Contacts of the helix formed by residues 181 - 204 (chain A) in PDB entry 4JDA
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 THR 181 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 4.1 2.8 - - - +
180A ASN* 1.3 77.5 - - - +
182A GLU* 1.3 67.9 + - - +
183A GLU* 3.9 8.9 + - - +
184A ASP* 2.7 40.8 + - - +
185A THR* 3.0 22.2 + - - -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ARG* 4.9 10.6 + - - -
49A THR 3.6 14.3 - - - +
50A CYS* 4.0 15.6 - - + -
51A THR 5.3 1.9 + - - -
176A ILE* 4.0 24.7 - - + +
181A THR* 1.3 72.1 - - - +
183A GLU* 1.3 54.9 + - - +
185A THR* 2.9 6.6 + - - -
186A ARG* 2.7 56.9 + - - +
45C ARG* 4.6 10.4 + - - -
182C GLU* 6.2 2.5 - - - -
186C ARG* 5.0 9.6 + - - -
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A THR* 3.3 8.6 + - - +
182A GLU* 1.3 79.4 - - - +
184A ASP* 1.3 60.5 + - - +
186A ARG* 3.9 20.4 - - - +
187A MET* 2.9 34.7 + - + +
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Residues in contact with ASP 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASN* 5.3 9.6 + - + +
181A THR* 2.7 29.5 + - - +
182A GLU 3.1 1.0 - - - -
183A GLU* 1.3 77.3 - - - +
185A THR* 1.3 65.4 + - - +
187A MET* 3.5 24.8 - - - +
188A PHE* 3.2 23.6 + - - +
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS* 4.1 18.8 - - - -
141A LEU* 5.9 5.9 - - - +
174A VAL* 5.0 7.6 - - - -
176A ILE* 4.7 14.1 - - - -
177A PRO* 5.1 7.2 - - - -
180A ASN* 5.3 3.7 - - - +
181A THR 3.0 12.3 + - - -
182A GLU* 2.9 9.0 + - - -
184A ASP* 1.3 73.9 - - - +
186A ARG* 1.3 65.7 + - - +
188A PHE* 3.3 5.8 + - - +
189A VAL* 3.0 26.0 + - - +
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A CYS* 3.5 11.9 - - - -
51A THR 3.7 20.3 + - - -
52A SER* 3.9 9.2 - - - -
172A TYR* 3.5 11.6 + - - +
182A GLU* 2.7 53.2 + - - +
183A GLU* 3.9 18.1 - - - +
185A THR* 1.3 72.5 - - - +
187A MET* 1.3 62.9 + - - +
188A PHE 3.2 0.3 + - - -
190A ASP* 3.0 46.8 + - - +
45C ARG* 3.4 39.6 - - - +
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Residues in contact with MET 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A GLU* 2.9 21.2 + - + +
184A ASP* 3.5 28.0 - - - +
186A ARG* 1.3 76.4 - - - +
188A PHE* 1.3 62.4 + - - +
190A ASP* 4.0 4.8 - - - +
191A THR* 3.1 27.5 + - - +
59B ASP* 4.5 23.1 - - - +
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 5.2 9.9 - - + -
141A LEU* 4.3 32.1 - - + -
184A ASP 3.2 16.4 + - - +
185A THR* 3.7 5.2 - - - +
186A ARG 3.2 0.2 - - - -
187A MET* 1.3 78.6 - - - +
189A VAL* 1.3 70.5 + - + +
191A THR* 3.1 22.7 - - + -
192A VAL* 3.3 30.3 + - + +
301A A9S 4.4 16.6 - - + -
202B VAL* 4.8 13.5 - - + -
205B THR* 5.7 9.4 - - + -
206B ALA* 5.1 12.6 - - + -
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LEU* 5.4 8.7 - - + -
144A TYR* 3.9 18.4 - - + +
172A TYR* 3.3 48.0 - - + +
174A VAL* 5.4 3.6 - - + -
185A THR 3.0 14.5 + - - +
188A PHE* 1.3 81.6 - - + +
190A ASP* 1.3 68.2 + - - +
192A VAL* 3.0 9.0 + - - +
193A VAL* 3.0 19.9 + - + +
301A A9S 4.1 11.0 - - + -
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A SER* 3.0 17.6 + - - -
54A ILE* 3.9 19.2 - - + +
172A TYR* 2.7 28.0 + - - -
186A ARG* 3.0 33.2 + - - +
187A MET* 4.0 5.4 + - - +
189A VAL* 1.3 74.6 - - - +
191A THR* 1.3 53.3 + - - +
