Contacts of the helix formed by residues 234 - 250 (chain A) in PDB entry 6ACQ
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 GLY 234 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLY 2.8 14.1 + - - -
231A ASP 4.0 2.9 - - - -
232A PHE 3.3 2.4 - - - -
233A ILE* 1.3 77.4 - - - +
235A LEU* 1.3 65.8 + - - -
236A ASP* 3.3 14.4 - - - -
237A ILE 3.3 2.1 + - - -
238A CYS* 3.1 23.0 + - - -
269A LEU 3.4 11.9 - - - -
272A LYS* 4.0 9.9 - - - -
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ILE* 5.4 1.8 - - + -
230A GLY* 3.4 31.2 - - - +
231A ASP* 3.9 10.8 - - - +
234A GLY* 1.3 70.1 - - - -
236A ASP* 1.3 61.3 + - - +
238A CYS* 3.7 6.5 - - - +
239A LEU* 2.9 31.4 + - - +
260A LEU* 4.0 12.4 - - + +
263A TYR* 4.0 20.4 - - + -
264A VAL* 3.5 15.0 - - + +
268A TRP 3.5 19.5 - - - +
269A LEU* 2.8 23.2 + - - +
276A GLY* 4.3 1.1 - - - -
277A PHE* 3.7 33.7 - - + -
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Residues in contact with ASP 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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234A GLY* 3.5 6.4 - - - -
235A LEU* 1.3 73.9 + - - +
237A ILE* 1.3 69.2 + - - +
239A LEU* 3.6 3.0 + - - +
240A ALA* 3.0 26.7 + - - +
264A VAL* 3.7 23.1 - - + +
269A LEU* 3.7 26.0 - - + +
272A LYS* 3.3 30.0 + - - -
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Residues in contact with ILE 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 ILE* 3.2 35.0 - - + +
234A GLY 3.3 4.7 + - - +
235A LEU 3.2 0.2 - - - -
236A ASP* 1.3 87.0 + - - +
238A CYS* 1.3 60.8 + - - +
240A ALA* 3.3 5.6 + - + +
241A ILE* 2.9 45.9 + - + +
272A LYS* 3.7 19.3 - - - +
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Residues in contact with CYS 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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192A ILE* 3.4 21.3 - - + +
195A ILE* 4.1 22.2 - - + -
230A GLY* 3.9 24.0 - - - -
233A ILE* 3.6 17.9 - - - -
234A GLY 3.1 19.0 + - - +
235A LEU* 3.3 11.0 + - + +
237A ILE* 1.3 75.5 - - - +
239A LEU* 1.3 63.3 + - - +
241A ILE 3.4 0.7 + - - -
242A MET* 3.1 28.5 + - - +
260A LEU* 4.6 9.9 - - + -
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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
----------------------------------------------------------
235A LEU 2.9 19.3 + - - +
236A ASP 3.8 3.4 - - - +
238A CYS* 1.3 78.6 - - - +
240A ALA* 1.3 57.3 + - - +
242A MET* 3.3 1.8 + - - -
243A ASP* 2.9 39.4 + - - +
256A PRO* 3.7 28.5 - - + -
260A LEU* 3.9 19.0 - - + +
261A LYS* 3.9 28.7 - - + +
264A VAL* 4.0 29.4 - - + -
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Residues in contact with ALA 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 ASP 3.0 19.1 + - - +
237A ILE* 3.3 7.1 + - - +
239A LEU* 1.3 73.2 - - - +
241A ILE* 1.3 67.4 + - + +
243A ASP* 3.2 12.8 + - - +
244A VAL* 2.9 28.2 + - + +
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Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 5.4 7.0 - - - +
118A SER* 6.0 3.8 - - - -
184A GLY* 5.5 1.8 - - - -
188A ASN* 3.7 40.4 - - + +
192A ILE* 3.8 34.8 - - + -
233A ILE* 5.8 0.2 - - + -
237A ILE* 2.9 36.8 + - + +
238A CYS 3.8 4.0 - - - +
239A LEU 3.3 0.2 - - - -
240A ALA* 1.3 77.3 - - + +
242A MET* 1.3 62.0 + - - +
244A VAL* 3.2 10.4 + - + +
245A LEU* 3.0 35.5 + - + +
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Residues in contact with MET 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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192A ILE* 3.7 12.3 - - + +
193A PRO* 3.7 42.4 - - + -
196A ASN* 3.6 36.3 - - + +
238A CYS 3.1 19.1 + - - +
239A LEU* 3.8 4.5 - - - +
240A ALA 3.2 0.2 - - - -
241A ILE* 1.3 76.6 - - - +
243A ASP* 1.3 62.8 + - - +
245A LEU* 3.2 7.1 + - - +
246A TYR* 3.1 24.8 + - - +
