Contacts of the helix formed by residues 222 - 241 (chain D) in PDB entry 3HB8
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 222 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218D ASP* 3.4 3.5 + - - -
220D GLY 3.0 5.7 + - - -
221D LEU* 1.3 80.3 - - - +
223D VAL* 1.3 68.0 + - - +
224D PRO* 3.2 2.9 - - - -
225D PHE* 2.8 29.3 + - - +
226D ASN* 3.2 13.9 + - - -
565D UMP 5.3 12.1 - - - -
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Residues in contact with VAL 223 (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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33D TYR* 3.6 22.4 - - + -
36D GLN* 5.5 0.9 - - - +
214D GLN* 4.3 4.7 - - - +
217D GLY* 3.8 19.1 - - - -
218D ASP 3.1 27.2 + - - +
219D MET* 3.7 22.2 - - + +
222D GLY* 1.3 76.0 - - - +
224D PRO* 1.4 70.9 - - + +
226D ASN* 3.1 11.3 + - - +
227D ILE* 2.9 35.6 + - + +
250D HIS* 4.2 11.2 - - + +
252D LEU* 4.5 5.6 - - + -
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Residues in contact with PRO 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D TYR* 3.5 26.5 - - + +
74D LEU* 3.3 32.9 - - + +
77D LYS* 6.3 2.0 - - + -
79D VAL* 3.8 15.7 - - + -
220D GLY* 3.6 23.8 - - - +
222D GLY 3.3 4.3 - - - +
223D VAL* 1.4 96.2 - - + +
225D PHE* 1.3 61.0 + - - +
227D ILE* 3.3 6.4 + - + +
228D ALA* 3.0 24.3 + - - +
268D GLN* 6.0 1.1 - - - +
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Residues in contact with PHE 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D VAL* 4.1 16.5 - - + +
80D PHE* 4.2 15.9 - + + -
83D GLY* 3.8 7.9 - - - -
84D VAL* 3.4 43.5 - - + +
87D GLU* 3.2 35.4 - - + -
108D ILE* 5.2 15.7 - - + -
222D GLY* 2.8 24.1 + - - +
224D PRO* 1.3 74.7 - - - +
226D ASN* 1.3 63.0 + - - +
228D ALA* 3.2 4.9 + - - +
229D SER* 2.7 42.4 + - - -
565D UMP 5.1 2.2 - + - -
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Residues in contact with ASN 226 (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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196D HIS* 3.7 14.1 + - + -
212D LEU* 4.7 6.1 - - + -
214D GLN* 3.0 39.8 + - - +
222D GLY* 3.3 16.5 + - - +
223D VAL* 3.1 9.0 + - - +
225D PHE* 1.3 84.9 - - - +
227D ILE* 1.3 68.2 + - - +
229D SER* 2.8 17.8 + - - -
230D TYR* 2.9 19.6 + - - +
250D HIS* 4.7 1.3 - - - +
565D UMP 2.6 31.0 + - - +
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Residues in contact with ILE 227 (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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33D TYR* 4.3 8.5 - - + -
36D GLN* 5.8 1.1 - - - +
65D TYR* 3.4 53.2 - - + +
72D PRO* 4.1 21.5 - - + +
74D LEU* 4.8 8.1 - - + -
223D VAL* 2.9 33.4 + - + +
224D PRO* 3.5 10.1 - - + +
226D ASN* 1.3 77.1 - - - +
228D ALA* 1.3 61.5 + - - +
230D TYR 3.7 0.2 + - - -
231D ALA* 3.2 21.0 + - - +
248D PHE* 3.9 15.1 - - + -
250D HIS* 4.1 20.2 - - + +
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Residues in contact with ALA 228 (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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71D PHE* 3.3 18.2 - - + -
72D PRO 4.0 9.4 - - - +
73D LEU* 3.5 32.8 - - + -
74D LEU* 5.5 0.2 - - + -
79D VAL* 4.9 0.2 - - + -
84D VAL* 3.9 13.5 - - + +
224D PRO 3.0 14.0 + - - +
225D PHE* 3.6 6.5 - - - +
227D ILE* 1.3 75.1 - - - +
229D SER* 1.3 65.7 + - - +
231D ALA* 4.4 0.2 - - - -
232D LEU* 3.1 20.6 + - - +
