Contacts of the helix formed by residues 235 - 256 (chain B) in PDB entry 5WVD
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 235 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233B GLN 4.7 5.6 - - - +
234B ALA* 1.3 78.1 - - - +
236B PHE* 1.3 58.4 + - - +
237B TYR* 3.5 9.5 + - - +
238B ASP* 3.0 37.6 + - - +
239B LYS* 3.0 28.7 + - - +
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Residues in contact with PHE 236 (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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235B THR* 1.3 70.7 - - - +
237B TYR* 1.3 63.2 + - + +
239B LYS* 3.5 17.0 + - + +
240B ARG* 3.1 74.0 + - + +
318B ALA* 4.1 18.6 - - + -
319B LYS* 4.3 27.8 - - + -
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Residues in contact with TYR 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B THR* 3.3 7.7 + - - +
236B PHE* 1.3 82.5 - - + +
238B ASP* 1.3 66.1 + - - +
240B ARG* 3.4 4.5 + - - +
241B CYS* 3.0 53.2 + - - -
316B ARG 5.9 2.7 - - - -
318B ALA* 4.3 20.6 - - + -
321B ARG* 5.4 6.3 - - - -
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Residues in contact with ASP 238 (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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167B ALA* 3.5 25.1 - - + +
169B ARG* 3.2 36.1 + - + +
234B ALA* 4.4 3.6 - - + -
235B THR* 3.0 39.5 + - - +
237B TYR* 1.3 84.4 - - - +
239B LYS* 1.3 64.9 + - - +
241B CYS* 3.5 17.4 + - - +
242B ASP* 3.7 7.8 + - - +
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Residues in contact with LYS 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B HIS* 3.2 79.4 + - + +
165B GLY* 4.0 18.9 - - - -
166B ILE 4.6 1.1 - - - +
167B ALA* 4.5 1.8 - - + -
234B ALA* 3.6 28.6 + - + -
235B THR 3.0 16.7 + - - +
236B PHE* 3.7 16.4 - - + +
237B TYR 3.3 0.2 - - - -
238B ASP* 1.3 77.9 - - - +
240B ARG* 1.3 63.4 + - + +
241B CYS 3.6 0.5 + - - -
242B ASP* 3.6 8.1 - - - +
243B LEU* 3.7 4.2 - - - +
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PHE* 3.1 48.8 + - + +
237B TYR 3.4 2.7 + - - +
238B ASP 3.4 0.2 - - - -
239B LYS* 1.3 76.6 - - + +
241B CYS* 1.3 56.4 + - - +
242B ASP 3.3 0.9 - - - -
243B LEU* 3.4 18.0 + - - +
244B TRP 3.2 15.4 + - - -
318B ALA* 2.8 46.0 + - + +
319B LYS* 4.0 6.3 + - - +
321B ARG* 2.7 57.1 + - - +
322B LEU 4.0 6.1 - - - -
323B SER* 3.5 31.1 - - - +
326B GLN* 5.2 1.2 + - - -
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Residues in contact with CYS 241 (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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169B ARG* 6.4 2.7 - - + -
237B TYR* 3.0 54.9 + - - +
238B ASP* 3.7 11.7 - - - +
239B LYS 3.3 0.6 - - - -
240B ARG* 1.3 75.7 - - - +
242B ASP* 1.3 65.2 + - - +
244B TRP* 3.8 9.0 - - + +
245B SER* 3.2 26.0 + - - -
321B ARG* 4.1 6.5 - - - +
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Residues in contact with ASP 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B LEU* 3.6 22.5 - - + +
162B HIS* 3.4 15.7 + - - +
167B ALA* 3.5 3.1 - - - -
168B HIS* 2.7 32.6 + - - +
169B ARG* 3.0 27.5 + - - -
170B ASP 4.8 0.2 + - - -
171B LEU* 3.4 17.1 + - + +
238B ASP 3.7 9.5 + - - +
239B LYS 3.6 9.0 - - - +
241B CYS* 1.3 80.5 - - - +
243B LEU* 1.3 56.5 + - - +
245B SER* 3.3 5.0 + - - -
