Contacts of the helix formed by residues 225 - 245 (chain A) in PDB entry 4J6V
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 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE* 5.5 3.6 - - + -
26A VAL* 4.6 10.3 - - + -
35A TYR* 3.5 16.6 - - + +
114A MET* 4.0 18.3 - - + +
131A PHE* 3.7 46.9 - - + -
136A TRP* 4.1 9.2 - - + -
149A LEU* 4.5 5.2 - - + -
151A ARG* 4.8 0.2 - - - +
223A ASN 3.5 9.2 - - - +
224A ASP* 1.3 89.6 - - - +
226A VAL* 1.3 60.2 + - - +
228A PHE* 3.1 24.0 + - + +
229A LEU* 3.8 6.2 + - - +
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Residues in contact with VAL 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TRP* 3.9 18.2 - - + -
108A ILE* 4.1 14.6 - - + -
109A TRP* 3.8 34.5 - - + -
114A MET* 3.8 13.0 - - + -
211A VAL* 4.7 4.0 - - + -
215A MET* 4.1 17.7 - - + -
224A ASP* 3.0 29.4 + - - +
225A PRO* 1.3 74.8 - - - +
227A PHE* 1.3 57.8 + - - +
228A PHE 3.2 0.2 - - - -
229A LEU* 3.1 11.5 + - + -
230A HIS* 2.8 34.4 + - - +
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Residues in contact with PHE 227 (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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42A HIS* 3.4 35.7 - + - -
69A HIS* 4.4 1.8 - + - -
72A TYR* 3.4 34.1 - + - -
208A HIS* 3.8 14.8 - + - -
215A MET* 3.8 11.8 - - - -
221A ALA* 3.5 37.5 - - + +
222A PRO* 3.7 12.3 - - + -
224A ASP 3.0 17.4 + - - +
226A VAL* 1.3 80.0 - - - +
228A PHE* 1.3 71.1 + + + +
230A HIS* 3.5 2.6 + - - +
231A HIS* 2.9 54.8 + + + +
401A CU 3.8 0.2 - - - -
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Residues in contact with PHE 228 (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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22A PHE* 5.6 1.6 - - + -
35A TYR* 3.3 33.2 - + - -
38A TYR* 4.0 8.7 - - + -
72A TYR* 3.4 39.5 - + - -
73A LEU* 3.8 18.6 - - + +
76A PHE* 3.6 50.7 - + + -
89A LEU* 3.9 23.5 - - + +
222A PRO* 4.0 9.2 - - + -
225A PRO* 3.1 16.6 + - + +
227A PHE* 1.3 87.3 - + + +
229A LEU* 1.3 60.1 + - + +
231A HIS 3.8 0.3 - - - -
232A ALA* 2.9 29.1 + - - +
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Residues in contact with LEU 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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11A VAL* 4.2 5.6 - - + -
22A PHE* 3.9 11.9 - - + -
89A LEU* 3.9 7.6 - - + -
90A PRO* 3.4 44.2 - - + +
91A TYR* 3.6 1.4 - - - -
92A TRP* 3.0 37.3 + - + +
108A ILE* 4.2 6.3 - - + -
113A PHE* 3.7 28.9 - - + -
114A MET* 3.8 25.8 - - + -
225A PRO 4.1 9.2 - - - +
226A VAL* 3.1 7.8 + - + +
228A PHE* 1.3 74.8 - - - +
230A HIS* 1.3 62.5 + - - +
232A ALA 3.5 0.7 + - - -
233A ASN* 3.3 12.0 + - - +
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Residues in contact with HIS 230 (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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92A TRP* 4.3 16.0 - - + +
94A TRP* 2.9 34.1 + + - +
204A HIS* 3.0 30.0 + - - -
207A VAL* 3.5 25.6 - - + +
208A HIS* 3.8 24.1 - + - -
215A MET* 4.2 13.0 - - + -
226A VAL 2.8 16.5 + - - +
227A PHE 3.6 3.1 - - - +
229A LEU* 1.3 76.1 - - - +
231A HIS* 1.3 73.4 + + - +
233A ASN* 3.1 14.0 + - - +
234A VAL* 3.1 27.4 + - + +
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Residues in contact with HIS 231 (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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65A PHE* 3.9 9.6 - + - -
69A HIS* 3.2 44.9 + + + +
73A LEU* 3.4 25.0 - - + +
204A HIS* 3.5 33.8 - + - -
208A HIS* 3.9 0.6 + - - -
227A PHE* 2.9 55.3 + + + +
230A HIS* 1.3 85.4 - + - +
232A ALA* 1.3 57.2 + - - +
