Contacts of the helix formed by residues 214 - 232 (chain B) in PDB entry 1RBO
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 TRP 214 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207B ASN 3.5 18.2 - - - +
208B SER* 3.1 28.6 + - - -
212B MET 3.9 0.4 + - - -
213B ARG* 1.3 72.9 - - + +
215B ARG* 1.3 94.8 + - + +
217B ARG* 3.2 18.0 + - - +
218B PHE* 3.0 46.1 + + + -
252B LYS* 3.7 38.2 - - + +
253B ARG* 3.6 53.7 - - + +
256B PHE* 3.7 34.1 - + + -
286L ASP* 5.6 6.3 + - - -
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213B ARG* 3.4 2.9 - - + +
214B TRP* 1.3 105.8 - - + +
216B ASP* 1.3 65.1 + - - +
218B PHE* 3.4 3.2 + - - +
219B LEU* 3.1 40.6 + - - +
256B PHE* 3.4 49.7 - - + -
161L LYS* 5.6 1.2 - - - +
258L ARG* 3.4 24.2 - - - +
285L ARG* 3.6 21.8 - - - +
286L ASP* 3.0 25.4 + - - +
287L ASN 3.5 17.7 + - - -
288L GLY* 3.5 17.9 - - - +
58S SER* 4.8 7.3 + - - -
59S PRO 4.6 2.6 + - - -
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Residues in contact with ASP 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 3.6 20.2 - - + -
213B ARG* 3.3 24.0 + - - +
214B TRP 3.3 0.6 - - - -
215B ARG* 1.3 77.5 - - - +
217B ARG* 1.3 63.5 + - - +
219B LEU* 3.4 3.4 + - - +
220B PHE* 3.1 30.2 + - + -
152L PRO 5.1 2.8 - - - +
153L HIS* 3.6 13.4 + - - -
157L VAL* 3.5 30.0 - - + +
161L LYS* 2.8 34.5 + - - +
285L ARG* 6.0 0.7 - - - -
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Residues in contact with ARG 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ALA* 3.8 10.3 - - - +
185B TYR* 3.8 12.8 - - + -
202B ASP* 2.9 39.3 + - - +
206B VAL* 3.4 25.4 + - - +
207B ASN* 3.0 30.5 + - - +
209B GLN* 5.4 0.2 + - - -
212B MET* 3.5 37.6 + - - +
213B ARG 3.2 3.3 + - - +
214B TRP* 3.2 17.2 + - - +
216B ASP* 1.3 80.2 - - - +
218B PHE* 1.3 75.3 + - + +
220B PHE* 3.4 0.9 + - - +
221B CYS* 2.9 48.1 + - - +
240B LEU* 5.1 0.7 - - + -
241B ASN 4.2 5.1 + - - -
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Residues in contact with PHE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214B TRP* 3.0 53.1 + + + +
215B ARG 3.7 4.5 - - - +
217B ARG* 1.3 100.0 - - - +
219B LEU* 1.3 57.8 + - - +
221B CYS* 3.9 1.2 - - - +
222B ALA* 3.0 30.8 + - - +
240B LEU* 3.7 49.9 - - + +
241B ASN 3.6 20.2 - - - -
242B ALA* 5.2 0.4 - - + -
253B ARG* 3.3 30.3 - - + -
256B PHE* 3.8 19.7 - + + -
257B ALA* 4.4 8.1 - - + -
260B LEU* 3.8 8.1 - - + +
265B VAL* 5.8 0.7 - - + -
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Residues in contact with LEU 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ARG* 3.1 23.4 + - - +
216B ASP* 3.6 5.8 - - - +
218B PHE* 1.3 81.0 - - - +
220B PHE* 1.3 63.1 + - + +
222B ALA* 3.3 6.6 + - - +
223B GLU* 3.2 18.0 + - - +
256B PHE* 3.5 28.7 - - + -
260B LEU* 4.2 5.2 - - + -
161L LYS* 4.0 20.9 - - + +
58S SER* 4.2 13.2 - - - +
