Contacts of the helix formed by residues 228 - 246 (chain A) in PDB entry 5Z62
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 PRO 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A PRO* 4.0 9.0 - - + +
131A PRO* 3.9 26.9 - - + -
220A PHE* 4.0 17.5 - - + +
222A PRO* 3.7 31.0 - - + -
226A GLY 4.1 0.9 - - - +
227A ASP* 1.3 89.5 - - - +
229A ILE* 1.3 61.3 + - - +
230A LEU 3.3 0.7 - - - -
231A TYR* 3.8 15.2 + - + +
232A GLN* 4.2 10.7 + - - +
160B LEU* 4.9 6.8 - - + +
175B ILE* 4.4 19.5 - - + -
176B PRO* 4.5 6.5 - - + +
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Residues in contact with ILE 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ASP* 3.1 23.7 - - - +
228A PRO* 1.3 81.7 - - + +
230A LEU* 1.3 64.7 + - - +
231A TYR 3.2 0.9 - - - -
232A GLN* 3.0 31.9 + - + +
233A HIS* 3.1 40.8 + - + +
292A MET* 5.1 1.8 - - - -
295A VAL* 3.7 31.4 - - + -
160B LEU* 5.3 1.3 - - + -
175B ILE* 3.6 34.5 - - + -
178B ARG* 4.6 13.7 - - - +
103C HIS* 4.8 1.6 - - + +
303C CDL 6.0 0.9 - - - +
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Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 4.0 17.3 - - + +
220A PHE* 3.7 16.2 - - + -
227A ASP 3.3 14.0 + - - +
228A PRO 3.3 0.2 - - - -
229A ILE* 1.3 79.6 - - - +
231A TYR* 1.3 61.6 + - - +
233A HIS* 3.6 4.3 + - - +
234A LEU* 3.2 28.0 + - + +
99C TRP* 3.5 31.0 - - + +
100C ALA* 3.8 31.2 - - + +
103C HIS* 3.6 39.9 + - + +
104C SER* 6.0 0.7 - - - -
192C ILE* 5.7 4.3 - - + -
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Residues in contact with TYR 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A THR 2.9 28.3 + - - -
128A VAL* 3.3 22.8 - - - +
129A TYR* 3.2 30.7 - + - -
130A PRO* 3.5 25.8 - - + -
205A GLY* 4.4 11.7 - - - -
206A ILE* 3.3 25.0 - - + +
209A LEU* 4.2 7.4 - - + -
220A PHE* 3.5 33.0 - + + -
228A PRO 3.8 8.1 + - - +
229A ILE 3.2 0.4 - - - -
230A LEU* 1.3 80.8 - - - +
232A GLN* 1.3 52.1 + - - +
234A LEU* 3.1 4.0 + - + +
235A PHE* 2.7 53.4 + + + -
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Residues in contact with GLN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 3.6 45.1 - - + -
228A PRO 4.2 12.2 + - - +
229A ILE* 3.0 18.4 + - + +
231A TYR* 1.3 78.9 - - + +
233A HIS* 1.3 58.2 + - - +
235A PHE 4.4 0.4 - - - +
236A TRP* 3.0 40.1 + - + -
291A HIS 5.1 1.9 - - - +
292A MET* 3.2 22.8 - - + +
295A VAL* 3.4 28.3 - - - +
160B LEU* 4.0 19.4 - - - +
173B ASP* 5.6 2.2 + - - -
198B GLU* 5.6 2.0 + - - -
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Residues in contact with HIS 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 3.1 45.9 + - + +
230A LEU* 3.9 3.6 - - - +
232A GLN* 1.3 78.2 - - - +
234A LEU* 1.3 60.2 + - - +
237A PHE* 3.3 25.6 + - - +
288A TRP* 4.0 14.1 + - - +
289A ALA* 5.1 0.7 - - + -
292A MET* 3.4 27.2 - - + +
297A MET* 5.1 8.5 - - + +
