Contacts of the helix formed by residues 214 - 232 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286H ASP* 5.6 6.1 - - - -
207L ASN 3.5 18.2 - - - +
208L SER* 3.1 29.4 + - - +
212L MET 3.9 0.4 + - - -
213L ARG* 1.3 72.9 - - + +
215L ARG* 1.3 93.0 + - + +
217L ARG* 3.2 17.6 + - - +
218L PHE* 3.0 46.4 + + + -
241L ASN 5.5 0.2 - - - +
252L LYS* 3.7 39.0 - - + +
253L ARG* 3.6 51.7 - - + +
256L PHE* 3.7 34.5 - + + -
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Residues in contact with ARG 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H LYS* 5.6 1.0 - - - +
258H ARG* 3.4 23.0 - - - +
285H ARG* 3.6 20.9 - - - +
286H ASP* 3.0 25.5 + - - +
287H ASN 3.5 17.9 + - - -
288H GLY* 3.5 17.1 - - - +
58I SER* 4.8 7.7 + - - -
59I PRO* 4.6 3.0 + - - +
213L ARG* 3.4 2.0 - - + +
214L TRP* 1.3 104.3 - - + +
216L ASP* 1.3 65.0 + - - +
218L PHE* 3.4 2.9 + - - +
219L LEU* 3.1 40.8 + - - +
256L PHE* 3.4 51.8 - - + -
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Residues in contact with ASP 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152H PRO 5.1 2.6 - - - +
153H HIS* 3.7 13.2 + - - -
157H VAL* 3.5 30.9 - - + +
161H LYS* 2.9 33.8 + - - +
285H ARG* 6.1 0.7 - - - -
182L ALA* 3.6 18.8 - - + -
213L ARG* 3.7 24.6 + - - +
214L TRP 3.3 0.2 - - - -
215L ARG* 1.3 78.8 - - - +
217L ARG* 1.3 64.3 + - - +
219L LEU* 3.4 3.1 + - - +
220L PHE* 3.1 29.2 + - + -
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Residues in contact with ARG 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182L ALA* 3.8 10.2 - - - +
185L TYR* 3.8 12.3 - - + -
202L ASP* 2.9 40.4 + - - +
206L VAL* 3.4 25.4 + - - +
207L ASN* 3.0 30.7 + - - +
209L GLN* 5.4 0.2 + - - -
212L MET* 3.5 39.1 + - - +
213L ARG 3.2 4.0 + - - +
214L TRP* 3.2 17.2 + - - +
216L ASP* 1.3 79.8 - - - +
218L PHE* 1.3 74.3 + - + +
220L PHE* 3.4 0.9 + - - +
221L CYS* 2.9 49.9 + - - +
240L LEU* 5.1 0.7 - - + -
241L ASN 4.2 4.8 + - - -
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Residues in contact with PHE 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214L TRP* 3.0 54.0 + + + +
215L ARG 3.7 4.7 - - - +
217L ARG* 1.3 98.0 - - - +
219L LEU* 1.3 57.8 + - - +
221L CYS* 3.5 1.6 + - - +
222L ALA* 3.0 29.8 + - - +
240L LEU* 3.7 49.9 - - + +
241L ASN 3.6 20.0 - - - -
242L ALA* 5.2 0.4 - - + -
253L ARG* 3.3 30.7 - - + -
256L PHE* 3.8 19.3 - + + -
257L ALA* 4.4 7.6 - - + -
260L LEU* 3.8 8.7 - - + +
265L VAL* 5.8 0.9 - - + -
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Residues in contact with LEU 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H LYS* 4.0 22.4 - - + +
58I SER* 4.2 10.8 - - - +
59I PRO 4.0 7.9 - - - +
60I GLY 3.6 30.7 - - - +
61I TYR* 3.9 27.3 - - + -
65I ARG* 5.1 3.1 - - - +
215L ARG* 3.1 21.4 + - - +
216L ASP* 3.6 5.4 - - - +
218L PHE* 1.3 79.3 - - - +
220L PHE* 1.3 63.8 + - + +
222L ALA* 3.3 6.9 + - - +
223L GLU* 3.2 17.5 + - - +
256L PHE* 3.5 28.9 - - + -
260L LEU* 4.2 7.2 - - + -
