Contacts of the helix formed by residues 231 - 251 (chain A) in PDB entry 3RQ5
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 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A HIS* 3.3 7.7 - - + +
230A GLU* 1.3 78.0 - - + +
232A PRO* 1.3 69.1 - - - +
233A LYS* 2.9 28.3 + - - +
234A HIS* 3.1 53.6 + - + +
235A ALA 3.2 8.5 + - - -
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Residues in contact with PRO 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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124A PRO* 4.5 6.5 - - + -
143A PRO* 4.1 28.5 - - + -
145A ILE* 5.6 0.7 - - + -
226A LEU* 3.5 26.4 - - + +
229A HIS 5.2 2.2 - - - +
230A GLU 3.4 10.3 - - - +
231A ASP* 1.3 88.7 - - - +
233A LYS* 1.3 66.3 + - + +
235A ALA* 3.3 4.0 + - + +
236A VAL* 3.1 28.9 + - - +
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Residues in contact with LYS 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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182A VAL* 6.0 0.2 - - + -
194A PHE* 3.5 45.8 - - + -
196A ASP* 2.8 32.3 + - - +
198A ASP* 2.9 24.0 + - - -
200A TRP* 6.0 0.9 - - - +
231A ASP* 2.9 17.0 + - - +
232A PRO* 1.3 84.5 - - + +
234A HIS* 1.3 65.1 + - + +
236A VAL* 3.3 4.2 + - - +
237A LEU* 3.1 32.9 + - + +
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TRP* 3.8 22.4 - + - -
14A THR* 3.5 35.8 + - + +
229A HIS* 3.9 15.5 - - + -
231A ASP* 3.1 38.5 + - + +
233A LYS* 1.3 78.3 - - + +
235A ALA* 1.3 60.0 + - - +
237A LEU* 4.5 6.3 - - + -
238A ASN* 2.8 36.3 + - - +
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Residues in contact with ALA 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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222A ILE* 4.8 1.3 - - - +
225A MET* 3.5 37.0 - - - +
226A LEU* 3.6 17.5 - - + +
229A HIS* 3.8 21.8 - - + -
231A ASP 3.2 6.2 + - - +
232A PRO* 3.5 10.3 - - + +
233A LYS 3.3 0.2 - - - -
234A HIS* 1.3 77.4 - - - +
236A VAL* 1.3 62.5 + - - +
239A ALA* 3.0 26.3 + - - +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A ILE* 3.7 33.0 - - + -
182A VAL* 4.5 6.7 - - + -
184A VAL* 3.6 30.7 - - + -
192A ILE* 3.8 17.0 - - + -
194A PHE* 4.8 4.5 - - + -
222A ILE* 3.9 20.4 - - + +
226A LEU* 4.6 1.6 - - + -
232A PRO 3.1 15.3 + - - +
233A LYS* 3.8 7.0 - - - +
234A HIS 3.3 0.4 - - - -
235A ALA* 1.3 76.2 - - - +
237A LEU* 1.3 62.9 + - - +
239A ALA* 3.3 2.6 + - - +
240A VAL* 3.1 26.4 + - + +
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Residues in contact with LEU 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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6A TRP* 3.5 55.8 - - + +
192A ILE* 3.8 28.1 - - + +
194A PHE* 4.1 11.4 - - + -
200A TRP* 3.8 41.5 - - + +
202A ASN* 4.8 0.5 - - - +
233A LYS* 3.1 24.0 + - + +
234A HIS* 3.9 4.5 - - + +
236A VAL* 1.3 78.5 - - - +
238A ASN* 1.3 55.7 + - - +
240A VAL* 3.4 4.8 + - - +
241A TYR* 3.0 29.3 + - - +
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Residues in contact with ASN 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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6A TRP* 2.9 22.4 + - - -
11A VAL* 3.4 17.2 - - - +
14A THR* 2.9 21.6 + - - -
15A LEU* 3.6 25.9 - - + +
225A MET* 3.7 6.5 - - - -
229A HIS* 3.0 31.2 + - - +
234A HIS 2.8 21.1 + - - +
