Contacts of the helix formed by residues 247 - 260 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246H THR* 1.3 73.8 - - - +
248H GLU* 1.3 64.7 + - - +
250H MET* 3.3 17.1 + - + +
251H MET* 3.0 36.8 + - + +
275H THR* 5.5 7.6 - - - -
276H ALA* 4.8 22.4 - - - +
279H THR* 5.5 7.9 - - + -
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Residues in contact with GLU 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246H THR* 3.3 21.6 - - - +
247H CYS* 1.3 84.9 + - + +
249H ASP* 1.3 65.3 + - - +
251H MET* 3.4 7.3 + - - +
252H LYS* 3.1 29.9 + - + +
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Residues in contact with ASP 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244H ALA* 3.5 20.0 - - + -
245H GLY* 4.8 3.3 + - - -
246H THR* 3.1 26.5 + - - +
248H GLU* 1.3 74.0 - - - +
250H MET* 1.3 66.4 + - - +
252H LYS* 3.3 20.4 + - - +
253H ARG* 3.3 42.8 + - - +
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Residues in contact with MET 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242H ALA* 3.4 35.2 - - + +
244H ALA* 3.5 7.1 - - + +
246H THR 3.1 13.7 + - - +
247H CYS* 3.4 18.8 - - + +
249H ASP* 1.3 76.6 - - - +
251H MET* 1.3 67.4 + - + +
253H ARG* 3.3 5.5 + - - +
254H ALA* 3.1 20.1 + - - +
267H HIS* 3.9 22.4 - - + -
276H ALA* 3.4 39.3 - - + +
279H THR* 3.8 23.6 - - + -
280H LEU* 4.0 18.2 - - + -
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Residues in contact with MET 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247H CYS* 3.0 22.5 + - + +
248H GLU* 3.7 6.7 - - - +
250H MET* 1.3 84.8 - - + +
252H LYS* 1.3 59.6 + - + +
254H ALA* 3.2 2.7 + - + +
255H VAL* 2.9 41.5 + - + +
279H THR* 3.9 25.4 - - + -
280H LEU* 4.8 6.5 - - - -
283H TYR* 3.2 51.4 - - + -
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Residues in contact with LYS 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286E ASP* 4.1 32.4 + - - +
214H TRP* 3.7 25.7 - - + +
248H GLU* 3.1 22.5 + - + +
249H ASP* 3.3 23.5 + - - +
251H MET* 1.3 76.5 - - - +
253H ARG* 1.3 61.8 + - - +
255H VAL* 3.7 7.5 - - - +
256H PHE* 3.2 17.8 + - - +
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Residues in contact with ARG 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H ASN* 4.0 14.3 - - - +
208H SER* 3.9 20.2 - - - +
214H TRP* 3.6 54.8 - - + +
218H PHE* 3.3 24.5 - - + -
241H ASN 4.3 11.4 + - - -
242H ALA* 4.1 17.9 - - - -
243H THR 3.4 18.8 + - - -
244H ALA* 3.9 11.7 - - - +
245H GLY 5.6 0.4 - - - +
249H ASP* 3.3 33.3 + - - +
250H MET 3.7 6.1 - - - +
251H MET 3.2 0.6 - - - -
252H LYS* 1.3 75.2 - - - +
254H ALA* 1.3 64.9 + - - +
256H PHE* 3.4 1.4 + - - +
257H ALA* 3.2 17.8 + - - +
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Residues in contact with ALA 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242H ALA* 4.5 7.3 - - + +
250H MET 3.1 12.4 + - - +
251H MET* 3.2 9.8 + - - +
253H ARG* 1.3 75.2 - - - +
255H VAL* 1.3 62.8 - - - +
257H ALA* 3.2 9.1 + - - +
258H ARG* 3.1 20.8 + - - +
265H VAL* 4.9 6.3 - - + -
280H LEU* 3.8 24.0 - - + -
283H TYR* 3.8 23.3 - - + -
289H LEU* 4.1 7.8 - - + +
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Residues in contact with VAL 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251H MET* 2.9 30.2 + - + +
252H LYS* 3.7 7.6 - - - +
254H ALA* 1.3 76.4 - - - +
256H PHE* 1.3 58.1 + - - +
258H ARG* 3.2 5.3 + - + +
259H GLU* 3.0 27.7 + - + +
283H TYR* 3.6 30.3 - - + +
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Residues in contact with PHE 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ARG* 5.0 0.4 - - - -
58F SER* 4.9 3.1 - - - -
214H TRP* 3.7 28.9 - + + -
215H ARG* 3.4 57.9 - - + -
218H PHE* 3.8 20.4 - + + -
219H LEU* 3.5 26.7 - - + -
252H LYS 3.2 10.4 + - - +
253H ARG 3.4 0.8 + - - +
255H VAL* 1.3 74.5 - - - +
257H ALA* 1.3 65.6 + - - +
259H GLU* 3.2 29.2 + - - -
260H LEU* 3.0 44.0 + - + +
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Residues in contact with ALA 257 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H PHE* 4.4 5.3 - - + -
240H LEU* 4.4 7.9 - - + -
253H ARG 3.2 10.9 + - - +
254H ALA 3.2 11.1 + - - +
256H PHE* 1.3 76.0 - - - +
258H ARG* 1.3 62.2 + - - +
260H LEU* 3.2 8.0 + - - +
261H GLY 3.2 15.8 + - - -
262H VAL* 3.5 29.0 + - + +
265H VAL* 3.5 29.6 - - + -
289H LEU* 4.7 3.6 - - + -
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Residues in contact with ARG 258 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254H ALA 3.1 8.5 + - - +
255H VAL* 3.3 10.3 - - + +
257H ALA* 1.3 75.4 - - - +
259H GLU* 1.3 59.6 + - - +
261H GLY* 2.9 22.2 + - - -
283H TYR* 3.7 21.8 - - - +
286H ASP 5.3 0.4 + - - -
287H ASN* 3.1 33.5 + - + +
289H LEU* 4.5 5.7 - - + +
58I SER* 3.8 16.4 - - - +
59I PRO* 3.8 21.7 - - + +
215L ARG* 3.4 23.9 - - - +
256L PHE* 4.7 0.8 - - - -
259L GLU* 3.0 39.3 + - - -
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Residues in contact with GLU 259 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ARG* 3.0 42.4 + - - -
56F HIS* 3.1 35.2 + - + +
58F SER* 4.2 1.4 - - - -
255H VAL* 3.0 15.8 + - + +
256H PHE* 3.2 25.5 + - + +
258H ARG* 1.3 79.5 - - - +
260H LEU* 1.3 59.4 + - - +
261H GLY* 3.4 0.7 + - - -
57I ASN 5.6 0.2 - - - +
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Residues in contact with LEU 260 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F HIS 5.1 1.4 - - - +
56F HIS* 3.8 37.8 - - + +
61F TYR* 4.9 2.5 - - + -
218H PHE* 3.8 26.9 - - + +
219H LEU* 4.2 9.9 - - + -
222H ALA* 4.2 15.7 - - + -
226H TYR* 2.9 24.5 + - + -
240H LEU* 4.9 4.9 - - + -
256H PHE* 3.0 54.1 + - + +
257H ALA* 3.2 11.2 + - - +
259H GLU* 1.3 75.3 - - - +
261H GLY* 1.3 58.3 + - - +
262H VAL* 4.1 9.9 - - + -
53I ARG* 4.7 0.2 + - - -
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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