Contacts of the helix formed by residues 250 - 265 (chain F) in PDB entry 1WOH
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 250 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247D ASP* 4.1 8.5 - - - -
233F PHE* 3.5 3.8 - - - -
234F ASP* 5.3 1.8 - - + -
237F VAL* 4.6 12.8 - - + -
248F GLY 4.9 2.9 - - - +
249F LEU* 1.3 78.1 - - - +
251F TYR* 1.3 66.3 + - - +
252F ALA* 3.5 7.8 + - - +
253F GLN* 2.9 44.2 + - - +
254F GLY 3.1 15.9 + - - -
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Residues in contact with TYR 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D PRO* 3.5 27.6 - - + -
247D ASP* 3.1 22.7 + - - +
233F PHE* 3.7 12.7 - - - -
237F VAL* 4.4 16.2 - - + +
249F LEU 4.0 0.2 + - - -
250F THR* 1.3 73.8 - - - +
252F ALA* 1.3 60.0 + - - +
254F GLY* 3.3 0.9 + - - -
255F MET* 2.9 34.5 + - + +
288F LEU* 3.3 30.3 - - + -
289F MET* 4.3 11.4 - - + -
291F ARG* 3.1 24.8 + - - +
292F LEU* 3.2 41.4 + - + +
295F GLU* 2.8 29.5 + - - +
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Residues in contact with ALA 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D ASP* 3.1 27.3 + - + +
250F THR* 3.1 5.8 - - - +
251F TYR* 1.3 82.8 - - - +
253F GLN* 1.3 56.7 + - + +
255F MET* 3.4 4.5 + - - +
256F LYS* 2.9 52.5 + - - +
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Residues in contact with GLN 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204F MET* 3.6 10.4 - - - +
207F VAL* 3.9 30.1 + - + +
208F THR* 4.7 6.5 + - - +
211F LEU* 4.8 10.8 - - + +
248F GLY 4.0 1.0 - - - +
249F LEU* 3.5 16.5 - - + -
250F THR* 2.9 46.8 + - + +
252F ALA* 1.3 74.3 - - + +
254F GLY* 1.3 68.1 + - - +
256F LYS* 3.2 11.9 + - + +
257F ILE* 3.1 29.0 + - - +
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Residues in contact with GLY 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142F LEU* 3.8 16.1 - - - +
233F PHE* 3.9 17.7 - - - -
249F LEU* 4.2 9.5 - - - +
250F THR 3.1 8.5 + - - -
251F TYR 3.8 1.8 - - - -
253F GLN* 1.3 78.1 - - - +
255F MET* 1.3 61.5 + - - +
257F ILE* 3.3 7.0 + - - +
258F LEU* 3.1 28.7 + - - +
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Residues in contact with MET 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F TYR* 2.9 25.3 + - + +
252F ALA* 3.7 5.6 - - - +
254F GLY* 1.3 74.8 - - - +
256F LYS* 1.3 55.5 + - + +
258F LEU* 3.1 9.4 + - + +
259F ALA* 2.7 45.5 + - + +
292F LEU* 3.7 23.1 - - + +
295F GLU* 3.4 48.5 - - + +
296F THR* 3.4 37.7 - - - +
299F GLU* 4.2 9.2 - - + +
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Residues in contact with LYS 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F LEU* 4.2 28.9 - - + -
215F LEU* 3.8 9.3 - - + +
252F ALA* 2.9 42.8 + - - +
253F GLN* 3.2 9.3 + - + +
255F MET* 1.3 76.1 - - + +
257F ILE* 1.3 57.0 + - - +
259F ALA* 3.8 6.2 - - - +
260F ALA* 3.0 30.1 + - - +
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Residues in contact with ILE 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 4.7 6.5 - - + -
142F LEU* 3.8 22.9 - - + -
179F VAL* 3.9 27.8 - - + -
207F VAL* 4.7 1.8 - - + -
211F LEU* 4.3 14.1 - - + -
214F VAL* 4.7 4.5 - - + -
215F LEU* 3.7 20.2 - - + -
218F LEU* 3.5 28.5 - - + +
249F LEU* 3.9 20.0 - - + -
253F GLN 3.1 15.4 + - - +
254F GLY* 3.5 9.2 - - - +
255F MET 3.1 0.2 - - - -
256F LYS* 1.3 74.7 - - - +
258F LEU* 1.3 65.4 + - - +
261F ALA* 3.1 20.1 + - - +
