Contacts of the helix formed by residues 232 - 248 (chain C) in PDB entry 1RFU
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 GLY 232 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C TYR 3.8 6.3 - - - -
19C VAL* 3.3 20.4 - - - -
23C ALA* 4.1 3.3 - - - +
231C VAL* 1.3 77.0 - - - +
233C THR* 1.3 64.7 + - - +
234C GLY 3.3 2.0 - - - -
235C ASP* 3.2 8.1 + - - +
236C LEU* 3.0 22.2 + - - +
291C LEU* 4.1 6.5 - - - -
2401C PLP 2.9 18.7 + - - -
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Residues in contact with THR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C PHE* 3.8 18.9 + - + -
231C VAL 3.3 1.2 - - - -
232C GLY* 1.3 77.6 + - - +
234C GLY* 1.3 61.9 + - - +
236C LEU 3.0 2.4 + - - -
237C PHE* 2.9 20.3 + - - +
263C MET* 3.0 17.4 - - + +
267C LEU* 3.8 27.4 - - + -
291C LEU* 4.1 10.0 - - + +
2401C PLP 3.9 1.9 + - - -
2402C ADP 2.8 63.7 + - + +
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Residues in contact with GLY 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ASP* 3.9 8.8 - - - +
148C THR* 5.2 0.5 + - - -
186C THR* 5.6 2.5 - - - -
233C THR* 1.3 73.2 + - - +
235C ASP* 1.3 62.3 + - - +
237C PHE* 3.0 21.5 - - - +
238C ALA* 3.1 9.2 + - - +
2401C PLP 3.1 1.7 + - - -
2402C ADP 2.8 48.8 + - - -
2403C ZN 4.0 0.7 - - - -
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Residues in contact with ASP 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLN* 3.4 22.2 + - - +
20C GLY* 3.8 28.9 + - - +
23C ALA* 4.5 1.8 - - + -
24C ALA* 4.3 6.2 - - + +
81C LEU* 5.5 0.3 - - - +
83C GLY* 5.0 0.5 - - - -
84C TYR 4.8 2.4 + - - -
113C ASP* 3.7 15.1 - - - +
115C VAL* 4.1 10.4 - - - +
232C GLY* 3.2 12.0 + - - +
234C GLY* 1.3 74.4 - - - +
236C LEU* 1.3 62.4 + - - +
238C ALA* 3.6 3.3 + - - +
239C ALA* 3.2 22.9 + - - +
2401C PLP 2.4 41.2 + - - +
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Residues in contact with LEU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA* 3.5 13.6 - - + +
27C PRO* 3.3 35.0 - - + -
232C GLY 3.0 12.4 + - - +
233C THR* 3.4 8.1 - - - +
235C ASP* 1.3 76.1 - - - +
237C PHE* 1.3 63.7 + - - +
239C ALA* 3.4 2.5 + - - +
240C MET* 3.0 46.6 + - + +
263C MET* 3.4 17.0 - - + -
266C VAL* 4.0 25.6 - - + -
291C LEU* 4.0 19.3 - - + -
293C MET* 4.3 10.8 - - + -
300C ILE* 4.6 2.0 - - + -
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Residues in contact with PHE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C THR* 4.3 7.2 - - + -
184C VAL* 3.8 24.5 - - + -
186C THR* 3.3 33.0 - - + -
221C MET* 6.2 1.3 - - + -
233C THR 2.9 11.1 + - - +
234C GLY* 3.0 13.9 - - - +
236C LEU* 1.3 75.9 - - - +
238C ALA* 1.3 63.4 + - - +
240C MET* 2.9 5.4 + - - +
241C LEU* 2.5 55.8 + - + +
256C CYS* 5.8 3.6 - - - -
259C THR* 3.2 30.9 - - + +
260C VAL* 3.9 21.1 - - + -
263C MET* 3.9 19.0 - - + +
2402C ADP 4.2 15.7 - - - -
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Residues in contact with ALA 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LEU* 4.1 20.4 - - + -
111C VAL* 4.4 4.0 - - + +
113C ASP* 4.5 10.3 - - + +
148C THR* 3.8 29.6 - - + +
234C GLY 3.1 8.0 + - - +
235C ASP* 4.0 4.0 - - - +
237C PHE* 1.3 78.8 - - - +
239C ALA* 1.3 53.8 + - - +
241C LEU* 2.9 9.6 + - - +
242C LEU* 2.5 38.7 + - - +
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Residues in contact with ALA 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ALA* 3.8 36.1 - - + +
27C PRO* 4.7 4.9 - - + -
28C LEU* 3.1 28.2 - - + +
81C LEU* 3.8 14.5 - - + +
235C ASP 3.2 11.9 + - - +
236C LEU* 3.5 9.2 - - - +
237C PHE 3.2 0.4 - - - -
238C ALA* 1.3 79.0 - - - +
240C MET* 1.3 65.0 + - - +
242C LEU* 3.0 8.5 + - - +
243C ALA 3.1 1.4 + - - -
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Residues in contact with MET 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C PRO* 4.2 18.2 - - + -
31C LEU* 4.6 8.3 - - + -
236C LEU* 3.0 39.2 + - + +
237C PHE* 2.9 6.1 + - - +