234A VAL* 3.3 11.9 + - - +
235A ASP* 2.8 29.6 + - - +
401A CU 3.9 1.0 - - - -
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Residues in contact with ALA 232 (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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8A ARG* 4.9 0.7 - - - +
73A LEU* 3.5 9.1 - - + +
89A LEU* 4.0 14.6 - - + +
90A PRO 3.3 27.6 - - - +
91A TYR* 3.6 10.1 - - + -
228A PHE 2.9 15.3 + - - +
229A LEU 3.7 1.3 - - - +
230A HIS 3.2 0.2 - - - -
231A HIS* 1.3 76.4 - - - +
233A ASN* 1.3 58.6 + - - +
236A ARG* 2.8 27.7 + - - +
286A TYR* 3.3 18.7 + - + +
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Residues in contact with ASN 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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91A TYR* 3.5 13.2 - - - +
92A TRP 3.1 28.2 + - - +
93A GLU* 3.6 3.0 - - - -
94A TRP* 3.2 28.0 - - - +
95A GLU* 2.9 24.5 + - - -
229A LEU 3.3 3.6 + - - +
230A HIS 3.1 10.8 + - - +
232A ALA* 1.3 76.5 - - - +
234A VAL* 1.3 64.7 + - - +
236A ARG* 3.0 31.9 + - - +
237A ILE* 2.9 33.5 + - - +
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Residues in contact with VAL 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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65A PHE* 4.2 15.5 - - + -
66A LEU* 3.7 25.4 - - + -
69A HIS* 6.3 1.3 - - + -
94A TRP* 4.2 8.7 - - + -
194A LEU* 4.0 14.7 - - + +
204A HIS* 4.3 12.3 - - + +
230A HIS* 3.1 40.7 + - + +
231A HIS* 3.3 15.9 + - - +
233A ASN* 1.3 74.8 - - - +
235A ASP* 1.3 62.4 + - - +
237A ILE* 3.3 10.6 + - - +
238A TRP* 3.0 21.5 + - - +
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Residues in contact with ASP 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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8A ARG* 3.7 2.3 + - - -
66A LEU* 5.0 1.2 - - - +
70A ARG* 2.6 45.9 + - - +
73A LEU* 4.2 7.6 - - + -
231A HIS 2.8 18.3 + - - +
234A VAL* 1.3 76.1 - - - +
236A ARG* 1.3 59.2 + - - +
238A TRP* 3.4 10.7 + - - +
239A ALA* 2.9 27.5 + - - +
279A HIS* 5.1 0.2 - - - +
284A TYR* 2.6 25.1 + - - -
286A TYR* 2.6 28.5 + - - +
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Residues in contact with ARG 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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91A TYR* 3.4 34.2 - - - -
93A GLU* 3.6 16.2 + - - -
95A GLU* 2.9 28.7 + - - -
168A VAL* 5.7 0.2 - - - +
232A ALA 2.8 18.5 + - - +
233A ASN* 3.0 29.4 + - - +
235A ASP* 1.3 76.8 - - - +
237A ILE* 1.3 68.9 + - - +
239A ALA* 3.1 4.0 + - - +
240A VAL* 2.9 51.1 + - + +
286A TYR* 3.6 35.6 + - + -
288A ILE* 3.9 19.1 - - - +
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Residues in contact with ILE 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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94A TRP* 3.7 31.0 - - + -
95A GLU* 4.1 1.8 - - - +
168A VAL* 4.1 30.1 - - + +
171A ALA* 5.7 1.6 - - + -
172A LEU* 3.6 20.0 - - + +
190A PHE* 4.3 4.3 - - + -
194A LEU* 4.1 24.9 - - + -
233A ASN* 2.9 29.6 + - - +
234A VAL* 3.7 4.9 - - - +
236A ARG* 1.3 89.8 - - - +
238A TRP* 1.3 65.1 + - - +
240A VAL* 3.3 10.2 + - - +
241A TRP* 3.0 18.0 + - - +
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Residues in contact with TRP 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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66A LEU* 3.6 45.8 - - + -
67A PRO* 3.7 23.1 - - + -
70A ARG* 3.2 45.1 - - - -
177A TYR* 3.7 28.4 - + - -
190A PHE* 3.7 26.6 - + + -
194A LEU* 4.3 0.2 - - - +
234A VAL 3.0 13.3 + - - +
235A ASP* 3.6 11.9 - - - +
237A ILE* 1.3 77.0 - - - +
