Contacts of the helix formed by residues 225 - 245 (chain A) in PDB entry 2Q8F
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 VAL 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A CYS 3.3 9.6 + - - +
224A ASN* 1.3 71.0 - - - +
226A LEU* 1.3 64.2 + - + +
228A VAL* 3.2 4.0 + - - +
229A ILE* 3.0 40.3 + - + +
264A ILE* 3.4 29.4 + - + +
266A VAL* 4.1 11.9 - - + -
273A LEU* 4.2 21.0 - - + +
305A VAL* 4.1 17.3 - - + -
312A LEU* 3.8 24.7 - - + -
314A VAL* 4.3 10.1 - - + -
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ASN 3.4 0.4 - - - -
225A VAL* 1.3 81.8 - - + +
227A GLU* 1.3 59.0 + - + +
229A ILE* 3.3 6.0 + - - +
230A LYS* 2.9 44.7 + - - +
252A LEU* 3.8 35.0 - - + -
253A GLU 5.3 0.4 - - - -
254A GLU* 3.4 45.8 - - + +
264A ILE* 4.7 6.9 + - + +
305A VAL* 3.9 34.3 - - + -
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ASN* 3.0 42.9 + - + +
225A VAL 3.3 0.2 - - - -
226A LEU* 1.3 77.0 - - + +
228A VAL* 1.3 65.7 + - + +
230A LYS* 3.4 12.7 + - + +
231A ASP* 3.1 22.3 + - - +
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A CYS* 4.1 20.4 - - - -
224A ASN 3.1 14.9 + - - +
225A VAL 3.2 6.5 + - - +
227A GLU* 1.3 74.8 - - + +
229A ILE* 1.3 58.4 + - - +
231A ASP* 3.2 9.2 + - - +
232A GLY* 3.0 25.6 + - - -
270A PRO* 4.1 15.7 - - + +
273A LEU* 3.7 17.7 - - + +
274A TYR* 3.6 40.0 - - + +
277A VAL* 4.1 2.6 - - + +
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Residues in contact with ILE 229 (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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225A VAL* 3.0 32.4 + - + +
226A LEU* 3.5 10.1 - - + +
228A VAL* 1.3 75.4 - - + +
230A LYS* 1.3 57.4 + - - +
232A GLY* 3.2 1.4 + - - -
233A TYR* 2.8 26.2 + - - +
250A LEU* 5.1 1.3 - - + -
252A LEU* 4.1 22.7 - - + -
273A LEU* 5.4 1.6 - - + -
277A VAL* 4.0 27.4 - - + -
281A PHE* 3.4 25.2 - - + -
303A VAL* 4.3 6.1 - - + -
305A VAL* 3.4 32.3 - - + -
314A VAL* 4.0 13.9 - - + -
316A MET* 6.2 0.2 - - + -
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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
----------------------------------------------------------
226A LEU* 2.9 30.2 + - - +
227A GLU* 3.9 11.2 - - + +
228A VAL 3.3 0.2 - - - -
229A ILE* 1.3 76.6 - - - +
231A ASP* 1.3 56.1 + - - +
233A TYR* 3.5 8.1 + - + +
234A GLU* 3.0 38.4 + - + +
250A LEU* 4.6 8.7 - - + -
252A LEU* 3.6 29.6 - - + -
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Residues in contact with ASP 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU 3.1 13.4 + - - +
228A VAL* 3.3 12.1 - - - +
230A LYS* 1.3 72.3 - - - +
232A GLY* 1.3 65.2 + - - +
234A GLU* 3.4 4.9 + - - +
235A ASN* 3.1 38.3 + - - +
274A TYR* 3.5 20.8 - - + -
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Residues in contact with GLY 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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228A VAL 3.0 13.0 + - - -
229A ILE 3.5 3.6 - - - -
231A ASP* 1.3 75.1 - - - +
233A TYR* 1.3 56.6 + - - +
235A ASN 3.6 0.2 + - - -
236A ALA* 3.0 31.9 + - - +
274A TYR* 3.5 18.0 - - - -
277A VAL* 4.2 12.6 - - - -
278A PHE* 3.7 11.5 - - - -
281A PHE* 3.7 6.6 - - - -
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Residues in contact with TYR 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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229A ILE 2.8 19.2 + - - +
230A LYS* 3.6 4.5 - - - +
232A GLY* 1.3 71.1 - - - +
234A GLU* 1.3 80.9 + - + +
236A ALA* 3.4 1.0 + - - +
237A ARG* 2.8 69.4 + - + +
248A PRO 2.6 25.0 + - - -
249A GLU* 3.3 7.5 - - - -
250A LEU* 3.4 45.0 + - + -
281A PHE* 3.4 30.1 - + + -
285A MET* 3.4 28.3 - - + -
301A ILE* 5.4 1.8 - - + -
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Residues in contact with GLU 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* 3.0 24.2 + - + +
231A ASP* 3.4 5.8 + - - +
233A TYR* 1.3 95.1 - - + +
235A ASN* 1.3 64.2 + - - +
237A ARG* 3.5 16.6 + - - +
238A ARG* 3.1 37.9 + - - +
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Residues in contact with ASN 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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231A ASP* 3.1 29.3 + - - +
234A GLU* 1.3 79.5 - - - +
236A ALA* 1.3 64.0 + - - +
238A ARG* 3.5 27.9 + - - +