239C ALA* 1.3 76.9 - - - +
241C LEU* 1.3 67.4 + - - +
243C ALA* 2.7 19.2 + - - +
244C TRP* 2.9 26.8 + - + +
259C THR* 4.1 13.9 - - + +
262C ALA* 3.5 33.4 - - + -
263C MET* 3.4 24.5 - - - +
266C VAL* 5.4 1.1 - - + -
300C ILE* 4.4 18.4 - - + +
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C VAL* 5.6 1.1 - - + -
146C ILE* 4.2 17.3 - - + -
148C THR* 3.5 29.4 - - + -
182C THR* 5.8 0.7 - - + -
184C VAL* 4.4 12.1 - - + -
237C PHE* 2.5 35.9 + - + +
238C ALA* 3.2 9.6 - - - +
240C MET* 1.3 73.4 - - - +
242C LEU* 1.3 63.8 + - - +
243C ALA 3.1 1.0 + - - -
245C THR* 3.1 44.6 + - + +
252C LEU* 5.4 0.9 - - + -
255C ALA 4.6 7.4 - - - +
256C CYS* 4.6 17.3 - - - -
259C THR* 3.7 19.0 + - + +
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Residues in contact with LEU 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C VAL* 3.6 29.2 - - + -
28C LEU* 3.9 12.6 - - + -
33C PHE* 3.9 26.5 - - + -
79C TYR* 3.8 27.4 - - + -
80C VAL 5.0 0.4 - - - +
81C LEU* 4.2 17.3 - - + -
111C VAL* 3.9 27.8 - - + +
146C ILE* 5.9 0.7 - - - -
238C ALA 2.5 16.2 + - - +
239C ALA* 3.0 11.9 + - - +
241C LEU* 1.3 75.5 - - - +
243C ALA* 1.3 59.9 + - - +
245C THR* 3.6 8.5 + - - -
246C HIS* 3.4 15.2 - - - +
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Residues in contact with ALA 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU* 4.2 3.4 - - + -
31C LEU* 3.5 29.2 - - + -
33C PHE* 3.4 31.9 - - + -
239C ALA 3.1 7.7 + - - +
240C MET 2.7 15.9 + - - +
242C LEU* 1.3 73.3 - - - +
244C TRP* 1.3 67.0 + - + +
246C HIS* 3.5 5.8 - - - +
247C LYS* 3.5 15.4 + - - +
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Residues in contact with TRP 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 4.1 27.8 - - + +
240C MET* 2.9 27.3 + - - +
241C LEU 4.3 0.9 - - - +
243C ALA* 1.3 78.0 - - + +
245C THR* 1.3 54.3 + - - +
246C HIS 3.0 2.0 - - - -
247C LYS* 2.7 41.5 + - + +
248C HIS* 2.7 19.0 + - + -
255C ALA* 3.7 23.6 - - + +
258C LYS* 3.5 44.5 - - + +
259C THR* 3.2 35.5 - - - +
300C ILE 4.1 4.4 + - - -
301C GLU 4.0 13.2 - - - -
302C SER* 5.5 0.4 - - - -
303C PRO* 4.1 23.7 - - + +
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Residues in contact with THR 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C TYR* 5.4 3.5 - - - -
146C ILE* 3.9 24.9 - - + +
182C THR* 5.3 3.4 - - + -
205C GLN* 6.3 1.8 - - - +
241C LEU* 3.1 36.8 + - + +
242C LEU* 3.6 7.3 + - - -
244C TRP* 1.3 76.7 - - - +
246C HIS* 1.3 58.6 + - - +
248C HIS 3.8 10.3 - - - +
249C PRO* 2.9 35.8 - - - +
252C LEU* 5.0 10.5 - - + -
255C ALA* 3.7 17.0 - - + +
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Residues in contact with HIS 246 (chain C).
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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1C MET* 4.4 8.7 - - + -
3C GLU* 3.7 28.4 + - - -
5C CYS* 3.2 33.2 - - - -
33C PHE* 3.8 19.5 - + + -
79C TYR* 2.5 38.3 + + + +
242C LEU 3.4 15.7 + - - +
243C ALA 3.5 7.2 - - - +
244C TRP 3.0 0.6 - - - -
245C THR* 1.3 82.1 + - - +
247C LYS* 1.3 65.0 + - + +
249C PRO* 3.9 7.0 - - - +
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Residues in contact with LYS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C MET* 6.4 1.8 - - + -
243C ALA 3.5 6.5 + - - +
244C TRP* 2.7 28.7 + - + +
246C HIS* 1.3 86.4 - - + +
248C HIS* 1.3 85.7 + - + +
249C PRO* 3.4 7.1 - - - +
258C LYS* 4.2 14.2 - - - +
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Residues in contact with HIS 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C TRP 2.7 16.9 + - - +
245C THR* 3.1 13.4 - - - +
247C LYS* 1.3 105.9 + - + +
249C PRO* 1.3 66.6 - - - +
250C ASN 3.1 3.5 + - - -
251C ASN* 3.2 40.7 + - + +
252C LEU* 4.5 0.7 + - - -
254C VAL* 3.6 20.8 - - + +
255C ALA* 4.3 5.8 - - + +
258C LYS* 2.7 37.5 + - + -
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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