59S PRO 3.9 7.9 - - - +
60S GLY 3.6 31.6 - - - +
61S TYR* 3.9 26.8 - - + -
65S ARG* 5.1 3.1 - - - +
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Residues in contact with PHE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B ALA* 3.7 28.3 - - + +
183B LYS* 3.8 20.4 - - + -
186B GLY* 4.4 2.2 - - - -
216B ASP* 3.1 25.2 + - + +
217B ARG 4.1 0.9 - - - +
219B LEU* 1.3 74.8 - - + +
221B CYS* 1.3 60.6 + - - +
223B GLU* 3.3 5.5 + - - +
224B ALA* 3.0 27.9 + - - +
157L VAL* 5.2 3.4 - - + -
160L ASP* 3.6 42.6 - - + -
161L LYS* 3.8 26.9 - - + -
65S ARG* 3.9 28.9 - - + -
66S TYR* 3.4 32.5 - + - +
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Residues in contact with CYS 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B TYR* 3.9 13.0 - - - -
186B GLY* 4.5 7.4 - - - -
189B VAL* 4.2 11.6 - - + +
217B ARG* 2.9 34.1 + - - +
218B PHE 3.9 2.9 - - - +
220B PHE* 1.3 75.5 - - - +
222B ALA* 1.3 61.1 + - - +
224B ALA* 3.4 6.5 + - - +
225B LEU* 2.9 33.7 + - + +
238B HIS* 3.7 39.5 - - + +
240B LEU* 4.2 7.2 - - + -
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B PHE 3.0 17.6 + - - +
219B LEU 3.6 5.6 - - - +
220B PHE 3.3 0.2 - - - -
221B CYS* 1.3 77.3 - - - +
223B GLU* 1.3 62.2 + - - +
225B LEU* 3.4 11.2 + - - +
226B TYR* 3.0 45.9 + - + -
240B LEU* 6.0 0.8 - - - +
260B LEU* 4.2 24.5 - - + -
262B VAL* 4.3 9.0 - - + -
61S TYR* 4.3 4.7 - - + -
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Residues in contact with GLU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B LEU 3.2 10.5 + - - +
220B PHE* 3.6 10.2 - - - +
221B CYS 3.3 0.2 - - - -
222B ALA* 1.3 79.3 - - - +
224B ALA* 1.3 61.5 + - - +
226B TYR* 3.9 2.1 - - - +
227B LYS* 3.1 24.6 + - + +
61S TYR* 3.4 22.6 - - + +
62S TYR 3.1 16.8 - - - +
63S ASP* 4.2 7.8 - - - +
64S GLY 3.5 5.4 + - - +
65S ARG* 2.9 58.9 + - - +
66S TYR* 3.2 28.5 + - + +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B GLY* 3.1 30.7 - - - +
189B VAL* 4.0 5.6 - - + -
190B TYR* 3.8 23.3 - - + +
220B PHE 3.0 17.0 + - - +
221B CYS 3.7 3.4 - - - +
223B GLU* 1.3 76.5 - - - +
225B LEU* 1.3 62.4 + - - +
227B LYS* 3.3 5.1 + - - +
228B ALA* 3.1 22.7 + - - +
66S TYR* 4.0 9.2 - - + -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B VAL* 4.9 0.2 - - + -
193B LEU* 3.8 25.7 - - + +
221B CYS 2.9 20.7 + - - +
222B ALA* 3.4 10.5 + - - +
224B ALA* 1.3 72.0 - - - +
226B TYR* 1.3 81.6 + - + +
228B ALA* 3.4 2.3 + - - +
229B GLN* 3.0 36.0 + - - +
236B LYS* 3.8 23.9 - - + +
237B GLY* 4.3 1.8 - - - -
238B HIS* 3.9 30.7 - - + +
240B LEU* 6.1 0.9 - - + -
262B VAL* 3.9 26.9 - - + -
263B PRO* 4.8 4.9 - - + -
62C TYR* 6.1 0.2 - - - +
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Residues in contact with TYR 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ALA* 3.0 39.0 + - + +
223B GLU 3.9 3.1 - - - +
225B LEU* 1.3 90.5 - - + +
