
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Residues in contact with THR 356 (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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254A PHE 3.8 2.9 - - - +
255A ARG 4.4 0.2 - - - -
352A VAL* 2.8 34.6 + - + +
353A GLU* 3.8 0.2 - - - -
355A HIS* 1.3 76.8 - - - +
357A GLY* 1.3 59.0 + - - +
358A GLU* 3.1 34.8 + - - +
426A ILE* 4.0 20.0 - - + +
427A LEU* 4.1 7.4 - - + -
434A PRO* 3.7 24.5 - - + -
437A ARG* 2.9 25.4 + - - +
212B LYS* 5.6 1.4 - - - +
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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