99C TRP* 3.5 31.1 - + + +
103C HIS* 4.4 18.7 - + - -
303C CDL 4.0 33.3 + - - -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A VAL* 3.9 29.8 - - + +
202A LEU* 4.7 1.7 + - - -
205A GLY* 4.1 21.1 - - - -
208A MET* 3.8 31.6 - - + -
220A PHE* 4.4 9.0 - - + -
230A LEU* 3.2 25.2 + - + +
231A TYR* 3.1 7.0 + - + +
233A HIS* 1.3 77.3 - - - +
235A PHE* 1.3 64.8 + - - +
237A PHE* 3.8 4.8 + - - -
238A PHE* 3.9 8.1 + - - +
96C GLY* 4.0 16.4 - - - +
99C TRP* 3.8 37.0 - - + -
100C ALA* 4.9 0.7 - - + -
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Residues in contact with PHE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TRP* 4.1 30.5 - + - -
127A THR* 3.0 35.2 - - + -
129A TYR* 4.3 1.8 - + + -
150A LEU* 5.5 5.4 - - + -
202A LEU* 4.0 28.3 - - + +
206A ILE* 5.3 0.7 - - + -
231A TYR* 2.7 54.7 + + + +
232A GLN 4.3 1.6 - - - +
234A LEU* 1.3 74.6 - - - +
236A TRP* 1.3 93.9 + + + +
238A PHE* 3.0 19.4 + + - +
239A GLY* 2.8 21.4 + - - -
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Residues in contact with TRP 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TRP* 4.4 7.6 - + - -
127A THR* 3.6 13.7 - - + -
129A TYR* 2.0 34.1 + + - -
232A GLN* 3.0 34.0 + - + +
235A PHE* 1.3 91.1 - + - +
237A PHE* 1.3 64.0 + - - +
239A GLY* 3.5 20.9 - - - +
240A HIS* 3.4 16.6 + - - +
243A VAL* 6.1 2.5 - - + -
288A TRP* 3.3 30.1 - - + +
291A HIS* 3.4 52.8 + + + +
292A MET* 4.5 11.2 - - + -
604A HEA 3.2 37.9 - + + -
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Residues in contact with PHE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU 5.3 2.7 - - - -
198A SER* 4.4 3.7 - - - -
201A VAL* 3.7 35.4 - - + -
233A HIS 3.3 20.9 + - - +
234A LEU 4.1 5.2 - - - +
235A PHE 3.2 0.8 - - - -
236A TRP* 1.3 78.3 - - - +
238A PHE* 1.3 56.5 + - - +
241A PRO* 3.3 20.8 - - - +
285A PHE* 3.5 44.9 - + + -
288A TRP* 3.6 38.2 - + + +
92C PHE* 6.4 1.3 - + - -
99C TRP* 4.9 9.6 - + + -
303C CDL 4.2 34.3 - - + -
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 4.3 18.8 - + - -
126A TRP* 5.6 2.0 - + - -
198A SER* 3.7 35.6 + - - +
199A LEU* 3.6 28.9 - - + -
201A VAL* 5.0 0.6 - - - +
202A LEU* 3.5 46.0 - - + +
234A LEU 3.9 2.5 + - - +
235A PHE* 3.0 21.4 + + - +
237A PHE* 1.3 79.4 - - - +
239A GLY* 1.3 68.5 + - - +
240A HIS 3.4 1.1 - - - -
241A PRO* 3.3 5.5 - - - +
242A GLU* 3.1 58.8 + - + +
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Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TRP* 5.5 4.5 - - - -
235A PHE* 2.8 23.4 + - - -
236A TRP* 3.4 23.0 + - - -
238A PHE* 1.3 83.5 - - - +
240A HIS* 1.3 59.8 + - - +
242A GLU* 3.3 11.1 - - - +
243A VAL* 3.3 22.5 - - - +
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Residues in contact with HIS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A TRP* 3.4 12.9 + - - +
239A GLY* 1.3 74.0 - - - +
241A PRO* 1.3 71.0 - - + +