227B LYS* 1.3 62.4 + - - +
229B GLN* 3.5 16.6 + - - +
230B ALA* 3.1 24.9 + - - +
260B LEU* 2.9 27.9 + - + -
261B GLY 3.4 8.6 + - - -
262B VAL* 3.8 8.0 + - + +
263B PRO* 6.3 0.7 - - + -
53C ARG* 3.1 31.0 + - - -
62C TYR* 5.8 3.1 - + - -
55S HIS* 3.5 61.8 + + + +
56S HIS* 6.1 1.1 - + + -
61S TYR* 3.9 6.1 - + - +
63S ASP* 4.8 0.4 - - - +
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Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B TYR* 3.4 44.9 - - + -
223B GLU* 3.1 19.8 + - + +
224B ALA* 3.6 6.1 - - - +
225B LEU 3.3 0.2 - - - -
226B TYR* 1.3 77.2 - - - +
228B ALA* 1.3 61.5 + - - +
230B ALA* 3.4 6.1 + - - +
231B GLU* 3.0 24.5 + - + +
45S GLU* 2.9 33.4 + - - -
48S HIS* 5.8 3.4 + - - +
52S TYR* 6.1 0.4 - - - +
55S HIS* 5.2 1.1 - - - -
64S GLY* 5.6 4.4 - - - +
66S TYR* 3.0 34.3 + - + +
67S TRP 4.4 2.2 - - - -
68S THR* 4.7 1.1 - - - -
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Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B TYR* 3.8 17.1 - - + +
193B LEU* 3.4 34.3 - - + -
194B ARG* 3.8 12.1 - - - +
224B ALA 3.1 14.6 + - - +
225B LEU 3.8 3.4 - - - +
227B LYS* 1.3 76.2 - - - +
229B GLN* 1.3 61.5 + - - +
231B GLU* 3.3 3.6 + - - +
232B THR* 3.0 32.6 + - - +
236B LYS* 4.3 3.4 - - + -
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Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B LEU* 3.0 23.3 + - - +
226B TYR* 3.8 15.8 - - - +
227B LYS 3.3 0.2 - - - -
228B ALA* 1.3 74.8 - - - +
230B ALA* 1.3 60.6 + - - +
233B GLY* 2.9 30.2 + - - -
234B GLU 3.3 21.8 - - - +
235B ILE* 3.5 15.1 - - + +
236B LYS* 3.0 38.5 + - + +
51C VAL* 4.2 11.3 - - + +
52C TYR* 6.1 0.2 - - - -
53C ARG* 5.6 1.9 - - - +
62C TYR* 3.8 24.4 + - - -
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Residues in contact with ALA 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TYR 3.1 17.2 + - - +
227B LYS* 3.8 6.1 - - - +
229B GLN* 1.3 78.0 - - - +
231B GLU* 1.3 63.2 + - - +
233B GLY* 4.0 0.3 + - - -
10C LYS* 3.2 22.3 + - - -
55S HIS* 5.6 7.4 - - + +
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B TYR* 2.6 30.1 + - - -
194B ARG* 2.9 43.7 + - - +
227B LYS* 3.0 17.8 + - + +
228B ALA* 3.6 6.5 - - - +
229B GLN 3.3 0.2 - - - -
230B ALA* 1.3 77.2 - - - +
232B THR* 1.3 61.7 + - + +
4C TRP* 5.2 0.3 - - - -
5C PRO 4.0 4.5 - - - +
6C ILE* 3.6 30.9 - - - +
9C LEU* 4.2 12.9 + - + +
10C LYS* 3.3 20.1 + - - +
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LEU 4.3 4.5 - - - +
194B ARG* 3.5 35.2 - - + +
228B ALA 3.0 17.4 + - - +
231B GLU* 1.3 84.2 - - + +
233B GLY* 1.3 63.6 + - - +
234B GLU* 3.3 16.2 + - - -
236B LYS* 3.3 17.9 - - - +
9C LEU 4.4 9.6 - - - +
10C LYS* 3.5 4.3 - - - -
11C LYS* 2.8 31.1 + - - +
17C TYR* 4.7 11.0 - - - +
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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