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Residues in contact with SER 229 (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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84D VAL* 3.6 24.4 + - - +
87D GLU* 4.0 15.4 + - - -
88D LEU* 3.9 21.8 - - - +
91D PHE* 5.6 1.6 - - - -
196D HIS* 6.0 0.9 - - - -
225D PHE* 2.7 27.6 + - - -
226D ASN* 2.8 11.5 + - - -
228D ALA* 1.3 74.3 - - - +
230D TYR* 1.3 64.3 + - - -
232D LEU* 3.5 5.2 - - - +
233D LEU 3.3 17.8 + - - -
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Residues in contact with TYR 230 (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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88D LEU* 6.3 1.3 - - + -
91D PHE* 5.8 1.2 - + - -
135D TYR* 4.5 3.6 - - - -
139D TRP* 3.7 22.6 + + - -
196D HIS* 3.4 44.7 - + - +
199D CYS* 4.1 26.4 - - + -
210D CYS* 4.8 6.0 - - - -
212D LEU* 3.2 37.2 - - + -
226D ASN 2.9 11.9 + - - +
229D SER* 1.3 82.3 - - - +
231D ALA* 1.3 62.0 + - - +
232D LEU 3.1 2.0 - - - -
233D LEU* 3.9 25.6 - - + +
234D THR* 2.8 26.9 + - - -
248D PHE* 3.3 29.3 - - + -
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Residues in contact with ALA 231 (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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67D LEU* 4.1 9.6 - - + +
71D PHE* 3.9 7.6 - - + -
72D PRO* 3.5 33.2 - - + -
227D ILE 3.2 19.8 + - - +
228D ALA 3.4 4.4 + - - +
230D TYR* 1.3 77.2 - - - +
232D LEU* 1.3 58.8 + - - +
234D THR* 3.4 7.7 - - - -
235D TYR* 2.9 34.5 + - - -
248D PHE* 4.7 7.6 - - + -
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Residues in contact with LEU 232 (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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71D PHE* 3.8 6.5 - - + -
81D TRP* 3.9 20.2 - - + -
84D VAL* 4.2 7.9 - - + -
85D LEU* 3.9 33.0 - - + -
88D LEU* 3.3 23.8 - - + -
228D ALA 3.1 15.7 + - - +
229D SER 3.5 5.2 - - - +
231D ALA* 1.3 74.8 - - - +
233D LEU* 1.3 61.3 + - - +
234D THR 3.1 1.1 - - - -
235D TYR* 2.9 5.5 + - - +
236D MET* 2.8 32.7 + - - +
279D LEU* 3.6 28.3 - - + -
296D PHE* 4.0 20.0 - - + -
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Residues in contact with LEU 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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88D LEU* 3.9 15.4 - - + +
92D ILE* 4.8 2.7 - - + -
139D TRP* 3.9 31.2 - - + -
161D LEU* 4.6 7.6 - - + -
179D MET* 5.2 4.9 - - - -
199D CYS* 5.0 2.2 - - - -
201D PHE* 4.1 21.3 - - + -
229D SER 3.3 10.8 + - - +
230D TYR* 4.0 26.5 - - + +
231D ALA 3.5 0.2 - - - -
232D LEU* 1.3 78.8 - - - +
234D THR* 1.3 56.9 + - - +
236D MET* 3.2 9.2 + - - +
237D ILE* 2.8 56.8 + - + +
288D ILE* 4.6 11.9 - - + -
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Residues in contact with THR 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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67D LEU* 3.5 28.4 - - + +
201D PHE* 4.9 3.6 - - - -
208D LEU* 3.7 29.2 - - + +
210D CYS* 3.4 26.6 - - + +
230D TYR 2.8 18.2 + - - -
231D ALA* 3.4 11.8 - - - -
232D LEU 3.1 0.4 - - - -
233D LEU* 1.3 78.9 - - - +
235D TYR* 1.3 56.5 + - - +
237D ILE* 3.2 6.0 + - - +
238D ALA* 2.8 30.1 + - - +
245D PRO* 4.7 5.2 - - + -
248D PHE* 4.6 1.9 - - - -
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Residues in contact with TYR 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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67D LEU* 3.0 39.0 + - + -
69D ASP* 4.6 0.9 + - - -
70D GLU 2.9 30.1 + - - -
71D PHE* 3.6 27.8 - + + -