193A VAL* 2.9 7.3 + - - +
194A LYS* 2.8 37.5 + - + +
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Residues in contact with THR 191 (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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187A MET* 3.1 15.0 + - - +
188A PHE* 3.1 18.8 - - + +
190A ASP* 1.3 79.3 - - - +
192A VAL* 1.3 55.1 + - + +
194A LYS* 3.5 2.8 + - - -
195A SER* 3.0 27.0 + - - -
198B GLN* 3.7 20.2 + - - +
201B ALA* 5.2 2.7 - - + +
202B VAL* 3.0 36.1 - - + +
205B THR* 6.3 1.8 - - - -
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PHE* 5.0 8.5 - - + -
111A LEU* 6.4 0.4 - - + -
188A PHE* 3.3 41.7 + - + +
189A VAL* 3.0 8.1 + - - +
191A THR* 1.3 73.3 - - + +
193A VAL* 1.3 62.3 + - - +
195A SER* 3.2 9.3 + - - -
196A ASN* 2.8 37.6 + - - +
301A A9S 3.9 48.9 - - + -
202B VAL* 4.6 13.7 - - + -
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Residues in contact with VAL 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 4.7 15.3 - - + -
144A TYR* 4.2 15.7 - - - +
170A GLU* 3.6 31.6 - - + +
172A TYR* 4.4 14.6 - - + -
189A VAL* 3.0 16.4 + - + +
190A ASP* 2.9 10.4 + - - +
192A VAL* 1.3 75.8 - - - +
194A LYS* 1.3 63.9 + - - +
196A ASN* 2.9 8.8 + - - +
197A LEU* 2.9 29.5 + - + +
301A A9S 4.7 5.6 - - + -
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Residues in contact with LYS 194 (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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54A ILE* 4.1 22.8 - - + +
56A HIS* 5.2 11.6 - - + -
190A ASP* 2.8 19.4 + - + +
191A THR* 3.8 6.7 - - - +
193A VAL* 1.3 72.2 - - - +
195A SER* 1.3 57.4 + - - +
197A LEU* 3.2 6.7 + - - +
198A GLN* 2.8 37.6 + - - +
198B GLN* 3.9 21.5 - - - +
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Residues in contact with SER 195 (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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80A HIS* 4.8 1.2 + - - +
81A PHE* 3.8 11.6 - - - -
191A THR 3.0 15.0 + - - -
192A VAL* 3.2 14.3 + - - -
194A LYS* 1.3 77.1 - - - +
196A ASN* 1.3 64.3 + - - -
198A GLN* 3.5 1.9 + - - +
199A ASN* 2.9 31.6 + - - -
198B GLN* 3.5 18.7 - - - +
199B ASN* 2.6 28.2 + - - -
202B VAL* 4.3 9.2 - - - -
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Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.3 30.0 - - + +
79A LYS* 3.4 37.8 - - - +
80A HIS 4.6 1.6 + - - -
81A PHE* 6.0 1.4 - - - -
170A GLU* 4.7 9.0 - - - +
192A VAL* 2.8 35.3 + - - +
193A VAL* 2.9 10.3 + - - +
195A SER* 1.3 75.4 + - - +
197A LEU* 1.3 61.0 + - + +
199A ASN* 4.4 0.4 - - - +
200A LEU* 3.0 26.0 + - - +
301A A9S 4.7 8.7 - - - -
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 3.8 27.1 - - + +
56A HIS* 3.7 40.1 + - + +
58A VAL* 4.9 1.4 - - - +
78A TYR* 5.7 2.0 - - + -
148A THR* 5.2 0.4 - - + -
168A VAL* 3.6 30.5 - - + +
170A GLU* 4.4 30.5 - - + +
193A VAL* 2.9 18.5 + - - +
194A LYS* 3.8 3.8 - - - +
196A ASN* 1.3 77.7 - - + +
198A GLN* 1.3 60.5 + - - +
200A LEU* 3.7 15.5 - - + +
201A ALA* 3.0 26.9 + - - +
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Residues in contact with GLN 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 3.3 35.2 + - + -
194A LYS* 2.8 19.5 + - - +
195A SER* 4.2 4.5 - - - +
