Contacts of the helix formed by residues 340 - 347 (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 LEU 340 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B LEU 5.3 0.7 - - - +
276B LEU* 3.8 9.9 - - + +
277B ALA* 3.5 40.2 - - + +
282B SER* 4.0 15.9 - - - +
283B ILE 3.8 15.0 - - - +
284B ILE* 3.4 26.0 - - + +
314B LEU* 3.7 24.5 - - + -
339B ASP* 1.3 77.5 + - - +
341B ALA* 1.3 63.1 + - - +
342B ILE 3.0 1.6 + - - -
343B ASP* 3.0 22.3 + - + +
344B MET* 3.8 2.3 + - - +
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Residues in contact with ALA 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU* 4.2 0.7 - - - +
339B ASP* 3.0 16.3 + - - +
340B LEU* 1.3 77.3 - - - +
342B ILE* 1.3 61.0 + - - +
344B MET* 2.9 21.5 + - - +
345B TRP 3.1 5.4 + - - -
464B PRO* 3.9 23.8 - - + +
467B ARG* 3.1 35.7 + - + +
468B ILE 6.1 0.4 - - - +
469B GLN* 6.3 2.9 - - + +
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Residues in contact with ILE 342 (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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284B ILE* 3.7 25.4 - - + -
286B CYS* 4.3 2.9 - - - -
322B ILE* 3.7 28.7 - - + -
323B GLN* 3.2 32.7 + - + +
329B SER* 3.4 23.8 - - - +
331B GLU* 3.5 14.6 - - + +
332B VAL* 4.2 0.9 - - + -
338B TYR* 3.4 30.3 - - + -
339B ASP 3.4 15.3 - - - +
340B LEU 3.0 1.2 + - - -
341B ALA* 1.3 77.7 - - - +
343B ASP* 1.3 65.8 + - - +
345B TRP* 3.5 4.0 + - - +
346B SER* 3.2 13.3 + - - -
467B ARG* 4.1 2.2 - - - +
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Residues in contact with ASP 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 4.0 20.0 - - + +
276B LEU* 4.4 6.1 - - - +
283B ILE 4.3 3.1 - - - +
284B ILE* 3.6 13.8 - - - +
285B HIS* 2.7 34.2 + - - +
286B CYS* 2.9 26.9 + - - -
287B ASP 4.5 0.7 + - - -
288B LEU* 3.6 12.7 + - + +
323B GLN* 4.8 1.6 + - - -
340B LEU* 3.0 11.2 + - - +
342B ILE* 1.3 83.4 - - - +
344B MET* 1.3 57.3 + - - +
346B SER* 3.3 8.5 + - - -
347B LEU* 2.9 27.0 + - - +
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Residues in contact with MET 344 (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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270B CYS* 5.0 2.0 - - - -
273B LEU* 4.0 20.3 - - + +
340B LEU 3.8 1.4 + - - +
341B ALA* 2.9 16.7 + - - +
343B ASP* 1.3 76.5 - - - +
345B TRP* 1.3 64.5 + - - +
347B LEU* 3.2 6.9 + - - +
348B GLY 3.0 18.0 + - - -
459B MET* 3.7 48.9 - - + +
467B ARG* 4.2 6.3 - - - -
468B ILE* 3.4 31.0 - - + +
469B GLN 4.0 1.1 - - - -
470B PRO* 3.6 40.2 - - + -
473B ALA* 4.6 4.9 - - + -
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Residues in contact with TRP 345 (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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326B PHE 5.2 0.6 + - - -
327B TYR 3.8 12.3 + - - -
328B ARG 3.4 12.9 + - - -
329B SER* 3.7 17.9 - - - -
330B PRO* 3.7 26.5 - - + -
341B ALA 3.1 5.3 + - - -
342B ILE 3.6 7.9 - - - +
344B MET* 1.3 74.2 - - - +
346B SER* 1.3 68.3 + - - +
348B GLY* 3.1 10.7 + - - -
349B CYS* 3.1 25.7 + - - -
361B PHE* 3.9 13.8 - + - -
369B GLN* 6.1 0.2 - - - +
373B ILE* 3.7 32.6 - - + +
377B LEU* 3.6 22.0 - - + -
459B MET 3.7 10.2 + - - -
460B LEU* 3.5 46.8 - - + +
461B ASP 4.2 4.5 - - - -
462B TYR* 4.8 2.5 - + - -
467B ARG* 3.8 25.1 - - - +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 3.5 35.5 + - - +
323B GLN* 2.9 19.1 + - - +
327B TYR* 2.8 29.0 + - - -
342B ILE 3.2 3.0 + - - -
343B ASP* 3.3 9.2 + - - -
345B TRP* 1.3 80.7 - - - +
347B LEU* 1.3 57.9 + - - +
349B CYS* 3.3 3.3 + - - +
350B ILE* 2.9 33.8 + - - +
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Residues in contact with LEU 347 (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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266B ALA 4.7 0.2 - - - +
269B MET* 3.5 46.0 - - + -
270B CYS* 4.0 22.7 - - - -
273B LEU* 3.9 20.0 - - + -
288B LEU* 4.6 3.1 - - + +
343B ASP 2.9 14.0 + - - +
344B MET* 3.5 11.4 - - - +
345B TRP 3.2 0.2 - - - -
346B SER* 1.3 77.9 - - - +
348B GLY* 1.3 56.8 + - - +
350B ILE* 3.3 14.7 + - + -
351B LEU* 2.9 51.0 + - + +
459B MET* 4.1 11.0 - - + -
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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