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Residues in contact with PHE 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H VAL* 5.2 3.4 - - + -
160H ASP* 3.7 42.6 - - + -
161H LYS* 3.8 27.1 - - + -
65I ARG* 3.9 28.7 - - + -
66I TYR* 3.4 33.7 - + - +
182L ALA* 3.7 27.6 - - + +
183L LYS* 3.8 20.4 - - + -
186L GLY* 4.4 0.9 - - - -
216L ASP* 3.1 27.1 + - + +
217L ARG 4.1 0.9 - - - +
219L LEU* 1.3 73.9 - - + +
221L CYS* 1.3 60.0 + - - +
223L GLU* 3.3 5.6 + - - +
224L ALA* 3.0 28.8 + - - +
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Residues in contact with CYS 221 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185L TYR* 3.9 13.9 - - - -
186L GLY* 4.5 6.7 - - - -
189L VAL* 4.2 11.3 - - + +
217L ARG* 2.9 34.8 + - - +
218L PHE 3.9 2.9 - - - +
220L PHE* 1.3 75.0 - - - +
222L ALA* 1.3 59.8 + - - +
224L ALA* 3.7 6.0 - - - +
225L LEU* 2.9 33.8 + - - +
238L HIS* 3.7 41.0 - - + +
240L LEU* 4.2 7.2 - - + -
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Residues in contact with ALA 222 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I TYR* 4.3 4.9 - - + -
218L PHE 3.0 18.5 + - - +
219L LEU 3.6 4.9 - - - +
220L PHE 3.3 0.2 - - - -
221L CYS* 1.3 76.0 - - - +
223L GLU* 1.3 64.0 + - - +
225L LEU* 3.4 11.9 + - - +
226L TYR* 3.0 46.0 + - + -
240L LEU* 6.0 0.4 - - - +
260L LEU* 4.2 24.5 - - + -
262L VAL* 4.3 8.5 - - + -
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Residues in contact with GLU 223 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61I TYR* 3.4 21.6 - - + +
62I TYR 3.2 16.8 - - - +
63I ASP* 4.2 7.7 - - - +
64I GLY 3.5 4.9 + - - +
65I ARG* 2.9 59.6 + - - +
66I TYR* 3.2 28.3 + - + +
219L LEU 3.2 10.5 + - - +
220L PHE* 3.6 10.7 - - - +
222L ALA* 1.3 80.2 - - - +
224L ALA* 1.3 61.1 + - - +
226L TYR* 3.5 2.3 + - - +
227L LYS* 3.1 23.2 + - + +
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Residues in contact with ALA 224 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66I TYR* 4.0 9.2 - - + -
186L GLY* 3.1 32.1 - - - +
189L VAL* 4.0 5.6 - - + -
190L TYR* 3.8 22.0 - - + +
220L PHE 3.0 15.8 + - - +
221L CYS 3.7 4.0 - - - +
223L GLU* 1.3 78.8 - - - +
225L LEU* 1.3 62.1 + - - +
227L LYS* 3.3 5.4 + - - +
228L ALA* 3.1 22.7 + - - +
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Residues in contact with LEU 225 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L VAL* 4.9 0.4 - - + -
193L LEU* 3.8 24.7 - - + +
221L CYS 2.9 21.3 + - - +
222L ALA* 3.4 10.3 + - - +
224L ALA* 1.3 73.2 - - - +
226L TYR* 1.3 81.8 + - + +
228L ALA* 3.4 2.3 + - - +
229L GLN* 3.0 35.4 + - - +
236L LYS* 3.8 23.8 - - + +
237L GLY* 4.3 2.2 - - - -
238L HIS* 3.9 31.4 - - + +
240L LEU* 6.1 0.7 - - + -
262L VAL* 3.9 26.7 - - + -
263L PRO* 4.8 4.5 - - + -
62S TYR* 6.1 0.2 - - - +
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Residues in contact with TYR 226 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55I HIS* 3.6 61.1 + + + +
56I HIS* 6.1 0.9 - - + -
61I TYR* 3.9 6.5 - + - +
63I ASP* 4.8 0.7 - - - +
222L ALA* 3.0 39.5 + - + +
223L GLU 3.9 3.4 - - - +
