Contacts of the helix formed by residues 226 - 245 (chain B) in PDB entry 6S6A
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 HIS 226 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 4.8 9.2 - - + +
168B THR* 6.3 2.3 - - + +
171B LYS* 5.0 7.7 - - + +
224B ASP* 3.1 14.2 + - - +
225B VAL* 1.3 101.4 + - + +
227B ARG* 1.3 62.4 + - - +
229B GLU* 3.1 33.1 + - - +
230B LYS* 3.5 23.0 + - - +
354C TYR* 3.2 5.6 - - - -
358C CYS* 4.5 12.0 - - + -
361C LYS* 5.2 7.3 + - - +
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Residues in contact with ARG 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 2.6 39.2 + - - -
218B GLN* 3.2 29.7 + - - +
222B GLN* 3.6 26.2 + - - +
224B ASP* 3.0 36.7 + - - +
225B VAL* 4.4 3.2 - - - +
226B HIS* 1.3 75.5 - - - +
228B PHE* 1.3 89.7 + - + +
230B LYS* 2.9 15.8 + - - +
231B ILE* 2.9 18.6 + - + +
354C TYR* 3.3 13.5 + - - -
357C HIS* 6.4 0.2 - - - +
298D ILE* 3.7 25.1 - - + -
299D TYR* 3.8 18.4 - - - +
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Residues in contact with PHE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 3.8 4.7 - - - -
204B LEU* 3.3 26.2 - - + -
213B VAL* 3.7 25.7 - - + +
216B HIS* 3.2 50.0 - + + -
227B ARG* 1.3 105.4 - - + +
229B GLU* 1.3 63.8 + - - +
231B ILE* 3.6 5.3 + - - +
232B SER* 3.1 28.4 + - - -
403B 9JE 4.3 15.9 - - + +
354C TYR* 3.1 47.1 + + + +
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Residues in contact with GLU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 3.1 31.4 - - + +
168B THR* 5.1 0.2 - - - -
170B TYR* 4.1 10.2 - - + +
171B LYS* 3.3 46.5 - - + +
226B HIS* 3.1 40.3 + - - +
228B PHE* 1.3 74.2 - - - +
230B LYS* 1.3 66.9 + - - +
232B SER* 3.5 3.9 + - - -
233B ASN* 3.0 24.6 + - - +
403B 9JE 4.2 2.1 + - - -
354C TYR* 2.5 31.2 + - - -
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 3.7 36.1 - - + +
224B ASP* 2.7 40.8 + - - +
226B HIS* 3.5 18.5 + - - +
227B ARG* 2.9 8.1 + - - +
229B GLU* 1.3 78.5 - - - +
231B ILE* 1.3 57.5 + - - +
233B ASN* 3.2 6.0 + - - +
234B ILE* 2.9 40.3 + - + +
298D ILE* 4.1 17.2 - - + +
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Residues in contact with ILE 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B LEU* 4.8 6.1 - - + -
206B PHE* 3.4 22.0 - - + -
227B ARG* 2.9 22.7 + - + +
228B PHE* 3.9 4.9 - - - +
230B LYS* 1.3 73.4 - - - +
232B SER* 1.3 65.3 - - - +
234B ILE* 3.1 12.0 + - + +
235B ILE* 2.9 51.5 + - + +
273B MET* 4.1 11.0 - - + -
295D VAL* 4.4 18.8 - - + -
298D ILE* 3.6 24.9 - - + -
299D TYR* 4.3 21.8 - - + +
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Residues in contact with SER 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B TYR* 3.8 22.4 - - - -
174B SER* 6.1 0.2 - - - -
206B PHE* 3.8 1.6 - - - -
211B PHE* 2.6 37.2 + - - +
212B LEU* 4.1 0.5 - - - -
213B VAL* 3.7 16.8 + - - +
228B PHE 3.1 17.4 + - - -
229B GLU* 3.6 7.4 - - - -
231B ILE* 1.3 76.9 - - - +
233B ASN* 1.3 54.3 + - - +
236B LYS* 3.1 32.4 + - - +
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Residues in contact with ASN 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B ILE 5.7 0.8 + - - -
166B ASP* 3.6 33.3 + - - +
167B GLU* 3.7 5.1 - - + +
170B TYR* 4.4 21.1 - - + -
229B GLU 3.0 14.6 + - - +
230B LYS* 3.4 11.2 - - - +
232B SER* 1.3 70.7 - - - +
234B ILE* 1.3 56.3 + - + +
236B LYS* 3.4 6.8 - - - +
237B GLN* 2.9 60.6 + - - +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LYS* 2.9 37.3 + - + +
231B ILE* 3.4 13.9 - - + +
233B ASN* 1.3 73.3 - - + +
235B ILE* 1.3 66.9 + - + +
237B GLN* 3.6 7.1 + - - +
238B PHE* 3.3 20.6 + - - +
290D ASP 5.5 0.4 - - - -
291D VAL* 4.1 35.3 - - + +
294D ASP* 3.8 33.4 - - + +
295D VAL* 4.4 9.6 - - + +
298D ILE* 4.2 17.3 - - + -
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 4.6 3.6 - - + -
211B PHE* 2.9 54.3 - - + -
231B ILE* 2.9 39.3 + - + +
234B ILE* 1.3 81.7 - - + +
236B LYS* 1.3 57.1 + - - +
238B PHE* 3.2 7.1 + - - +
239B LYS* 2.7 33.0 + - + +
249B PHE* 4.1 18.4 - - + -
252B MET* 5.1 2.2 - - + -
263B ILE* 3.7 32.1 - - + -
291D VAL* 5.1 7.0 - - + -
