Contacts of the helix formed by residues 226 - 246 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 4.9 3.8 - - + +
171A LYS* 4.4 13.1 + - + -
224A ASP* 3.0 13.3 - - - +
225A VAL* 1.3 96.6 + - + +
227A ARG* 1.3 57.6 + - - +
229A GLU* 3.1 37.5 + - - +
230A LYS* 3.2 29.3 + - + +
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Residues in contact with ARG 227 (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 GLU* 2.7 42.5 + - - -
218A GLN* 2.8 23.4 + - - -
221A GLU* 5.7 2.2 + - - -
222A GLN* 3.4 35.0 + - - +
224A ASP* 3.1 37.3 + - + +
225A VAL* 3.3 7.5 - - - +
226A HIS* 1.3 77.4 - - - +
228A PHE* 1.3 89.3 + - + +
230A LYS* 3.2 8.2 + - - +
231A ILE* 3.0 27.9 + - - +
298C ILE* 4.0 21.5 - - + -
299C TYR* 3.8 21.3 - - - +
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Residues in contact with PHE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 4.1 0.2 - - - -
204A LEU* 3.4 34.1 - - + -
213A VAL* 3.6 22.4 - - + +
216A HIS* 3.6 37.0 - + + -
218A GLN* 4.1 0.9 - - - -
225A VAL* 3.9 20.4 - - - -
226A HIS 3.4 0.6 - - - -
227A ARG* 1.3 115.1 - - + +
229A GLU* 1.3 67.3 + - - +
231A ILE* 3.4 5.1 + - - +
232A SER* 3.1 24.8 + - - -
403A 9JE 3.5 30.7 - - + +
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 3.5 28.5 - - + +
168A THR* 5.6 0.9 - - - +
170A TYR* 4.0 10.0 - - - +
171A LYS* 3.2 53.2 + - + +
174A SER* 5.9 1.1 - - - -
225A VAL 4.1 3.6 - - - +
226A HIS* 3.1 47.4 + - - +
228A PHE* 1.3 87.8 + - - +
230A LYS* 1.3 61.0 + - - +
232A SER* 3.3 4.3 + - - -
233A ASN* 3.0 24.3 + - - +
403A 9JE 4.1 6.4 + - - +
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Residues in contact with LYS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 3.6 37.2 - - + +
224A ASP* 2.8 38.7 + - - +
226A HIS* 3.2 23.8 + - - +
227A ARG* 3.2 8.7 + - - +
229A GLU* 1.3 75.4 - - - +
231A ILE* 1.3 58.2 + - - +
233A ASN* 3.2 4.2 + - - +
234A ILE* 2.9 41.7 + - + +
298C ILE* 4.1 17.7 - - + -
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Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 4.3 14.6 - - + -
206A PHE* 3.8 18.2 - - + -
227A ARG 3.0 18.9 + - - +
228A PHE 3.9 3.6 - - - +
230A LYS* 1.3 75.5 - - - +
232A SER* 1.3 63.3 + - - +
233A ASN 3.1 0.3 + - - -
234A ILE* 3.2 5.4 + - + -
235A ILE* 2.9 51.7 + - + +
273A MET* 3.9 11.2 - - + -
295C VAL* 4.2 20.2 - - + -
298C ILE* 3.6 25.1 - - + -
299C TYR* 4.1 21.5 - - + +
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Residues in contact with SER 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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170A TYR* 3.9 22.2 - - - -
174A SER* 4.7 1.7 + - - -
206A PHE* 3.8 1.8 - - - -
211A PHE* 2.5 36.3 + - - +
212A LEU* 4.0 0.4 - - - -
213A VAL* 3.3 27.9 + - - +
228A PHE 3.1 7.2 + - - -
229A GLU* 3.5 9.2 - - - -
231A ILE* 1.3 73.9 - - - +
233A ASN* 1.3 52.3 + - - +
235A ILE* 4.1 0.2 - - - -
236A LYS* 2.9 38.5 + - - +
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Residues in contact with ASN 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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165A TRP 5.8 0.2 - - - -
166A ASP* 4.2 9.6 - - - +
167A GLU* 4.2 24.2 + - + +
170A TYR* 3.4 30.2 - - + -
229A GLU 3.0 12.5 + - - +
230A LYS* 3.5 9.0 - - - +
232A SER* 1.3 74.8 - - - +
234A ILE* 1.3 67.9 + - + +
236A LYS* 3.9 4.0 - - - +
237A GLN* 2.6 58.7 + - - +
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Residues in contact with ILE 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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230A LYS* 2.9 37.3 + - + +
231A ILE* 3.7 5.6 - - + +
233A ASN* 1.3 75.2 - - + +
235A ILE* 1.3 67.4 + - + +
237A GLN* 3.3 5.6 + - - +
238A PHE* 3.1 20.6 + - - +
291C VAL* 3.8 26.9 - - + +
294C ASP* 3.2 43.3 - - + +
295C VAL* 4.2 21.5 - - + -
298C ILE* 4.5 5.4 - - + -
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Residues in contact with ILE 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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206A PHE* 4.7 2.0 - - + -
211A PHE* 3.3 44.4 - - + -
231A ILE* 2.9 41.4 + - + +
234A ILE* 1.3 82.0 - - + +
236A LYS* 1.3 67.7 + - - +
238A PHE* 3.2 8.4 + - + +
239A LYS* 2.9 23.3 + - + +
249A PHE* 4.5 17.7 - - + -
252A MET* 5.0 8.7 - - + -
263A ILE* 3.4 29.4 - - + -
291C VAL* 4.8 1.3 - - + -
295C VAL* 5.3 3.1 - - + -
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Residues in contact with LYS 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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26A ILE 4.1 11.9 - - - -
27A ILE 4.6 4.6 + - - -
28A PHE 6.3 0.2 - - - -
30A ASN* 2.7 39.6 + - - +
170A TYR* 3.2 28.7 - - + +
209A ALA 3.6 14.8 + - - +
210A THR 3.9 18.8 - - - +
211A PHE* 4.3 12.7 - - + -
232A SER 2.9 22.4 + - - +
233A ASN* 3.9 5.4 - - - +
235A ILE* 1.3 75.6 - - - +
