Contacts of the helix formed by residues 329 - 334 (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 329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323B GLN* 2.7 19.6 + - - -
327B TYR 3.8 1.2 + - - -
328B ARG* 1.3 76.4 - - - +
330B PRO* 1.3 77.8 - - - +
331B GLU* 3.4 16.1 - - - +
332B VAL* 3.1 17.8 + - - +
333B LEU* 3.0 23.0 + - - +
342B ILE* 3.4 17.4 - - - +
345B TRP* 3.7 17.9 - - - -
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Residues in contact with PRO 330 (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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329B SER* 1.3 90.0 - - - +
331B GLU* 1.3 60.1 + - - +
333B LEU* 2.8 15.9 + - + +
334B LEU* 2.6 51.7 + - + +
345B TRP* 3.7 41.3 - - + -
370B MET* 4.4 6.7 - - + -
373B ILE* 5.0 3.4 - - + -
380B PRO* 6.0 0.2 - - + -
384B ILE* 6.4 0.7 - - + -
462B TYR* 3.9 29.4 - - + +
467B ARG* 4.5 2.5 - - - +
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Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER* 3.4 17.5 - - - +
330B PRO* 1.3 83.8 - - - +
332B VAL* 1.3 57.5 + - - +
334B LEU* 4.5 0.6 - - - +
335B GLY 3.2 2.9 + - - -
336B MET* 2.8 50.5 + - + +
337B PRO 4.0 15.0 - - - +
338B TYR* 4.0 7.2 - - + -
339B ASP* 5.0 0.5 + - - +
341B ALA* 4.2 0.5 - - - +
342B ILE* 3.5 22.4 + - + +
462B TYR 4.5 1.7 - - - +
464B PRO* 3.9 25.7 - - + +
467B ARG* 2.6 46.6 + - - -
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Residues in contact with VAL 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B GLN* 3.4 26.8 - - - +
321B PTR 5.0 0.4 - - - -
322B ILE* 3.5 38.1 - - + +
323B GLN* 3.3 10.5 - - - +
328B ARG* 3.7 11.9 - - + -
329B SER* 3.1 25.2 + - - +
330B PRO 3.2 0.4 - - - -
331B GLU* 1.3 75.0 - - - +
333B LEU* 1.4 62.9 + - - +
335B GLY* 3.6 9.1 + - - -
336B MET 5.1 0.7 - - - +
338B TYR* 4.2 15.0 - - + -
342B ILE* 4.2 11.2 - - + -
366B GLU* 4.6 2.3 - - - +
390B LYS* 4.2 6.6 + - - -
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Residues in contact with LEU 333 (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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328B ARG* 4.0 17.7 - - - +
329B SER 3.0 17.8 + - - +
330B PRO* 2.8 7.8 + - + +
332B VAL* 1.4 75.7 - - - +
334B LEU* 1.3 57.1 + - - +
335B GLY 3.2 1.3 - - - -
366B GLU* 3.7 48.9 - - + +
369B GLN* 4.0 15.7 - - + -
370B MET* 3.8 25.1 - - + +
373B ILE* 3.7 30.1 - - + -
390B LYS* 2.9 22.9 + - - -
394B PHE* 3.3 16.6 - - + -
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Residues in contact with LEU 334 (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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330B PRO* 2.6 31.0 + - + +
332B VAL 3.4 0.2 - - - -
333B LEU* 1.3 72.2 - - - +
335B GLY* 1.3 61.5 + - - +
336B MET* 3.4 9.6 - - + -
370B MET* 4.0 10.5 - - + -
380B PRO* 5.1 4.9 - - + -
384B ILE* 4.1 17.5 - - + -
385B LEU* 3.9 22.9 - - + -
388B ALA* 3.6 19.5 - - + -
389B PRO* 3.4 6.4 - - - +
390B LYS* 2.9 30.4 + - - -
391B ALA* 3.7 28.9 - - - +
394B PHE* 4.0 16.4 - - + -
395B PHE* 4.3 4.7 - - + -
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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