197A LEU* 1.3 78.4 - - - +
199A ASN* 1.3 61.9 + - - +
201A ALA* 3.5 4.2 + - + +
202A VAL* 3.5 23.0 + - - +
191B THR* 4.4 10.7 + - + +
194B LYS* 3.1 35.3 - - - +
195B SER* 3.7 28.6 + - - +
198B GLN* 4.7 12.3 - - + +
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Residues in contact with ASN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TYR* 3.1 29.1 + - - +
80A HIS* 3.8 17.0 - - - +
195A SER* 2.9 19.4 + - - +
196A ASN 3.6 0.9 - - - +
197A LEU 3.2 0.4 - - - -
198A GLN* 1.3 76.6 - - - +
200A LEU* 1.3 64.6 + - - +
202A VAL* 3.1 13.9 + - - +
203A ILE* 3.3 12.6 + - - +
80B HIS* 3.9 19.1 + - - +
81B PHE* 3.6 7.9 - - - -
195B SER* 2.5 28.9 + - - +
199B ASN* 3.2 26.8 + - - -
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Residues in contact with LEU 200 (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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58A VAL* 5.6 1.6 - - + -
65A ILE* 3.5 34.5 - - + +
68A PHE* 3.6 33.7 - - + -
69A VAL* 3.9 14.6 - - + -
78A TYR* 3.8 29.1 - - + +
148A THR* 5.9 0.4 - - + -
168A VAL* 4.3 10.8 - - + -
196A ASN 3.0 16.0 + - - +
197A LEU* 3.7 26.2 - - + +
198A GLN 3.4 0.2 - - - -
199A ASN* 1.3 76.7 - - - +
201A ALA* 1.3 53.6 + - - +
203A ILE* 3.6 3.1 + - - +
204A SER* 2.6 37.0 + - - -
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Residues in contact with ALA 201 (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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56A HIS* 4.1 13.9 - - + -
57A ARG 4.8 0.2 - - - +
58A VAL* 3.8 34.1 - - + +
197A LEU 3.0 17.7 + - - +
198A GLN* 3.6 7.9 - - + +
199A ASN 3.2 0.2 - - - -
200A LEU* 1.3 77.8 - - - +
202A VAL* 1.3 58.2 + - - +
204A SER* 3.6 0.9 + - - -
205A THR* 3.1 29.3 + - - +
191B THR* 4.3 12.9 - - + +
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Residues in contact with VAL 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A GLN 3.5 9.6 + - - +
199A ASN 3.1 2.0 + - - +
201A ALA* 1.3 76.1 - - - +
203A ILE* 1.3 65.4 + - - +
205A THR* 3.2 27.0 + - - +
81B PHE* 3.3 43.5 - - + -
111B LEU* 4.6 11.6 - - + +
188B PHE* 4.6 12.2 - - + -
191B THR* 3.3 40.2 - - + +
192B VAL* 4.2 15.5 - - + +
195B SER* 4.2 2.5 - - - -
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Residues in contact with ILE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 3.5 51.8 - - + -
77A LYS* 3.4 27.6 - - + +
78A TYR* 3.8 13.5 - - + -
199A ASN 3.3 8.8 + - - +
200A LEU* 3.6 10.8 - - - +
202A VAL* 1.3 79.2 - - - +
204A SER* 1.3 62.3 + - - +
205A THR 3.5 4.9 + - - +
81B PHE* 3.6 23.1 - - + -
108B VAL* 5.7 2.7 - - + -
110B GLY* 4.3 27.3 - - - +
111B LEU* 4.7 7.7 - - + +
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Residues in contact with SER 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 3.6 9.5 - - - +
60A ALA* 3.4 15.2 - - - +
64A ALA* 3.7 15.9 - - - +
65A ILE* 3.4 43.3 - - - +
68A PHE* 3.8 11.9 - - - -
200A LEU 2.6 25.2 + - - -
201A ALA 3.6 0.2 + - - -
203A ILE* 1.3 77.5 - - - +
205A THR* 1.3 59.6 + - - +
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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
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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