237A GLN* 1.3 66.9 + - + +
239A LYS* 3.2 22.3 + - + +
240A LEU* 3.2 32.3 + - + +
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Residues in contact with GLN 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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32A ILE* 5.6 7.4 - - + -
233A ASN* 2.6 54.5 + - - +
234A ILE* 3.7 5.4 - - - +
235A ILE 3.1 0.2 - - - -
236A LYS* 1.3 77.2 - - + +
238A PHE* 1.3 63.5 - - - +
240A LEU* 3.1 18.1 + - + +
241A SER* 3.0 24.5 + - - -
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Residues in contact with PHE 238 (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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234A ILE 3.1 6.0 + - - +
235A ILE* 3.2 9.2 + - + +
237A GLN* 1.3 77.4 - - - +
239A LYS* 1.3 55.8 + - - +
241A SER* 3.2 5.8 + - - -
242A CYS* 2.9 54.1 + - - -
249A PHE* 3.8 18.8 - + - -
252A MET* 4.7 3.8 - - + -
284C LEU* 4.0 16.4 - - + -
287C ASP* 3.7 23.6 - - + -
288C MET* 3.6 25.4 - - + -
291C VAL* 3.5 26.2 - - + -
318C ILE* 3.5 42.2 - - + -
326C LEU* 4.9 3.8 - - + -
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Residues in contact with LYS 239 (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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208A ARG* 3.5 24.8 + - - +
209A ALA* 5.1 5.3 + - - +
211A PHE* 3.7 24.9 - - + -
235A ILE* 2.9 12.7 + - + +
236A LYS* 3.3 18.8 - - + +
238A PHE* 1.3 77.4 - - - +
240A LEU* 1.3 58.9 + - + +
242A CYS* 3.4 3.6 + - - +
243A SER* 3.1 27.9 + - - -
248A SER* 5.4 0.3 - - - -
249A PHE* 3.9 35.7 + - + +
271A TYR* 3.9 31.5 - - - -
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Residues in contact with LEU 240 (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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30A ASN* 3.6 44.6 - - + +
31A TYR 3.9 13.9 - - - +
32A ILE* 3.8 26.9 - - + -
236A LYS* 3.2 28.2 + - + +
237A GLN* 3.1 15.3 + - + +
239A LYS* 1.3 74.3 - - + +
241A SER* 1.3 65.0 + - - +
243A SER* 3.6 7.4 + - - +
244A LYS* 3.1 45.6 + - + +
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Residues in contact with SER 241 (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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237A GLN 3.0 16.9 + - - -
238A PHE* 3.2 6.9 + - - -
240A LEU* 1.3 73.8 - - - +
242A CYS* 1.3 57.2 + - - +
244A LYS* 4.6 3.4 - - - -
245A LEU* 2.8 48.7 + - - +
284C LEU* 4.0 6.7 - - - -
287C ASP* 2.8 38.0 + - - +
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Residues in contact with CYS 242 (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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238A PHE* 2.9 55.5 + - - -
239A LYS 3.6 8.3 - - - +
240A LEU 3.3 0.4 - - - -
241A SER* 1.3 73.4 - - - +
243A SER* 1.3 57.8 + - - +
246A ALA* 2.8 29.3 + - - -
247A ALA 3.2 25.1 + - - +
249A PHE* 3.8 14.6 - - - +
284C LEU* 3.9 12.6 - - - -
320C LEU* 3.6 16.6 - - + -
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Residues in contact with SER 243 (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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239A LYS 3.1 17.5 + - - -
240A LEU* 3.6 11.1 + - - +
242A CYS* 1.3 74.5 - - - +
244A LYS* 1.3 64.2 + - - +
246A ALA 4.0 9.9 - - - +
247A ALA* 4.0 2.3 + - - +
248A SER* 4.2 20.8 - - - +
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Residues in contact with LYS 244 (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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30A ASN 4.9 11.0 + - - -
32A ILE* 4.4 18.3 - - + +
35A ASP* 4.2 16.6 + - - -
240A LEU* 3.1 45.4 + - + +
241A SER* 4.0 3.6 - - - +
243A SER* 1.3 77.7 - - - +
245A LEU* 1.3 71.5 + - + +
246A ALA 4.0 0.2 + - - -
280C GLN* 4.3 7.6 - - - +
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Residues in contact with LEU 245 (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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241A SER* 2.8 33.7 + - - +
244A LYS* 1.3 84.3 - - + +
246A ALA* 1.3 61.3 + - - +
280C GLN* 3.4 55.2 + - + +
281C SER 5.3 0.3 + - - -
283C GLU* 3.3 46.2 - - + +
284C LEU* 3.5 19.6 - - + +
287C ASP* 4.3 1.8 - - - +
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Residues in contact with ALA 246 (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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242A CYS 2.8 9.5 + - - +
243A SER 4.0 7.4 - - - +
244A LYS 3.7 1.1 - - - +
245A LEU* 1.3 80.0 - - - +
247A ALA* 1.3 61.9 - - + +
284C LEU* 4.1 14.6 - - + -
320C LEU* 3.9 21.1 - - + -
322C ASN* 4.9 6.7 - - - +
324C THR* 5.9 2.2 - - + -
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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) + - + + + + + -
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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