246B LEU* 2.9 23.9 + - - +
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Residues in contact with LEU 243 (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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155B ALA* 5.5 0.2 - - + -
158B LEU* 4.4 8.1 - - + -
162B HIS* 3.9 10.8 - - + +
239B LYS 3.7 17.9 - - - +
240B ARG* 3.4 21.8 + - - +
241B CYS 3.3 0.4 - - - -
242B ASP* 1.3 74.3 - - - +
244B TRP* 1.3 63.4 + - - +
246B LEU* 3.7 17.4 + - + +
247B GLY 3.4 14.4 + - - -
313B LEU* 3.4 24.4 - - + +
321B ARG* 4.5 3.4 - - - -
322B LEU 3.4 27.6 - - - +
323B SER* 3.8 2.7 - - - -
324B ALA* 3.8 33.4 - - + +
327B VAL* 3.9 18.6 - - + -
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Residues in contact with TRP 244 (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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240B ARG 3.2 5.5 + - - -
241B CYS* 3.8 11.9 - - + +
242B ASP 3.3 0.2 - - - -
243B LEU* 1.3 75.3 - - - +
245B SER* 1.3 74.8 + - - +
247B GLY 3.2 12.6 + - - -
248B VAL* 3.2 33.4 + - + +
313B LEU 3.5 19.5 - - - -
314B LEU* 3.5 35.6 + - + +
315B VAL 4.4 0.6 - - - -
316B ARG* 5.9 0.8 - - - +
321B ARG* 3.6 35.1 - - - +
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Residues in contact with SER 245 (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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171B LEU* 3.4 32.4 + - - +
241B CYS 3.2 17.4 + - - -
242B ASP* 3.3 6.0 + - - -
244B TRP* 1.3 94.5 - - - +
246B LEU* 1.3 57.9 + - - +
248B VAL* 3.3 7.9 + - - +
249B VAL* 3.1 29.8 + - - +
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B VAL* 6.2 0.2 - - + -
151B VAL* 4.2 26.2 - - + +
154B VAL* 3.8 25.4 - - + -
155B ALA* 4.3 18.6 - - + -
158B LEU* 4.2 19.7 - - + -
171B LEU* 3.8 9.8 - - + +
242B ASP 2.9 15.3 + - - +
243B LEU* 3.7 21.5 - - + +
244B TRP 3.3 0.2 - - - -
245B SER* 1.3 73.7 - - - +
247B GLY* 1.3 58.7 + - - +
249B VAL* 3.3 15.1 + - + +
250B LEU* 3.0 26.9 + - + +
313B LEU* 4.2 13.4 - - + +
327B VAL* 4.5 6.3 - - + -
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Residues in contact with GLY 247 (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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243B LEU 3.4 4.8 + - - -
244B TRP 3.2 10.9 + - - -
246B LEU* 1.3 78.0 - - - +
248B VAL* 1.3 60.5 + - - +
249B VAL 3.4 0.2 - - - -
250B LEU* 4.2 5.6 - - - +
251B TYR* 3.3 22.7 + - - +
310B ILE* 4.7 6.7 - - - +
313B LEU* 3.9 23.5 - - - +
314B LEU* 3.8 16.9 - - - +
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Residues in contact with VAL 248 (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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171B LEU 5.9 0.2 - - - +
173B PRO* 5.9 1.6 - - + -
244B TRP* 3.2 44.1 + - + +
245B SER* 3.5 10.1 - - - +
246B LEU 3.3 0.2 - - - -
247B GLY* 1.3 75.2 - - - +
249B VAL* 1.3 58.8 + - + +
251B TYR* 3.3 6.8 + - - +
252B ILE* 2.9 46.5 + - + +
258B PRO* 4.9 11.7 - - + -
314B LEU* 3.9 12.1 - - + -
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Residues in contact with VAL 249 (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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132B ILE* 5.2 4.7 - - + -
150B VAL* 4.9 3.8 - - + -
154B VAL* 6.0 0.2 - - + -
171B LEU* 4.0 11.0 - - + +