237A LEU* 1.3 69.6 - - - +
239A ALA* 1.3 60.3 + - - +
241A TYR* 4.3 3.4 - - - -
242A LEU* 2.8 36.5 + - + +
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Residues in contact with ALA 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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218A LEU* 3.8 2.4 - - + +
221A MET* 3.6 8.0 - - + +
222A ILE* 3.6 41.1 - - + +
225A MET* 3.4 20.1 - - - -
235A ALA 3.0 18.0 + - - +
236A VAL 3.7 0.9 - - - +
238A ASN* 1.3 74.1 - - - +
240A VAL* 1.3 67.2 + - - +
243A HIS* 2.9 28.2 + - - +
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Residues in contact with VAL 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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184A VAL* 3.9 27.1 - - + -
190A THR* 3.8 20.2 - - + +
192A ILE* 4.2 14.6 - - + -
202A ASN* 3.6 33.3 + - + +
218A LEU* 3.9 22.4 - - + -
222A ILE* 4.7 3.1 - - + -
236A VAL* 3.1 18.1 + - + +
237A LEU 3.9 3.4 - - - +
239A ALA* 1.3 74.9 - - - +
241A TYR* 1.3 63.0 + - - +
243A HIS* 3.7 4.7 + - - +
244A GLY 3.2 17.3 + - - -
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Residues in contact with TYR 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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6A TRP* 3.2 30.1 - + + -
7A THR 3.9 0.7 - - - -
8A GLU* 3.5 35.7 + - - +
11A VAL* 3.5 21.5 - - + -
202A ASN* 3.1 16.3 + - - +
203A PRO* 3.7 9.0 - - + +
204A THR* 2.7 46.3 + - + +
237A LEU 3.0 17.8 + - - +
238A ASN 3.7 3.8 - - - +
240A VAL* 1.3 78.2 - - - +
242A LEU* 1.3 67.6 + - + +
244A GLY 3.3 0.3 + - - -
245A ALA* 3.0 15.3 + - + -
275A PHE* 3.6 30.4 - + - -
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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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11A VAL* 4.7 4.3 - - + -
15A LEU* 4.0 24.2 - - + -
221A MET* 4.0 7.2 - - + -
225A MET* 3.6 23.1 - - + -
238A ASN* 2.8 19.9 + - + +
241A TYR* 1.3 80.6 - - + +
243A HIS* 1.3 59.4 + - - +
245A ALA* 3.1 3.0 + - - +
246A CYS* 2.9 34.2 + - - -
268A LEU* 3.8 13.2 - - + -
271A VAL* 3.8 14.8 - - + +
272A TRP* 4.2 22.0 - - + -
275A PHE* 3.6 36.3 - - + -
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Residues in contact with HIS 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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186A LYS* 6.3 0.7 - - + -
209A LEU* 3.8 28.5 - - + +
214A THR* 2.8 30.1 + - - -
215A GLY* 5.5 0.7 - - - -
217A THR* 4.2 1.6 - - + -
218A LEU* 3.7 41.1 - - + +
221A MET* 3.5 22.9 - - + +
239A ALA 2.9 18.9 + - - +
240A VAL* 3.7 5.7 + - - +
242A LEU* 1.3 77.1 - - - +
244A GLY* 1.3 63.1 + - - +
246A CYS* 3.3 12.7 + - - +
247A ALA* 3.5 9.0 + - - +
264A LEU* 3.7 28.7 - - + +
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Residues in contact with GLY 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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202A ASN* 4.8 0.9 - - - -
204A THR* 3.3 17.9 - - - -
205A GLY* 3.4 27.6 + - - -
209A LEU* 4.2 9.6 - - - -
240A VAL 3.2 12.2 + - - -
243A HIS* 1.3 77.1 + - - +
245A ALA* 1.3 62.5 + - - +
247A ALA* 3.1 3.3 + - - +
248A GLU* 3.1 18.0 + - - +
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Residues in contact with ALA 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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204A THR* 3.5 15.4 + - + -