295D VAL* 5.7 1.6 - - + -
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Residues in contact with LYS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE 3.6 15.0 + - - -
27B ILE 3.4 20.6 + - - -
28B PHE 5.5 0.2 - - - -
29B ALA 5.0 0.6 - - - +
30B ASN* 4.0 22.2 + - - +
31B TYR 5.1 0.7 - - - -
170B TYR* 3.4 18.6 + - + +
209B ALA 3.3 23.9 + - - +
210B THR 4.0 10.7 + - - +
211B PHE* 4.4 10.9 - - + -
232B SER 3.1 22.0 + - - +
233B ASN* 3.4 8.1 - - - +
235B ILE* 1.3 77.7 - - - +
237B GLN* 1.3 60.8 + - + +
239B LYS* 3.5 14.2 - - + +
240B LEU* 3.2 42.8 + - + +
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Residues in contact with GLN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 4.1 24.1 - - - +
233B ASN* 2.9 45.5 + - - +
234B ILE* 3.7 7.9 - - - +
235B ILE 3.2 0.2 - - - -
236B LYS* 1.3 72.8 - - + +
238B PHE* 1.3 61.5 - - - +
240B LEU* 3.1 13.2 + - + +
241B SER* 2.9 29.5 + - - -
287D ASP* 6.3 0.2 - - - -
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ILE 3.3 6.0 + - - +
235B ILE* 3.2 10.2 + - - +
237B GLN* 1.3 75.0 - - - +
239B LYS* 1.3 66.1 + - - +
241B SER* 2.9 15.5 + - - +
242B CYS* 2.9 43.4 + - - -
249B PHE* 3.7 28.3 - + - -
252B MET* 4.4 2.9 - - + -
284D LEU* 3.9 23.6 - - + -
287D ASP* 3.7 15.3 - - + -
288D MET* 3.9 9.9 - - + -
291D VAL* 3.5 30.7 - - + -
318D ILE* 3.4 32.5 - - + -
326D LEU* 4.1 13.5 - - + -
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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
----------------------------------------------------------
30B ASN* 5.5 6.7 - - - +
208B ARG* 2.8 36.7 + - - +
209B ALA* 4.5 12.9 - - - +
211B PHE* 4.9 7.6 - - + -
235B ILE* 2.7 18.7 + - + +
236B LYS* 3.5 17.3 - - + +
238B PHE* 1.3 72.6 - - - +
240B LEU* 1.3 59.6 + - + +
242B CYS* 3.4 8.8 + - - +
243B SER* 3.1 29.4 + - - +
248B SER* 5.6 5.4 - - - +
249B PHE* 5.0 17.9 - - + -
271B TYR* 3.9 26.6 + - - -
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASN* 3.4 45.8 - - + +
31B TYR 4.3 2.2 - - - +
32B ILE* 4.0 26.0 - - + -
236B LYS* 3.2 37.8 + - + +
237B GLN* 3.1 14.5 + - - +
238B PHE 3.0 0.6 - - - -
239B LYS* 1.3 77.4 - - + +
241B SER* 1.3 58.5 + - - +
242B CYS 3.3 0.2 - - - -
243B SER* 3.5 11.6 + - - +
244B LYS* 3.3 34.6 + - + +
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B GLN 2.9 12.8 + - - -
238B PHE* 2.9 9.9 + - - -
240B LEU* 1.3 75.2 - - - +
242B CYS* 1.3 59.7 + - - +
243B SER 3.4 0.2 - - - -
244B LYS* 3.6 6.1 + - - -
245B LEU* 3.1 34.9 - - - +
284D LEU* 3.5 10.2 - - - +
287D ASP* 2.2 43.2 + - - -
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Residues in contact with CYS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PHE* 2.9 53.4 + - - -
239B LYS* 3.5 11.7 - - - +
241B SER* 1.3 76.2 - - - +
243B SER* 1.3 57.4 + - - +
246B ALA* 3.1 24.5 - - - +
247B ALA 3.0 14.1 + - - +
248B SER 3.0 25.7 - - - +
249B PHE* 4.5 3.6 - - + -
284D LEU* 3.9 10.5 - - - -
320D LEU* 4.0 12.8 - - + -
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Residues in contact with SER 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASN* 5.7 2.1 + - - -
239B LYS* 3.1 17.6 + - - +
240B LEU* 3.5 17.7 + - - +
241B SER 3.4 0.2 - - - -
242B CYS* 1.3 75.3 - - - +
244B LYS* 1.3 70.0 + - - +
245B LEU 3.2 2.5 + - - -
246B ALA 3.9 9.8 + - - +
247B ALA 3.4 13.9 - - - -
248B SER* 5.6 1.1 - - - -
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Residues in contact with LYS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B LEU* 3.3 22.4 + - + +
241B SER* 3.6 8.2 + - - +
242B CYS 3.6 0.2 - - - -
243B SER* 1.3 82.4 + - - +
245B LEU* 1.3 67.2 + - + +
246B ALA 3.9 0.2 - - - -
280D GLN* 4.9 2.4 - - - +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B SER* 3.1 25.8 + - - +
243B SER 3.2 0.2 - - - -
244B LYS* 1.3 87.9 - - + +
246B ALA* 1.3 63.3 + - + +
280D GLN* 3.1 56.7 - - + +
281D SER* 5.3 0.4 - - - -
283D GLU* 4.3 17.9 - - + -
284D LEU* 3.7 28.7 - - + +
287D ASP* 5.8 0.2 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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