225L LEU* 1.3 91.7 - - + +
227L LYS* 1.3 62.4 + - - +
229L GLN* 3.5 17.8 + - - +
230L ALA* 3.1 24.3 + - - +
260L LEU* 2.9 27.9 + - + -
261L GLY 3.4 8.5 + - - -
262L VAL* 3.8 8.1 + - + +
263L PRO* 6.3 0.2 - - + -
53S ARG* 3.1 30.7 + - - -
62S TYR* 5.8 2.7 - + - -
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Residues in contact with LYS 227 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I GLU* 2.9 33.6 + - - -
48I HIS* 5.9 3.4 + - - +
52I TYR* 6.2 0.2 - - - +
55I HIS* 5.3 1.1 - - - -
64I GLY* 5.6 4.6 - - - -
66I TYR* 3.0 35.1 + - + +
67I TRP 4.4 2.5 - - - -
68I THR* 4.7 0.9 - - - -
190L TYR* 3.4 44.6 - - + -
223L GLU* 3.1 19.2 + - + +
224L ALA* 3.6 6.1 - - - +
225L LEU 3.3 0.2 - - - -
226L TYR* 1.3 78.1 - - - +
228L ALA* 1.3 60.2 + - - +
230L ALA* 3.4 6.3 + - - +
231L GLU* 3.0 24.7 + - + +
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Residues in contact with ALA 228 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L TYR* 3.8 16.1 - - + +
193L LEU* 3.4 34.1 - - + -
194L ARG* 3.8 12.6 - - - +
224L ALA 3.1 16.5 + - - +
225L LEU 3.8 3.6 - - - +
227L LYS* 1.3 76.1 - - - +
229L GLN* 1.3 61.6 - - - +
231L GLU* 3.3 3.1 + - - +
232L THR* 3.0 32.4 + - - +
236L LYS* 4.3 2.7 - - + -
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Residues in contact with GLN 229 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L LEU* 3.0 23.5 + - - +
226L TYR* 3.8 15.8 - - + +
227L LYS 3.3 0.2 - - - -
228L ALA* 1.3 74.3 - - - +
230L ALA* 1.3 60.3 + - - +
233L GLY* 2.9 29.7 + - - -
234L GLU 3.3 23.3 - - - +
235L ILE* 3.5 13.6 - - + +
236L LYS* 3.0 38.1 + - + +
51S VAL* 4.2 10.8 - - + +
53S ARG* 5.6 2.6 - - - +
62S TYR* 3.8 25.1 + - - -
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Residues in contact with ALA 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55I HIS* 5.6 7.4 - - + +
226L TYR 3.1 18.1 + - - +
227L LYS* 3.8 6.1 - - - +
229L GLN* 1.3 77.7 - - - +
231L GLU* 1.3 61.6 + - - +
233L GLY* 4.0 0.5 + - - -
10S LYS* 3.2 22.3 + - - -
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Residues in contact with GLU 231 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190L TYR* 2.6 30.0 + - - -
194L ARG* 2.9 43.4 + - - +
227L LYS* 3.0 18.3 + - + +
228L ALA* 3.6 5.6 - - - +
229L GLN 3.3 0.2 - - - -
230L ALA* 1.3 78.3 - - - +
232L THR* 1.3 60.5 + - + +
4S TRP* 5.2 0.5 - - - -
5S PRO 4.0 4.6 - - - +
6S ILE* 3.6 31.3 - - - +
9S LEU* 4.2 13.6 + - + +
10S LYS* 3.3 19.5 + - - +
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Residues in contact with THR 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193L LEU 4.3 4.7 - - - +
194L ARG* 3.5 35.4 - - + +
228L ALA 3.0 17.7 + - - +
231L GLU* 1.3 84.2 - - + +
233L GLY* 1.3 62.7 + - - +
234L GLU* 3.3 15.9 + - - -
236L LYS* 3.3 17.8 - - - +
9S LEU 4.4 8.3 - - - +
10S LYS* 3.5 4.1 - - - -
11S LYS* 2.8 32.0 + - - +
17S TYR* 4.7 10.3 - - - +
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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