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Residues in contact with LEU 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 5.2 1.8 - - + +
142F LEU* 4.1 18.8 - - + -
226F PHE* 3.6 40.3 - - + -
228F VAL* 4.2 20.4 - - + -
254F GLY 3.1 13.9 + - - +
255F MET* 3.1 9.7 + - + +
257F ILE* 1.3 77.6 - - - +
259F ALA* 1.3 57.9 + - - +
261F ALA 3.3 0.9 + - - -
262F ALA* 2.8 32.8 + - - +
270F LEU* 5.2 1.8 - - + -
292F LEU* 4.1 29.8 - - + -
296F THR* 3.4 30.1 - - + +
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Residues in contact with ALA 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F MET* 2.7 24.3 + - + +
256F LYS* 3.8 8.3 - - - +
258F LEU* 1.3 73.8 - - - +
260F ALA* 1.3 62.1 + - - +
262F ALA* 3.3 1.9 + - - +
263F ALA* 3.0 24.9 + - - +
299F GLU* 3.8 42.7 - - + +
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Residues in contact with ALA 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F LEU* 4.0 19.1 - - + +
218F LEU* 3.8 16.2 - - + -
256F LYS 3.0 18.3 + - - +
257F ILE 3.7 4.3 - - - +
259F ALA* 1.3 78.2 - - - +
261F ALA* 1.3 62.5 + - - +
263F ALA* 3.2 12.0 + - - +
264F ASN* 3.1 28.3 + - - +
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Residues in contact with ALA 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F VAL* 4.5 13.7 - - + -
218F LEU* 4.0 15.6 - - + +
219F PRO 5.2 0.2 - - - -
224F VAL* 5.3 1.3 - - + -
226F PHE* 3.4 31.0 - - + -
257F ILE 3.1 11.1 + - - +
260F ALA* 1.3 79.5 - - - +
262F ALA* 1.3 62.2 + - - +
263F ALA 3.3 0.2 + - - -
264F ASN* 3.3 0.7 + - - +
265F ASN* 2.9 43.4 + - - +
267F VAL* 4.9 0.2 - - - +
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Residues in contact with ALA 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226F PHE* 3.7 7.1 - - + -
258F LEU 2.8 17.7 + - - +
259F ALA 3.7 4.3 - - - +
261F ALA* 1.3 76.4 - - - +
263F ALA* 1.3 60.7 + - - +
265F ASN 3.6 12.4 - - - +
267F VAL* 4.0 12.2 - - - +
296F THR* 4.6 2.2 - - + +
299F GLU* 4.1 11.9 - - + +
300F VAL* 3.9 45.1 - - + +
303F HIS* 4.7 4.2 - - - +
304F VAL* 5.7 1.9 - - - +
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Residues in contact with ALA 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259F ALA 3.0 17.0 + - - +
260F ALA* 3.2 7.5 + - - +
262F ALA* 1.3 78.7 - - - +
264F ASN* 1.3 68.6 + - - +
265F ASN 3.7 0.6 + - - -
299F GLU* 5.5 0.9 - - - +
303F HIS* 4.1 43.0 - - + +
305F LEU* 5.5 4.0 - - - +
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Residues in contact with ASN 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F PRO 4.6 5.0 + - - +
220F ARG* 4.6 17.6 - - + +
221F GLY* 2.7 34.3 + - - -
260F ALA* 3.1 24.3 + - - +
261F ALA* 3.3 3.0 + - - +
263F ALA* 1.3 89.0 - - - +
265F ASN* 1.3 60.3 + - - +
305F LEU* 5.7 4.0 - - - -
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Residues in contact with ASN 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F PRO* 2.7 34.0 + - - +
220F ARG 3.4 1.0 - - - -
221F GLY* 3.0 8.4 + - - +
222F GLN* 2.8 37.6 + - - +
224F VAL* 3.7 20.8 - - + +
261F ALA* 2.9 32.5 + - - +
262F ALA 3.6 13.0 - - - +
263F ALA 3.7 1.0 - - - -
264F ASN* 1.3 81.7 - - - +
266F THR* 1.3 63.6 + - - +
267F VAL* 3.5 6.5 + - + +
304F VAL* 5.8 4.9 - - - +
305F LEU* 4.6 12.2 - - - +
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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