Contacts of the helix formed by residues 230 - 237 (chain A) in PDB entry 1WK8
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 THR 230 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A THR* 3.0 11.1 + - - +
229A THR* 1.3 95.3 + - - +
231A PRO* 1.3 64.7 - - - +
232A TRP* 3.1 29.6 - - + +
233A THR* 2.9 37.6 + - + +
234A LEU* 5.1 0.2 - - - +
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Residues in contact with PRO 231 (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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202A ASP* 6.5 0.4 - - + -
203A PRO 4.2 10.8 - - - +
205A VAL* 3.8 24.2 - - + -
228A THR* 4.0 5.1 - - + +
229A THR 3.5 8.5 - - - +
230A THR* 1.3 89.7 - - - +
232A TRP* 1.3 55.0 + - - +
233A THR 3.1 0.4 - - - -
234A LEU* 3.0 40.8 + - + +
363A ASN* 3.4 21.3 - - - +
366A ILE* 3.7 24.0 - - + +
367A LEU* 4.0 20.9 - - + -
370A LEU* 5.1 0.4 - - + -
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Residues in contact with TRP 232 (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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230A THR* 3.7 26.2 - - + +
231A PRO* 1.3 75.0 - - - +
233A THR* 1.3 69.9 + - + +
234A LEU 3.3 0.4 - - - -
235A PRO* 3.2 14.3 - - - +
324A PHE* 3.2 41.3 - + - -
342A THR* 5.0 1.9 - - - +
343A VAL* 4.8 9.9 - - + -
349A LEU* 3.8 14.8 - - + +
359A PHE* 3.3 67.7 - + + +
362A ALA* 4.6 3.1 - - + -
363A ASN* 3.1 37.4 + - + +
366A ILE* 3.5 12.3 - - + -
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Residues in contact with THR 233 (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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230A THR* 2.9 33.7 + - - +
232A TRP* 1.3 91.6 - - + +
234A LEU* 1.3 59.1 + - - +
235A PRO* 3.2 2.5 - - - -
236A GLY* 2.8 22.9 + - - -
319A HIS* 2.8 33.9 + - - -
321A ALA* 5.0 0.2 - - - -
324A PHE* 3.4 49.2 - - + -
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Residues in contact with LEU 234 (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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207A VAL* 4.3 16.2 - - + -
209A PHE* 4.0 24.2 - - + -
226A ILE* 4.2 9.4 - - + -
228A THR* 4.6 3.4 - - + -
231A PRO* 3.0 29.7 + - + +
233A THR* 1.3 77.6 + - - +
235A PRO* 1.3 65.0 - - + +
237A ASN* 3.0 20.6 + - - +
291A PRO* 6.0 0.2 - - - +
292A PRO* 4.0 19.2 - - + +
293A TYR* 4.1 8.5 + - + +
319A HIS* 3.7 31.4 - - + +
366A ILE* 4.4 1.3 - - + -
370A LEU* 3.8 28.9 - - + -
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Residues in contact with PRO 235 (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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232A TRP 3.2 16.6 - - - +
233A THR 3.2 1.3 - - - -
234A LEU* 1.3 95.8 - - + +
236A GLY* 1.3 56.9 + - - +
237A ASN 3.3 2.4 + - - +
293A TYR* 3.8 23.7 - - + +
295A GLN* 3.9 10.4 + - - +
340A LEU* 3.7 11.8 - - - +
342A THR* 4.7 0.7 - - + -
349A LEU* 3.9 11.0 - - + -
351A VAL* 3.4 31.8 - - + +
352A GLU 5.0 0.2 - - - +
354A PHE* 3.7 28.7 - - + -
366A ILE* 3.7 12.1 - - + -
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Residues in contact with GLY 236 (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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233A THR 2.8 12.0 + - - -
235A PRO* 1.3 78.1 - - - +
237A ASN* 1.3 64.9 + - - +
238A VAL* 3.5 4.2 + - - +
321A ALA* 3.3 24.9 - - - +
322A PRO* 4.1 2.4 - - - +
323A ALA 5.5 0.2 + - - -
324A PHE* 4.6 0.7 - - - -
340A LEU* 3.7 13.1 - - - +
342A THR* 3.2 29.6 + - - +
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Residues in contact with ASN 237 (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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209A PHE* 3.6 17.0 - - + -
233A THR 3.8 1.2 + - - -
234A LEU 3.0 17.7 + - - +
235A PRO 3.3 1.9 - - - +
236A GLY* 1.3 79.8 - - - +
238A VAL* 1.3 65.0 + - - +
239A ALA 2.9 19.9 - - - +
289A TYR* 2.7 31.4 + - - -
291A PRO* 3.9 7.0 - - + +
292A PRO* 5.3 0.7 - - + -
301A TYR* 3.2 36.9 + - + -
319A HIS* 2.9 24.8 + - - +
320A GLN 3.4 6.4 + - - +
340A LEU* 3.9 4.2 - - - +
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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