Contacts of the helix formed by residues 230 - 247 (chain B) in PDB entry 3SF4
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 ASP 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221B ARG* 4.0 7.3 + - - +
225B ALA* 3.0 14.6 + - - +
228B PHE* 2.9 15.3 + - + +
229B GLY* 1.3 72.3 - - - +
231B LYS* 1.3 56.2 + - - +
232B ALA* 3.3 11.4 + - - +
233B ALA* 3.1 32.0 + - + +
234B GLU* 3.0 28.5 + - - +
236B ARG* 4.9 2.8 + - - -
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Residues in contact with LYS 231 (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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229B GLY* 3.1 15.8 + - - +
230B ASP* 1.3 68.9 + - - +
232B ALA* 1.3 64.8 + - - +
234B GLU* 3.0 32.6 + - - +
235B ARG* 3.1 23.7 + - - +
264B LEU* 3.6 28.3 - - + +
267B GLN* 4.5 8.8 - - - +
268B LEU* 3.6 29.5 - - + +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ASP* 3.3 8.4 + - - +
231B LYS* 1.3 77.6 - - - +
233B ALA* 1.3 60.2 + - - +
235B ARG* 3.2 9.0 + - - +
236B ARG* 2.9 44.4 + - - +
268B LEU* 4.6 8.2 - - + +
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ARG* 3.2 39.4 - - - +
225B ALA* 3.8 7.4 - - + +
230B ASP* 3.1 26.5 + - - +
232B ALA* 1.3 75.1 - - - +
234B GLU* 1.3 64.9 + - - +
236B ARG* 3.2 19.7 + - - +
237B ALA* 2.9 25.1 + - - +
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Residues in contact with GLU 234 (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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222B LEU* 3.6 15.4 - - + +
225B ALA* 3.5 15.4 - - + +
226B LYS* 3.6 23.1 + - + +
229B GLY 5.9 0.5 - - - -
230B ASP 3.0 16.5 + - - +
231B LYS* 3.0 41.2 + - - +
233B ALA* 1.3 76.5 - - - +
235B ARG* 1.3 62.8 + - - +
237B ALA* 3.3 4.0 + - - +
238B TYR* 3.1 56.7 + - + -
264B LEU* 3.9 7.6 - - + +
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Residues in contact with ARG 235 (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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231B LYS 3.1 18.8 + - - +
232B ALA* 3.3 7.2 + - - +
234B GLU* 1.3 75.1 - - - +
236B ARG* 1.3 77.6 + - - +
238B TYR* 3.2 7.3 + - - +
239B SER* 3.0 39.2 + - - -
261B THR* 4.3 17.3 - - - +
264B LEU* 3.6 21.7 - - + +
265B ALA* 4.7 2.2 - - - +
268B LEU* 4.6 11.0 - - + +
273B VAL* 3.7 42.9 - - + +
276B GLN* 4.1 5.1 + - - -
40E GLU* 2.5 40.3 + - - -
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Residues in contact with ARG 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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221B ARG* 4.1 1.2 - - + +
230B ASP* 4.9 2.8 + - - -
232B ALA* 2.9 35.8 + - - +
233B ALA* 3.2 26.6 + - - +
235B ARG* 1.3 93.3 - - - +
237B ALA* 1.3 58.4 + - - +
239B SER* 3.2 3.5 + - - -
240B ASN* 2.9 34.5 + - - +
40E GLU* 3.7 30.5 - - + +
41E CYS 3.4 21.6 + - - -
42E GLU* 3.0 43.8 + - - +
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Residues in contact with ALA 237 (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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218B HIS* 3.9 14.3 - - + +
221B ARG* 4.1 10.0 - - + +
222B LEU* 3.9 31.4 - - + +
233B ALA 2.9 13.2 + - - +
234B GLU 3.5 9.0 - - - +
236B ARG* 1.3 78.0 - - - +
238B TYR* 1.3 57.8 + - - +
240B ASN* 3.3 7.9 + - - +
241B LEU* 2.8 36.8 + - - +
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Residues in contact with TYR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 3.5 29.8 - - + -
226B LYS* 2.8 22.1 + - - -
234B GLU* 3.1 44.4 + - + -
235B ARG* 3.2 4.2 + - - +
237B ALA* 1.3 76.0 - - - +
239B SER* 1.3 56.0 + - - +
241B LEU* 3.4 4.3 + - + +
242B GLY* 3.0 22.3 + - - -
257B TYR* 3.4 32.6 - + - +
260B LYS* 3.7 48.1 - - + +
261B THR* 3.0 21.8 - - + +
264B LEU* 4.3 11.4 - - + -
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Residues in contact with SER 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 3.0 32.3 + - - -
236B ARG 3.7 6.7 - - - -
238B TYR* 1.3 76.6 - - - +
240B ASN* 1.3 64.3 + - - +
242B GLY* 3.4 1.3 + - - +
243B ASN* 3.0 35.4 + - - +
258B TYR* 4.1 9.1 - - - -
261B THR* 3.2 19.9 + - - +
276B GLN* 4.8 4.0 + - - -
277B SER* 5.4 0.7 + - - -
40E GLU* 3.9 11.0 - - - -
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Residues in contact with ASN 240 (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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199B GLY* 6.0 0.6 - - - -