173B PRO* 3.8 26.7 - - + -
176B ILE* 3.9 30.1 - - + -
245B SER 3.1 17.9 + - - +
246B LEU* 3.3 22.4 + - + +
248B VAL* 1.3 75.7 - - + +
250B LEU* 1.3 57.1 + - - +
252B ILE* 3.3 10.2 + - - +
253B MET* 2.9 48.7 + - + +
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Residues in contact with LEU 250 (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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147B ALA 4.6 1.1 - - - +
151B VAL* 3.9 24.0 - - + -
246B LEU* 3.0 17.0 + - + +
247B GLY* 4.2 4.9 - - - +
249B VAL* 1.3 74.0 - - - +
251B TYR* 1.3 60.7 + - - +
253B MET* 3.5 13.0 + - + -
254B LEU* 3.2 45.2 + - + +
309B LEU* 3.9 33.7 - - + -
310B ILE* 3.9 26.7 - - + +
313B LEU* 5.2 4.9 - - + -
332B TRP* 3.8 27.1 - - + -
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Residues in contact with TYR 251 (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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247B GLY 3.3 19.3 + - - +
248B VAL* 3.3 8.3 + - - +
250B LEU* 1.3 74.3 - - - +
252B ILE* 1.3 59.6 + - - +
254B LEU* 4.9 1.1 - - - +
255B SER* 2.5 40.9 + - - -
257B TYR* 3.3 48.1 + + - +
258B PRO 3.6 22.7 - - - -
310B ILE* 3.9 33.8 - - + +
314B LEU* 4.7 9.9 - - + -
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Residues in contact with ILE 252 (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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132B ILE* 6.0 1.1 - - + -
133B LEU* 6.2 1.1 - - + -
136B ILE* 4.0 33.3 - - + +
173B PRO* 3.9 33.4 - - + -
248B VAL* 2.9 38.2 + - + +
249B VAL 3.3 5.8 + - - +
251B TYR* 1.3 73.9 - - - +
253B MET* 1.3 60.4 + - + +
256B GLY* 2.9 31.4 + - - +
257B TYR 4.0 5.2 - - - -
258B PRO* 3.9 31.4 - - + -
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Residues in contact with MET 253 (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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132B ILE* 4.7 16.8 - - + -
136B ILE* 4.4 17.1 - - + +
147B ALA* 3.5 39.9 - - + +
150B VAL* 3.8 29.4 - - + -
151B VAL* 3.9 18.2 - - + -
249B VAL* 2.9 23.4 + - + +
250B LEU* 3.7 18.6 - - + +
251B TYR 3.4 0.2 - - - -
252B ILE* 1.3 78.9 - - + +
254B LEU* 1.3 61.6 + - + +
255B SER 3.8 0.2 + - - -
256B GLY 5.0 0.2 + - - -
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Residues in contact with LEU 254 (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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147B ALA* 3.9 27.6 - - + -
250B LEU* 3.2 34.5 + - + +
251B TYR* 4.9 1.6 - - - +
253B MET* 1.3 78.5 - - - +
255B SER* 1.3 60.7 + - - +
310B ILE* 4.0 18.8 - - + -
332B TRP* 4.7 15.5 - - + -
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B TYR* 2.5 31.7 + - - -
253B MET 5.3 0.2 - - - -
254B LEU* 1.3 81.8 - - - +
256B GLY* 1.3 57.6 + - - +
257B TYR* 3.0 47.2 + - - -
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Residues in contact with GLY 256 (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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136B ILE* 4.6 19.2 - - - +
252B ILE* 2.9 27.0 + - - +
253B MET 4.9 0.2 - - - -
254B LEU 4.0 0.2 - - - -
255B SER* 1.3 73.2 + - - +
257B TYR* 1.3 58.6 + - - +
258B PRO* 4.6 1.9 - - - +
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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