Contacts of the helix formed by residues 232 - 248 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D TYR 3.8 5.2 - - - -
19D VAL* 3.2 20.0 - - - -
23D ALA* 4.1 3.3 - - - +
231D VAL* 1.3 77.5 - - - +
233D THR* 1.3 65.4 + - - +
234D GLY 3.2 2.5 - - - -
235D ASP* 3.1 8.6 + - - +
236D LEU* 2.9 22.0 + - - +
291D LEU* 4.2 5.8 - - - -
3401D PLP 2.9 18.1 + - - -
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Residues in contact with THR 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D PHE* 3.8 18.8 + - + -
231D VAL 3.3 1.6 + - - -
232D GLY* 1.3 77.2 + - - +
234D GLY* 1.3 62.0 + - - +
236D LEU* 3.1 2.3 + - - -
237D PHE* 2.9 19.9 + - - +
263D MET* 3.0 17.4 - - + +
267D LEU* 3.7 27.4 - - + -
291D LEU* 4.1 9.3 - - + +
3401D PLP 4.0 1.6 + - - -
3402D ADP 2.7 67.2 + - + +
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Residues in contact with GLY 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ASP* 3.9 10.4 - - - +
148D THR* 5.3 0.5 + - - -
186D THR* 5.5 2.0 - - - -
233D THR* 1.3 72.1 + - - +
235D ASP* 1.3 58.2 + - - +
237D PHE* 2.8 28.9 + - - +
238D ALA* 3.1 6.4 + - - +
3401D PLP 3.0 2.3 + - - -
3402D ADP 2.7 48.9 + - - -
3403D ZN 4.0 0.9 - - - -
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Residues in contact with ASP 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D GLN* 3.4 22.1 + - - +
20D GLY* 3.8 27.1 + - - +
23D ALA* 4.5 2.5 - - + -
24D ALA* 4.2 5.5 - - + +
81D LEU* 5.5 0.3 - - - +
83D GLY* 5.0 0.2 - - - -
84D TYR 4.8 2.6 + - - -
113D ASP* 3.7 15.6 - - - +
115D VAL* 4.1 11.5 - - - +
232D GLY* 3.4 11.5 - - - +
234D GLY* 1.3 73.2 - - - +
236D LEU* 1.3 65.1 + - - +
238D ALA* 3.5 3.5 + - - +
239D ALA* 3.2 23.7 + - - +
3401D PLP 2.5 43.5 + - - +
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ALA* 3.5 14.0 - - + +
27D PRO* 3.2 35.9 - - + -
232D GLY 2.9 12.4 + - - +
233D THR* 3.5 8.1 - - - +
235D ASP* 1.3 76.4 - - - +
237D PHE* 1.3 63.3 + - - +
239D ALA* 3.5 1.9 + - - +
240D MET* 3.0 43.7 + - + +
263D MET* 3.5 16.6 - - + -
266D VAL* 4.1 25.6 - - + -
291D LEU* 4.0 21.8 - - + -
293D MET* 4.1 10.8 - - - -
300D ILE* 4.6 2.5 - - + -
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Residues in contact with PHE 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D THR* 4.3 9.2 - - + -
184D VAL* 3.8 24.0 - - + -
186D THR* 3.3 34.1 - - + -
221D MET* 6.5 0.7 - - + -
233D THR 2.9 11.2 + - - +
234D GLY* 2.8 17.7 + - - +
236D LEU* 1.3 74.0 - - - +
238D ALA* 1.3 54.0 + - - -
240D MET* 3.0 4.0 + - - +
241D LEU* 2.5 57.5 + - + +
256D CYS* 5.5 3.4 - - - -
259D THR* 3.3 30.7 - - + +
260D VAL* 4.0 20.2 - - + -
263D MET* 3.8 19.0 - - + +
3402D ADP 4.4 14.4 - - - -
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Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LEU* 4.0 20.6 - - + -
111D VAL* 4.4 4.8 - - + +
113D ASP* 4.4 10.1 - - + +
148D THR* 3.9 28.7 - - + +
234D GLY 3.1 5.6 + - - +
235D ASP* 3.5 6.5 + - - +
237D PHE* 1.3 78.9 - - - +
239D ALA* 1.3 54.0 + - - +
241D LEU* 3.0 8.0 + - - +
242D LEU* 2.5 39.4 + - - +
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Residues in contact with ALA 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ALA* 3.7 37.5 - - + +
27D PRO* 4.6 5.4 - - + -
28D LEU* 2.9 29.3 - - + +
81D LEU* 3.8 14.5 - - + +
235D ASP 3.2 16.8 + - - +
236D LEU 3.6 4.7 - - - +
238D ALA* 1.3 79.8 - - - +
240D MET* 1.3 62.9 + - - +
242D LEU* 3.1 6.9 + - - +
243D ALA 3.1 2.1 + - - -
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Residues in contact with MET 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PRO* 4.2 18.2 - - + -
31D LEU* 4.6 9.2 - - + -
236D LEU* 3.0 34.9 + - + +
237D PHE 3.6 1.8 - - - +
239D ALA* 1.3 72.3 - - - +
241D LEU* 1.3 67.8 + - - +
243D ALA* 2.8 18.5 + - - +
244D TRP* 2.9 27.4 + - + +
259D THR* 3.9 15.3 - - + +
262D ALA* 3.4 33.7 - - + -
