Contacts of the helix formed by residues 247 - 260 (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 CYS 247 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246L THR* 1.3 72.8 - - - +
248L GLU* 1.3 66.1 + - + +
250L MET* 3.3 15.8 + - + +
251L MET* 3.0 36.8 + - + +
275L THR* 5.5 7.6 - - - -
276L ALA* 4.8 22.9 - - - +
279L THR* 5.5 8.1 - - + -
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Residues in contact with GLU 248 (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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246L THR* 3.3 21.2 - - - +
247L CYS* 1.3 86.4 + - - +
249L ASP* 1.3 64.8 + - - +
251L MET* 3.4 8.0 + - - +
252L LYS* 3.1 29.6 + - + +
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Residues in contact with ASP 249 (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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244L ALA* 3.5 19.3 - - + -
245L GLY* 4.8 3.8 + - - -
246L THR* 3.1 26.0 + - - +
248L GLU* 1.3 74.8 - - - +
250L MET* 1.3 67.0 + - - +
252L LYS* 3.3 21.1 + - - +
253L ARG* 3.3 41.5 + - - +
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Residues in contact with MET 250 (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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242L ALA* 3.4 34.4 - - + +
244L ALA* 3.5 7.0 - - + +
246L THR 3.1 12.0 + - - +
247L CYS* 3.5 19.1 - - + +
249L ASP* 1.3 77.4 - - - +
251L MET* 1.3 67.7 + - - +
253L ARG* 3.3 5.6 + - - +
254L ALA* 3.1 20.6 + - - +
267L HIS* 3.9 22.2 - - + -
276L ALA* 3.4 39.5 - - + +
279L THR* 3.8 24.2 - - + -
280L LEU* 4.0 18.4 - - + -
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Residues in contact with MET 251 (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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247L CYS* 3.0 23.4 + - + +
248L GLU* 3.7 6.1 - - - +
249L ASP 3.2 0.2 - - - -
250L MET* 1.3 85.7 - - + +
252L LYS* 1.3 59.2 + - - +
254L ALA* 3.2 2.9 + - - +
255L VAL* 2.9 40.6 + - + +
279L THR* 3.9 25.6 - - + -
280L LEU* 4.8 6.7 - - - -
283L TYR* 3.2 48.9 - - + -
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Residues in contact with LYS 252 (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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286H ASP* 4.0 32.0 + - - +
214L TRP* 3.7 26.9 - - + +
248L GLU* 3.1 23.4 + - + +
249L ASP* 3.3 23.5 + - - +
251L MET* 1.3 76.2 - - - +
253L ARG* 1.3 62.5 + - - +
255L VAL* 3.5 7.4 + - - +
256L PHE* 3.2 17.8 + - - +
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Residues in contact with ARG 253 (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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207L ASN* 4.0 14.6 - - - +
208L SER* 3.9 20.0 - - - -
214L TRP* 3.6 56.1 - - + +
218L PHE* 3.3 25.7 - - + -
241L ASN 4.3 12.0 + - - -
242L ALA* 4.1 17.5 - - - -
243L THR 3.4 18.8 + - - -
244L ALA* 3.9 11.5 - - - +
245L GLY 5.6 0.6 - - - +
249L ASP* 3.3 34.5 + - - +
250L MET 3.7 5.8 - - - +
251L MET 3.2 0.6 - - - -
252L LYS* 1.3 74.3 - - - +
254L ALA* 1.3 64.7 + - - +
256L PHE 3.4 1.2 + - - -
257L ALA* 3.2 18.4 + - - +
265L VAL* 5.9 0.2 - - - -
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Residues in contact with ALA 254 (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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242L ALA* 4.5 6.8 - - + +