231D ALA 2.9 21.6 + - - -
232D LEU* 2.9 8.6 + - + +
234D THR* 1.3 79.1 - - - +
236D MET* 1.3 63.1 + - - +
238D ALA* 3.9 1.2 - - - +
239D HIS* 3.1 24.6 + - - +
245D PRO* 3.8 24.9 - - + +
278D LYS* 6.0 0.3 - - - +
279D LEU* 3.9 36.4 + - + -
281D ILE* 4.6 15.8 - - + +
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Residues in contact with MET 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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85D LEU* 5.2 0.7 - - + -
88D LEU* 3.4 30.1 - - + -
89D LEU* 3.9 11.9 - - + -
92D ILE* 3.6 25.8 - - + -
232D LEU* 2.8 17.2 + - + +
233D LEU* 3.5 12.3 - - + +
234D THR 3.2 0.2 - - - -
235D TYR* 1.3 78.4 - - - +
237D ILE* 1.3 64.1 + - + +
239D HIS* 3.4 3.3 + - - +
240D ILE* 3.2 28.3 + - - +
288D ILE* 5.2 3.1 - - + -
291D PHE* 3.5 42.5 - - + -
296D PHE* 3.3 39.3 - - + -
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Residues in contact with ILE 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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161D LEU* 4.6 5.4 - - + -
164D VAL* 5.0 3.8 - - + -
165D ILE* 3.2 29.8 - - + -
168D ILE* 3.4 33.2 - - + -
201D PHE* 4.6 13.2 - - + -
208D LEU* 3.5 15.9 - - + -
233D LEU* 2.8 36.2 + - + +
234D THR 3.7 0.4 - - - +
236D MET* 1.3 72.7 - - - +
238D ALA* 1.3 65.7 + - - +
240D ILE* 3.0 14.4 + - + +
241D THR* 3.0 24.1 + - + +
288D ILE* 3.7 21.1 - - + -
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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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208D LEU* 3.5 12.7 - - + +
234D THR 2.8 21.0 + - - +
235D TYR 3.9 1.8 - - - +
237D ILE* 1.3 72.0 - - - +
239D HIS* 1.3 56.2 + - - +
241D THR* 3.3 7.7 + - - -
242D GLY 3.1 9.0 + - - -
243D LEU* 2.8 49.7 + - - +
245D PRO* 3.7 27.4 - - + -
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Residues in contact with HIS 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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235D TYR 3.1 19.1 + - - +
236D MET 3.5 4.9 - - - +
238D ALA* 1.3 77.6 - - - +
240D ILE* 1.3 61.0 + - + +
241D THR 3.4 0.9 + - - -
242D GLY* 3.6 8.8 + - - +
281D ILE* 3.5 33.0 - - + +
282D LEU 5.0 2.0 - - - -
284D LYS* 3.6 37.3 + - + +
285D VAL* 3.4 31.0 + - + +
291D PHE* 3.4 27.6 - + + -
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Residues in contact with ILE 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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165D ILE* 4.1 24.7 - - + -
169D LYS* 4.4 10.1 - - + +
236D MET 3.2 15.0 - - - +
237D ILE* 3.0 9.9 + - - +
239D HIS* 1.3 77.6 - - + +
241D THR* 1.3 60.4 + - + +
242D GLY 3.5 0.8 + - - -
284D LYS* 5.5 2.0 + - - +
285D VAL* 3.8 25.1 - - + +
286D GLU 3.3 19.0 - - - +
287D LYS* 3.2 31.9 - - - +
288D ILE* 4.3 8.7 - - + +
291D PHE* 3.6 19.1 - - + -
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Residues in contact with THR 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D ILE* 4.4 13.2 - - + -
168D ILE* 3.9 31.7 - - + +
169D LYS* 4.4 20.0 - - + +
208D LEU* 4.8 0.7 - - - +
237D ILE* 3.1 26.2 + - + +
238D ALA* 3.3 11.4 + - - -
239D HIS 3.2 0.2 - - - -
240D ILE* 1.3 80.2 - - - +
242D GLY* 1.3 64.1 + - - +
243D LEU* 2.9 23.1 + - - +
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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
------------------------------------------------------------
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