263D MET* 3.4 33.9 - - - +
300D ILE* 4.4 19.7 - - + +
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Residues in contact with LEU 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D VAL* 5.5 1.1 - - + -
146D ILE* 4.1 19.3 - - + -
148D THR* 3.5 29.4 - - + -
182D THR* 5.8 0.4 - - + -
184D VAL* 4.3 11.0 - - + -
237D PHE* 2.5 38.6 + - + +
238D ALA* 3.3 6.1 - - - +
240D MET* 1.3 72.6 - - - +
242D LEU* 1.3 63.9 + - - +
243D ALA 3.1 1.0 + - - -
244D TRP 4.6 0.2 - - - +
245D THR* 3.1 47.7 + - + +
252D LEU* 5.4 0.7 - - + -
255D ALA 4.6 1.3 - - - +
256D CYS* 4.1 26.5 - - - -
259D THR* 3.5 20.3 + - + +
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Residues in contact with LEU 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D VAL* 3.7 28.7 - - + -
28D LEU* 3.8 16.8 - - + -
33D PHE* 4.0 20.6 - - + -
79D TYR* 3.9 22.9 - - + -
81D LEU* 4.1 17.0 - - + -
111D VAL* 3.8 33.0 - - + +
146D ILE* 6.0 0.7 - - - -
238D ALA 2.5 17.3 + - - +
239D ALA* 3.1 12.3 + - - +
241D LEU* 1.3 73.7 - - - +
243D ALA* 1.3 63.1 + - - +
245D THR* 3.7 5.9 + - - -
246D HIS* 3.5 17.7 + - - +
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Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D LEU* 4.2 3.1 - - + -
31D LEU* 3.5 28.7 - - + -
33D PHE* 3.5 30.9 - - + -
239D ALA 3.1 8.1 + - - +
240D MET 2.8 10.1 + - - +
242D LEU* 1.3 78.1 - - - +
244D TRP* 1.3 67.3 + - + +
246D HIS* 3.5 13.7 - - - +
247D LYS* 3.5 8.7 + - - +
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Residues in contact with TRP 244 (chain D).
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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31D LEU* 4.2 20.5 - - + +
240D MET* 2.9 27.3 + - + +
241D LEU 4.3 0.7 - - - +
243D ALA* 1.3 76.3 - - + +
245D THR* 1.3 54.5 + - - +
246D HIS 3.0 2.2 - - - -
247D LYS* 2.7 43.5 + - + +
248D HIS* 2.7 19.1 + - - -
255D ALA* 3.7 23.6 - - + +
258D LYS* 3.7 43.1 - - + +
259D THR* 3.1 36.9 - - - +
300D ILE 4.1 10.9 + - - -
301D GLU 4.0 13.2 - - - -
302D SER* 5.6 0.4 - - - -
303D PRO* 4.1 24.4 - - + +
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Residues in contact with THR 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D TYR* 5.4 3.5 - - - -
146D ILE* 4.0 25.1 - - + +
182D THR* 5.4 1.6 - - + -
205D GLN* 6.1 2.9 - - - +
241D LEU* 3.1 35.1 + - + +
242D LEU* 3.7 6.4 + - - -
244D TRP* 1.3 76.0 - - - +
246D HIS* 1.3 58.7 + - - +
248D HIS 3.6 12.1 - - - +
249D PRO* 2.8 35.7 - - - +
252D LEU* 5.0 11.2 - - + -
255D ALA* 3.7 16.8 - - + -
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Residues in contact with HIS 246 (chain D).
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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1D MET* 4.4 6.3 - - + -
3D GLU* 3.7 28.7 + - - -
5D CYS* 3.1 32.2 - - - -
33D PHE* 3.8 20.8 - + + -
79D TYR* 2.5 37.4 + + + +
242D LEU 3.5 11.6 + - - +
243D ALA 3.5 11.0 + - - +
245D THR* 1.3 82.9 + - - +
247D LYS* 1.3 63.2 + - + +
249D PRO* 4.0 6.9 - - - +
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Residues in contact with LYS 247 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D ALA 3.5 8.4 + - - +
244D TRP* 2.7 28.5 + - + +
246D HIS* 1.3 85.4 - - + +
248D HIS* 1.3 82.8 + - + +
249D PRO* 3.5 7.0 - - - +
258D LYS* 4.1 15.4 - - - +
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Residues in contact with HIS 248 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D GLN* 5.5 0.2 + - - -
244D TRP 2.7 18.1 + - - +
245D THR* 3.1 12.8 - - - +
247D LYS* 1.3 106.6 + - + +
249D PRO* 1.3 62.3 - - - +
250D ASN 3.1 6.5 + - - +
251D ASN* 3.2 42.2 + - + +
252D LEU* 4.4 0.7 + - - -
254D VAL* 3.6 24.1 - - + +
255D ALA* 4.3 4.9 - - + +
258D LYS* 2.7 35.9 + - + -
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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