250L MET 3.1 13.6 + - - +
251L MET* 3.7 9.4 - - + +
253L ARG* 1.3 75.4 - - - +
255L VAL* 1.3 63.1 + - - +
257L ALA* 3.2 9.9 + - - +
258L ARG* 3.1 21.1 + - - +
265L VAL* 4.9 7.0 - - + -
280L LEU* 3.8 24.0 - - + -
283L TYR* 3.8 21.5 - - + -
289L LEU* 4.1 7.6 - - + +
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Residues in contact with VAL 255 (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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251L MET* 2.9 29.4 + - + +
252L LYS* 3.7 7.6 - - - +
254L ALA* 1.3 76.1 - - - +
256L PHE* 1.3 57.3 + - - +
258L ARG* 3.2 4.7 + - - +
259L GLU* 3.0 28.0 + - + +
283L TYR* 3.6 29.2 - - + +
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Residues in contact with PHE 256 (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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258H ARG* 5.0 0.7 - - - -
58I SER* 4.9 2.7 - - - -
214L TRP* 3.7 29.4 - + + -
215L ARG* 3.4 58.3 - - + -
218L PHE* 3.8 20.0 - + + -
219L LEU* 3.5 27.4 - - + -
252L LYS 3.2 10.5 + - - +
253L ARG 3.4 0.6 + - - +
255L VAL* 1.3 74.3 - - - +
257L ALA* 1.3 65.2 + - - +
259L GLU* 3.2 30.4 + - - -
260L LEU* 3.0 43.7 + - + +
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Residues in contact with ALA 257 (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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218L PHE* 4.4 5.1 - - + -
240L LEU* 4.4 7.4 - - + -
253L ARG 3.2 11.3 + - - +
254L ALA 3.2 9.5 + - - +
256L PHE* 1.3 75.0 - - - +
258L ARG* 1.3 63.5 + - - +
260L LEU* 3.2 8.5 + - - +
261L GLY 3.2 15.8 + - - -
262L VAL* 3.5 28.5 + - + +
265L VAL* 3.5 30.5 - - + -
289L LEU* 4.7 3.6 - - + -
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Residues in contact with ARG 258 (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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215B ARG* 3.4 23.9 - - - +
256B PHE* 4.7 0.6 - - - -
259B GLU* 3.0 38.8 + - - -
254L ALA 3.1 8.1 + - - +
255L VAL 3.3 10.8 - - - +
257L ALA* 1.3 76.2 - - - +
259L GLU* 1.3 58.7 + - - +
261L GLY* 2.9 21.8 + - - -
283L TYR* 3.7 21.1 - - - +
286L ASP 5.3 0.4 + - - -
287L ASN* 3.1 34.1 + - + +
289L LEU* 4.5 6.4 - - + +
58S SER* 3.8 15.8 - - - +
59S PRO* 3.8 24.2 - - + +
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Residues in contact with GLU 259 (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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258H ARG* 3.0 42.7 + - - -
56I HIS* 3.1 35.8 + - + +
58I SER* 4.1 1.2 - - - -
255L VAL* 3.0 15.6 + - + +
256L PHE* 3.2 26.3 + - - +
258L ARG* 1.3 78.9 - - - +
260L LEU* 1.3 59.5 + - - +
261L GLY* 3.4 0.9 + - - -
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Residues in contact with LEU 260 (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 5.1 1.4 - - - +
56I HIS* 3.8 38.1 - - + +
61I TYR* 4.9 2.7 - - + -
218L PHE* 3.8 26.2 - - + +
219L LEU* 4.2 9.6 - - + -
222L ALA* 4.2 14.8 - - + -
226L TYR* 2.9 24.3 + - + -
240L LEU* 4.9 5.4 - - + -
256L PHE* 3.0 52.9 + - + +
257L ALA* 3.2 10.9 + - - +
259L GLU* 1.3 74.9 - - - +
261L GLY* 1.3 57.9 + - - +
262L VAL* 3.3 10.8 - - + -
53S ARG* 4.7 0.3 + - - -
57S ASN* 5.0 0.4 - - - +
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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