242A GLU 3.1 1.1 - - - -
243A VAL* 3.2 18.6 - - + +
244A TYR* 2.7 60.1 + + - -
284A GLY* 4.0 7.0 - - - -
287A VAL* 3.5 28.2 - - + +
288A TRP* 4.4 12.3 - - - +
290A HIS* 3.3 16.3 - + - -
291A HIS* 4.6 2.9 - - - +
309A THR* 5.9 1.0 - - + +
312A ILE* 4.9 0.6 - - - +
601A CU 2.1 33.8 - - - -
604A HEA 4.7 13.9 - + - -
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Residues in contact with PRO 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU* 3.8 19.3 - - + +
198A SER* 4.2 14.8 - - - +
236A TRP 4.4 0.4 - - - +
237A PHE* 3.3 21.8 - - - +
238A PHE 3.3 10.3 - - - +
240A HIS* 1.3 89.0 - - + +
242A GLU* 1.3 60.9 + - - +
243A VAL 3.3 0.2 - - - -
244A TYR* 3.4 13.4 + - + -
245A ILE* 3.3 21.8 + - - +
284A GLY 3.4 24.7 - - - +
285A PHE* 3.8 23.3 - - + -
288A TRP* 5.6 0.7 - - + -
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ILE* 3.6 16.0 - - + +
67A PHE* 3.6 9.4 - - + -
71A MET* 3.2 33.6 - - - +
126A TRP* 5.1 9.0 - - + -
198A SER* 5.2 0.4 + - - -
199A LEU* 4.6 2.4 - - - +
238A PHE* 3.1 49.6 + - + +
239A GLY* 3.3 14.6 - - - +
240A HIS 3.1 0.6 - - - -
241A PRO* 1.3 76.6 - - - +
243A VAL* 1.3 63.6 + - + +
245A ILE* 3.3 15.6 + - - +
246A LEU* 3.3 26.6 + - + +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TRP* 5.6 7.0 - - + -
236A TRP* 6.1 2.9 - - + -
239A GLY 3.3 15.7 - - - +
240A HIS* 3.2 33.4 - - + +
242A GLU* 1.3 81.7 - - + +
244A TYR* 1.3 64.4 + - + +
246A LEU* 3.7 15.9 + - + +
247A ILE* 3.6 7.4 + - - +
291A HIS* 6.2 1.6 - - + +
604A HEA 3.2 77.6 - - + +
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A LEU* 4.3 12.6 - - + -
240A HIS* 2.7 65.3 + + - -
241A PRO* 3.4 10.1 + - + +
242A GLU 3.2 0.4 - - - -
243A VAL* 1.3 78.6 - - + +
245A ILE* 1.3 55.5 + - - +
246A LEU 3.1 1.8 - - - -
247A ILE* 2.7 18.2 + - + -
248A LEU* 2.4 48.7 + - + +
251A PHE* 5.9 1.1 - + - -
280A ILE* 3.8 27.8 - - + -
284A GLY* 4.4 12.1 - - - -
312A ILE* 3.3 22.0 - - + +
604A HEA 3.6 34.5 + - + +
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A MET* 4.5 13.0 - - + -
74A MET* 5.5 1.0 - - - +
75A ILE* 3.9 20.4 - - + +
191A THR* 3.7 27.6 - - + +
194A LEU* 3.9 21.1 - - + +
195A LEU* 3.7 48.2 - - + +
198A SER* 4.8 2.5 - - - +
199A LEU* 4.9 1.1 - - + -
241A PRO 3.3 21.3 - - - +
242A GLU* 3.4 16.8 - - - +
244A TYR* 1.3 76.7 - - - +
246A LEU* 1.3 58.6 + - - +
248A LEU* 4.9 0.7 - - - -
249A PRO* 3.3 17.0 - - - +
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ILE* 3.8 36.1 - - + -
70A VAL* 3.7 34.8 - - + +
71A MET* 3.8 24.7 - - + -
74A MET* 4.9 8.0 - - - +
242A GLU* 3.3 19.9 + - + +
243A VAL* 3.8 19.1 - - + +
244A TYR 3.1 0.8 - - - -
245A ILE* 1.3 76.9 - - - +
247A ILE* 1.3 58.4 + - - +
249A PRO* 4.9 1.8 - - - -
381A LEU* 3.9 30.1 - - + -
385A ALA* 3.9 19.8 - - - +
603A HEA 5.8 0.2 - - + -
604A HEA 5.5 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