239A ALA* 1.3 55.2 + - - +
241A TRP* 3.1 6.9 + + - +
242A GLN* 2.9 55.0 + - + +
276A VAL 4.4 2.9 - - - -
277A MET* 4.0 19.7 - - + -
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Residues in contact with ALA 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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70A ARG* 3.8 5.3 - - - +
235A ASP 2.9 14.4 + - - +
236A ARG* 3.1 13.2 + - - +
238A TRP* 1.3 75.4 - - - +
240A VAL* 1.3 62.9 + - + +
242A GLN* 3.4 15.4 + - - +
243A ILE* 3.3 28.3 + - - +
279A HIS* 3.8 33.0 - - + +
286A TYR* 4.6 6.7 - - + -
289A GLU* 5.1 2.7 - - - +
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Residues in contact with VAL 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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172A LEU* 3.7 27.8 - - + -
236A ARG* 2.9 42.2 + - + +
237A ILE* 3.4 9.4 - - - +
239A ALA* 1.3 71.7 - - + +
241A TRP* 1.3 66.9 + - - +
243A ILE* 3.1 18.7 + - - +
244A ILE* 3.1 23.6 + - + +
288A ILE* 6.3 2.2 - - + -
289A GLU* 6.3 3.4 - - + -
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Residues in contact with TRP 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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172A LEU* 3.7 20.6 - - + +
174A ILE 2.9 19.9 + - - -
175A THR 3.8 13.7 - - - -
176A GLN 3.9 2.2 - - - -
177A TYR* 3.6 48.5 - + + -
190A PHE* 3.3 49.7 - + + +
237A ILE 3.0 6.9 + - - +
238A TRP* 3.1 14.8 + + - +
240A VAL* 1.3 76.6 - - - +
242A GLN* 1.3 77.8 + - + +
243A ILE 3.2 0.2 + - - -
244A ILE* 3.3 2.9 + - - -
245A HIS* 3.0 50.8 + + + -
248A GLN* 3.8 27.8 - - + -
249A ASN 5.4 1.8 - - - -
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Residues in contact with GLN 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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70A ARG* 3.1 30.5 + - - -
238A TRP* 2.9 35.4 + - + +
239A ALA* 3.6 12.3 - - - +
240A VAL 3.2 0.2 - - - -
241A TRP* 1.3 88.8 - - + +
243A ILE* 1.3 62.0 + - + +
245A HIS 3.4 2.3 - - - +
246A ARG* 3.4 22.5 - - - +
248A GLN 6.0 0.2 - - - -
277A MET* 3.1 42.9 + - - +
278A ASN* 5.2 0.4 - - - +
279A HIS* 4.8 3.8 + - - -
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Residues in contact with ILE 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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239A ALA 3.3 21.0 + - - +
240A VAL* 3.1 10.0 + - + +
242A GLN* 1.3 79.0 - - + +
244A ILE* 1.3 67.1 + - + +
245A HIS 3.6 0.2 + - - -
246A ARG* 3.7 18.8 + - + +
279A HIS* 5.2 4.3 - - + -
280A ARG* 6.4 0.4 - - - -
289A GLU* 4.2 21.5 - - + +
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Residues in contact with ILE 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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172A LEU* 4.2 27.6 - - + +
240A VAL* 3.1 34.0 + - + +
241A TRP* 3.8 1.6 - - - +
243A ILE* 1.3 79.1 - - + +
245A HIS* 1.3 84.7 + - + +
246A ARG* 3.5 2.8 + - - +
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Residues in contact with HIS 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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172A LEU 2.8 24.4 + - - -
173A LYS* 3.9 10.5 - - - -
174A ILE 3.4 19.1 + - - -
175A THR* 4.1 15.8 + - + +
241A TRP* 3.0 42.6 + + + +
242A GLN* 3.4 12.1 - - - +
244A ILE* 1.3 91.7 + - + +
246A ARG* 1.3 58.8 + - - +
247A ASN 3.2 3.4 - - - +
248A GLN* 3.2 40.6 + - + +
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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
------------------------------------------------------------
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