203B ASN* 3.3 12.8 + - - +
206B TYR* 5.0 2.8 - - - -
218B HIS* 3.4 37.4 + - + +
221B ARG* 6.3 0.4 - - - +
236B ARG* 2.9 25.9 + - - +
237B ALA* 3.8 3.7 - - - +
239B SER* 1.3 74.4 - - - +
241B LEU* 1.3 63.3 + - - +
243B ASN* 3.5 9.2 + - - +
244B ALA* 3.1 24.1 + - - +
38E MET 5.1 0.3 - - - +
39E THR* 4.0 2.9 - - - -
40E GLU* 3.1 49.5 + - - +
42E GLU* 5.8 0.4 + - - -
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Residues in contact with LEU 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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215B VAL* 3.6 45.5 - - + +
218B HIS* 3.7 23.6 - - + +
219B GLU* 4.3 8.1 - - + +
222B LEU* 4.3 15.5 - - + -
237B ALA 2.8 28.9 + - - +
238B TYR* 3.5 5.4 - - - +
239B SER 3.1 0.2 - - - -
240B ASN* 1.3 74.9 - - - +
242B GLY* 1.3 66.3 + - - +
244B ALA* 3.2 4.9 + - - +
245B TYR* 3.0 35.8 + - + -
257B TYR* 3.7 34.1 - - + +
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Residues in contact with GLY 242 (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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238B TYR 3.0 11.9 + - - -
239B SER 3.4 0.6 + - - -
241B LEU* 1.3 75.4 - - - +
243B ASN* 1.3 62.1 + - - +
245B TYR 3.3 1.2 + - - -
246B ILE* 3.0 21.3 + - - +
254B ALA* 3.4 20.5 - - - +
257B TYR* 3.8 16.5 - - - +
258B TYR* 3.4 21.3 - - - -
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Residues in contact with ASN 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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206B TYR* 3.5 20.1 + - + +
239B SER* 3.0 25.2 + - - +
240B ASN* 3.7 11.5 + - - +
242B GLY* 1.3 75.4 - - - +
244B ALA* 1.3 62.0 + - - +
246B ILE* 3.3 10.4 + - - +
247B PHE* 3.3 23.2 - - - -
258B TYR* 2.5 33.8 + - - -
280B SER* 5.0 0.9 + - - -
35E LEU* 3.5 24.9 - - + +
38E MET* 4.2 25.5 + - - +
40E GLU* 5.7 2.8 - - - +
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Residues in contact with ALA 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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206B TYR* 3.8 19.9 - - + -
211B PHE* 3.9 16.6 - - + +
214B ALA* 4.4 8.1 - - + -
215B VAL* 3.7 21.5 - - + +
218B HIS* 5.3 0.4 - - + -
240B ASN 3.1 18.1 + - - +
241B LEU* 3.5 4.9 - - - +
243B ASN* 1.3 75.4 - - - +
245B TYR* 1.3 62.9 + - - +
247B PHE* 3.3 4.7 + - - -
248B LEU* 3.3 25.6 + - - +
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Residues in contact with TYR 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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163A PHE* 5.6 0.7 - - + -
168A ARG* 4.4 4.5 + - - -
212B ARG* 3.7 13.5 + - - -
215B VAL* 3.3 37.9 - - + +
219B GLU* 4.3 6.6 + - - -
241B LEU* 3.0 30.5 + - + -
242B GLY 3.7 5.8 - - - +
243B ASN 3.3 0.2 - - - -
244B ALA* 1.3 75.3 - - - +
246B ILE* 1.3 67.4 + - - +
248B LEU* 2.8 17.4 + - + +
250B GLU* 3.0 63.7 + - + +
253B THR* 3.5 24.6 - - + +
254B ALA* 3.8 6.5 - - + -
257B TYR* 3.4 28.6 + + - -
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Residues in contact with ILE 246 (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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242B GLY 3.0 18.3 + - - +
243B ASN 3.4 8.7 - - - +
244B ALA 3.3 0.2 - - - -
245B TYR* 1.3 74.9 - - - +
247B PHE* 1.3 62.7 + - + +
249B GLY* 3.0 14.7 + - - -
251B PHE* 3.5 32.4 - - + -
254B ALA* 3.8 12.6 - - + -
258B TYR* 3.5 16.2 - - - +
284B THR* 3.4 24.9 - - + +
287B LEU* 4.1 7.4 - - + -
31E TRP* 3.8 12.1 - - + -
32E MET* 3.7 28.4 - - + +
35E LEU* 4.1 15.0 - - + -
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Residues in contact with PHE 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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211A PHE* 4.7 6.1 - - - -
247A PHE 4.8 4.7 - - - +
206B TYR* 3.2 29.8 - + - -
211B PHE* 3.5 40.6 - + + -
243B ASN 3.3 17.7 - - - -
244B ALA 3.3 4.6 + - - +
245B TYR 3.2 0.6 - - - -
246B ILE* 1.3 74.7 - - + +
248B LEU* 1.3 59.0 + - - +
249B GLY 3.1 5.1 + - - -
19E PRO* 5.5 10.8 - - + +
32E MET* 3.5 38.4 - - + -
35E LEU* 3.9 21.5 - - + -
36E LYS* 3.3 47.1 - - + -
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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
------------------------------------------------------------
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