239A LEU* 3.4 24.1 + - - +
274A TYR* 2.9 30.3 + - - +
278A PHE* 3.8 8.6 - - + -
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Residues in contact with ALA 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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232A GLY 3.0 18.1 + - - +
233A TYR 3.8 2.2 - - - +
235A ASN* 1.3 72.3 - - - +
237A ARG* 1.3 60.8 + - - +
239A LEU* 3.2 6.3 + - - +
240A CYS* 2.9 27.7 + - - +
278A PHE* 3.5 12.8 - - + -
281A PHE* 3.5 26.2 - - + -
282A LYS* 4.0 17.5 - - + -
285A MET* 3.7 12.3 - - - +
352A LEU* 4.6 2.6 - - - +
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Residues in contact with ARG 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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233A TYR* 2.8 55.8 + - + +
234A GLU* 3.7 16.8 + - - +
236A ALA* 1.3 72.6 - - - +
238A ARG* 1.3 58.2 + - + +
240A CYS* 3.6 2.2 - - - +
241A ASP* 2.8 38.7 + - - +
246A ASN* 5.6 0.4 + - - -
247A SER* 2.9 42.3 + - - +
248A PRO 4.0 0.2 + - - -
249A GLU* 2.8 42.6 + - - -
285A MET* 3.8 14.1 - - + +
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Residues in contact with ARG 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 GLU* 3.1 25.2 + - - +
235A ASN* 3.6 27.9 - - - +
236A ALA 3.2 0.4 - - - -
237A ARG* 1.3 77.8 - - + +
239A LEU* 1.3 59.1 + - + +
241A ASP* 3.4 7.5 + - - +
242A LEU* 3.1 36.0 + - + +
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Residues in contact with LEU 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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235A ASN 3.4 7.2 + - - +
236A ALA 3.2 4.5 + - - +
238A ARG* 1.3 77.1 - - + +
240A CYS* 1.3 62.8 + - - +
242A LEU* 3.3 19.7 + - + +
243A TYR* 3.1 24.4 + - - +
278A PHE* 3.7 34.3 - - + -
282A LYS* 4.1 13.0 - - + +
350A VAL* 4.7 15.8 - - + +
352A LEU* 3.6 18.6 - - + +
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Residues in contact with CYS 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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236A ALA 2.9 13.6 + - - +
237A ARG 3.6 7.6 - - - +
239A LEU* 1.3 73.0 - - - +
241A ASP* 1.3 58.8 + - - +
243A TYR 3.2 0.5 + - - -
244A TYR* 2.8 40.6 + - - +
246A ASN 3.4 15.2 - - - +
247A SER* 3.6 12.8 - - - -
248A PRO* 4.0 0.2 - - - -
285A MET* 3.8 27.4 - - - -
289A MET* 3.5 32.1 - - - -
352A LEU* 3.9 11.3 - - + +
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Residues in contact with ASP 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 ARG* 2.8 28.0 + - - +
238A ARG* 3.7 8.1 - - - +
240A CYS* 1.3 73.3 - - - +
242A LEU* 1.3 59.8 + - + +
245A ILE* 3.0 30.4 + - - +
246A ASN* 3.3 21.1 - - - +
247A SER* 2.7 26.5 + - - -
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Residues in contact with LEU 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 ARG* 3.1 25.0 + - + +
239A LEU* 3.5 21.8 - - + +
240A CYS 3.2 0.2 - - - -
241A ASP* 1.3 80.4 - - + +
243A TYR* 1.3 58.9 + - - +
245A ILE* 3.7 11.1 - - - +
349A ALA* 3.3 22.6 - - + +
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Residues in contact with TYR 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 LEU 3.1 15.8 + - - +
240A CYS* 4.1 1.6 - - - +
242A LEU* 1.3 80.3 - - - +
244A TYR* 1.3 102.5 + + + +
245A ILE* 3.5 7.3 + - - +
290A GLU* 4.9 2.9 - - - -
349A ALA* 3.6 23.6 - - + -
350A VAL 3.5 21.8 - - - +
351A PRO* 3.6 33.0 - - + +
352A LEU* 4.9 3.6 - - + -
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Residues in contact with TYR 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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240A CYS* 2.8 23.5 + - - +
243A TYR* 1.3 102.4 - + + +
245A ILE* 1.3 71.6 + - - +
246A ASN* 3.0 15.7 + - - +
286A ARG* 3.4 18.0 - - - +
289A MET* 3.5 40.6 - - + +
290A GLU* 2.9 44.1 + - + -
352A LEU* 4.0 25.8 + - + +
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Residues in contact with ILE 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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240A CYS 3.7 0.2 + - - -
241A ASP* 3.0 22.7 + - - +
242A LEU 3.7 20.0 - - - +
243A TYR 4.0 7.9 - - - +
244A TYR* 1.3 80.7 - - - +
246A ASN* 1.3 62.1 + - - +
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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