241A TYR* 3.0 26.5 + - + +
242A LEU* 3.1 8.5 + - - +
244A GLY* 1.3 76.0 - - - +
246A CYS* 1.3 57.2 + - - +
248A GLU* 3.3 9.2 + - - +
249A LEU* 2.9 28.9 + - - +
271A VAL* 3.8 21.0 - - + +
275A PHE* 4.5 6.3 - - + -
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Residues in contact with CYS 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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221A MET* 5.3 1.1 - - - -
242A LEU 2.9 18.6 + - - -
243A HIS* 3.5 10.5 - - - +
244A GLY 3.2 0.4 - - - -
245A ALA* 1.3 79.3 - - - +
247A ALA* 1.3 55.7 + - - +
249A LEU 3.4 0.7 + - - -
250A TRP* 3.0 27.4 + - - +
264A LEU* 3.5 37.2 - - + +
267A ILE* 3.8 24.3 - - + +
268A LEU* 3.5 34.5 - - - -
271A VAL* 4.1 5.8 - - - -
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Residues in contact with ALA 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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206A ASN* 3.4 24.7 + - - +
208A ALA* 4.5 6.0 - - + +
209A LEU* 3.8 37.0 - - + -
243A HIS 3.5 2.4 + - - +
244A GLY 3.1 9.2 + - - +
246A CYS* 1.3 76.4 - - - +
248A GLU* 1.3 66.1 + - - +
250A TRP* 3.4 8.3 - - - +
251A THR* 3.1 20.4 + - - +
259A LEU* 4.7 1.1 - - - -
264A LEU* 3.6 7.3 - - + +
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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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203A PRO 4.0 3.6 - - - +
204A THR* 3.1 22.7 - - - +
205A GLY* 2.9 29.4 + - - +
206A ASN* 3.7 15.7 - - - +
244A GLY 3.1 9.7 + - - +
245A ALA* 3.5 9.9 - - - +
246A CYS 3.2 0.2 - - - -
247A ALA* 1.3 75.6 - - - +
249A LEU* 1.3 66.6 + - - +
251A THR* 3.1 14.5 + - - -
252A ASP* 3.4 13.5 - - - +
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Residues in contact with LEU 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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245A ALA 2.9 16.8 + - - +
246A CYS 3.8 3.8 - - - +
248A GLU* 1.3 75.0 - - - +
250A TRP* 1.3 63.8 + - - +
252A ASP* 3.1 41.8 + - + +
253A GLU 4.4 0.3 + - - -
254A HIS* 5.0 1.2 + - - -
267A ILE* 4.0 12.1 - - + -
270A ARG* 4.7 16.8 - - + -
271A VAL* 3.4 26.0 - - + -
274A ARG* 3.6 42.0 - - - +
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Residues in contact with TRP 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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208A ALA* 4.5 2.7 - - + -
246A CYS 3.0 14.0 + - - +
247A ALA* 3.4 12.3 - - - +
249A LEU* 1.3 76.3 - - - +
251A THR* 1.3 71.4 + - + +
252A ASP 3.1 4.9 + - - -
253A GLU 3.4 0.3 + - - -
254A HIS* 2.8 73.7 + + + +
255A SER 3.1 24.0 + - - -
258A THR* 3.4 20.6 - - - -
259A LEU* 3.6 44.0 - - + +
263A GLU* 3.3 34.1 - - + -
267A ILE* 3.9 21.8 - - + +
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Residues in contact with THR 251 (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 ASN* 3.1 34.9 + - - +
208A ALA* 4.3 0.7 - - + -
247A ALA 3.1 5.1 + - - +
248A GLU* 3.1 10.2 + - - -
249A LEU 3.3 0.4 - - - -
250A TRP* 1.3 79.4 - - + +
252A ASP* 1.3 65.0 + - - +
253A GLU 3.2 1.2 + - - -
254A HIS 3.2 13.0 + - - +
256A ALA* 3.7 36.3 - - + +
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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