253A LYS 5.3 0.7 - - - +
254A TYR* 3.2 42.5 - - + +
255A ARG 4.2 0.4 - - - +
256A PRO* 3.9 18.1 - - + +
260A LEU* 5.0 2.7 - - + -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 2.9 34.0 + - - +
240A ALA* 3.3 12.9 - - - +
242A MET* 1.3 76.9 - - - +
244A VAL* 1.3 58.2 + - + +
246A TYR* 3.8 6.5 - - - +
247A SER* 2.9 31.9 + - - -
256A PRO* 3.7 18.2 - - - +
261A LYS* 5.1 3.5 + - - -
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Residues in contact with VAL 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER 5.6 0.2 - - - +
118A SER* 3.8 42.8 - - - +
183A PRO* 5.0 7.2 - - + -
184A GLY 5.3 4.5 - - - +
240A ALA* 2.9 18.9 + - + +
241A ILE* 3.2 11.0 + - + +
243A ASP* 1.3 78.1 - - + +
245A LEU* 1.3 61.3 + - + +
247A SER* 4.1 5.2 - - - -
248A GLU* 2.8 43.9 + - + +
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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
----------------------------------------------------------
183A PRO* 3.6 41.3 - - + +
184A GLY* 3.7 9.9 - - - +
188A ASN 4.6 3.1 - - - +
189A ARG* 3.9 14.8 - - - +
193A PRO* 4.1 18.8 - - + -
241A ILE* 3.0 30.5 + - + +
242A MET* 3.2 27.8 + - - +
244A VAL* 1.3 77.9 - - + +
246A TYR* 1.3 60.6 + - - +
249A THR* 2.8 34.8 + - + +
254A TYR* 3.9 21.9 - - + -
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Residues in contact with TYR 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 MET 3.1 15.8 + - - +
243A ASP* 3.8 5.6 - - - +
245A LEU* 1.3 75.5 - - - +
247A SER* 1.3 62.0 + - - +
249A THR* 4.2 1.1 - - - -
250A GLY* 2.9 27.0 + - - -
251A ASP 3.1 31.9 - - - -
252A SER* 3.8 10.6 + - - -
254A TYR* 3.8 13.9 - - - +
255A ARG* 4.4 12.1 - - + -
256A PRO* 4.4 7.6 - - + -
246C TYR* 4.2 18.8 + - - -
252C SER* 5.7 0.2 - - - -
246E TYR* 4.3 13.0 + - - -
247E SER 6.0 0.2 - - - -
250E GLY* 3.0 40.4 + - - -
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Residues in contact with SER 247 (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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243A ASP 2.9 19.2 + - - -
244A VAL* 3.5 7.9 - - - -
246A TYR* 1.3 81.3 - - - +
248A GLU* 1.3 69.3 + - - +
250A GLY* 3.9 4.2 + - - -
246C TYR* 6.1 0.3 - - - -
261C LYS* 3.5 11.1 + - - -
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Residues in contact with GLU 248 (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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118A SER 5.5 2.2 - - - +
183A PRO* 3.6 27.0 - - + +
244A VAL* 2.8 35.4 + - + +
245A LEU 4.3 0.2 - - - +
247A SER* 1.3 82.1 + - - +
249A THR* 1.3 58.7 + - - +
256C PRO 5.0 0.9 - - - +
258C THR* 3.9 8.0 + - - +
261C LYS* 2.8 38.9 + - - +
265C ARG* 2.8 43.7 + - - -
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Residues in contact with THR 249 (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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183A PRO* 3.9 23.1 - - + -
189A ARG* 4.0 22.0 - - - +
245A LEU* 2.8 23.9 + - - +
246A TYR 4.0 0.2 + - - -
248A GLU* 1.3 76.9 - - - +
250A GLY* 1.3 62.4 + - - +
251A ASP* 3.1 25.9 + - - +
254A TYR* 3.6 10.4 - - + -
255C ARG* 3.4 21.8 + - - +
256C PRO 4.6 6.1 - - - +
258C THR* 4.4 9.4 - - - +
261C LYS* 5.3 0.4 - - - -
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Residues in contact with GLY 250 (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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246A TYR* 2.9 16.9 + - - -
247A SER 3.9 3.7 + - - -
248A GLU 3.3 3.2 + - - -
249A THR* 1.3 78.3 - - - +
251A ASP* 1.3 57.1 + - - +
246C TYR* 3.0 35.5 + - - -
252C SER* 2.9 18.2 + - - -
255C ARG* 3.4 12.7 - - - -
256C PRO* 6.1 0.7 - - - -
261C LYS* 5.2 0.8 - - - +
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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