Contacts of the helix formed by residues 159 - 180 (chain C) in PDB entry 3J41
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 SER 159 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B ARG 3.5 7.2 - - - -
157B LEU 3.0 22.3 + - - -
158B GLY* 3.4 7.9 - - - -
159B SER 4.7 3.1 - - - -
57C GLN* 3.6 5.5 + - - +
157C LEU 3.7 4.0 + - - +
158C GLY* 1.3 70.7 - - - -
160C VAL* 1.3 61.4 + - - +
161C ALA* 3.3 11.3 + - - +
162C LEU* 3.1 32.6 + - - +
163C ALA* 3.2 18.9 + - - +
57D GLN* 4.7 0.2 + - - -
159D SER* 4.7 4.0 - - - -
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Residues in contact with VAL 160 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ASN* 5.7 4.5 - - - +
156B ARG* 3.3 37.9 + - + +
56C VAL* 4.6 6.1 - - + -
148C THR* 3.6 32.8 - - - +
149C TYR* 4.2 23.3 - - + -
157C LEU* 4.2 12.8 - - + -
158C GLY 4.3 3.1 - - - +
159C SER* 1.3 71.7 - - - +
161C ALA* 1.3 65.6 + - + +
163C ALA* 3.6 7.1 - - - +
164C VAL* 3.0 36.4 + - - +
57D GLN* 5.3 0.9 - - - +
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Residues in contact with ALA 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG 4.9 0.4 + - - -
53C ALA* 3.1 36.4 - - + +
56C VAL* 3.6 26.1 - - + +
57C GLN* 3.4 30.3 - - + +
159C SER* 3.5 0.7 - - - +
160C VAL* 1.3 83.5 - - + +
162C LEU* 1.3 57.7 + - - +
164C VAL* 3.8 2.1 - - - +
165C GLY 2.9 22.9 + - - -
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Residues in contact with LEU 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LEU* 3.9 25.6 - - + -
163B ALA* 6.3 2.0 - - - -
166B PHE* 3.9 19.3 - - + -
50C LEU* 4.3 3.1 - - + -
53C ALA* 3.8 16.1 - - + +
159C SER* 3.1 25.7 + - - +
161C ALA* 1.3 75.2 - - - +
163C ALA* 1.3 55.5 + - - +
165C GLY 3.5 0.3 - - - -
166C PHE* 2.7 83.9 + - + +
162D LEU* 3.9 17.7 - - + -
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Residues in contact with ALA 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C CYS* 3.9 6.3 - - - -
148C THR* 4.1 12.1 - - + -
159C SER 3.2 11.5 + - - +
160C VAL 3.6 8.5 - - - +
162C LEU* 1.3 78.8 - - - +
164C VAL* 1.3 57.9 + - - +
166C PHE* 3.3 6.5 + - - +
167C SER* 2.9 28.2 + - - -
54D THR* 4.7 3.4 + - - +
57D GLN* 3.8 34.3 - - + +
159D SER* 5.9 0.2 - - - +
162D LEU* 6.3 2.0 - - - +
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Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LEU* 3.6 26.9 - - + -
56C VAL* 4.5 9.0 - - + -
141C PHE* 3.5 15.2 - - + -
144C CYS* 4.4 3.1 - - - +
145C ILE* 3.9 24.2 - - + -
148C THR* 3.6 20.9 - - - +
149C TYR* 4.1 15.0 - - + +
160C VAL 3.0 21.2 + - - +
161C ALA* 3.8 5.4 - - - +
163C ALA* 1.3 75.9 - - - +
165C GLY* 1.3 61.1 + - - +
167C SER* 3.1 9.8 + - - -
168C LEU 3.0 17.8 + - - -
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Residues in contact with GLY 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLY* 3.1 37.7 - - - -
52C LEU* 4.2 6.7 - - - -
53C ALA* 4.1 6.3 - - - -
161C ALA 2.9 16.4 + - - -
162C LEU 3.2 2.9 + - - -
164C VAL* 1.3 77.6 - - - +
166C PHE* 1.3 56.6 + - - +
168C LEU* 3.0 2.3 + - - +
169C THR* 2.9 23.1 + - - -
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Residues in contact with PHE 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PHE* 4.1 16.4 - + - -
46C LEU* 4.2 20.6 - - + -
50C LEU* 4.3 9.4 - - + -
162C LEU* 2.7 58.0 + - + +
163C ALA* 3.8 5.4 - - - +
165C GLY* 1.3 70.5 - - - +
167C SER* 1.3 59.7 + - - +
169C THR* 3.3 11.3 + - - -
170C LEU* 2.9 27.2 + - - +
50D LEU* 3.7 38.5 - - + +
53D ALA* 6.1 2.2 - - + -
54D THR* 4.4 4.3 - - - +
162D LEU* 3.9 27.6 - - + -
166D PHE* 4.1 14.8 - + - -
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Residues in contact with SER 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLN* 2.6 41.3 + - - +
141C PHE* 3.3 20.1 - - - -
144C CYS* 4.0 12.3 - - - -
163C ALA 2.9 13.6 + - - -
164C VAL* 3.1 11.4 + - - -
166C PHE* 1.3 75.4 - - - +
168C LEU* 1.3 59.9 + - - +
170C LEU* 3.2 3.8 + - - +
171C GLY 3.0 23.0 + - - -
54D THR* 3.6 15.4 + - - +
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 3.2 30.1 - - + +
45C ALA 4.9 0.2 - - - -
48C PHE* 3.5 29.6 - - + +
49C GLY* 4.3 0.7 - - - -
52C LEU* 3.5 20.4 - - + -
141C PHE* 3.9 16.7 - - + -
164C VAL 3.0 11.5 + - - +
165C GLY 3.3 8.7 - - - +
167C SER* 1.3 78.0 - - - +
169C THR* 1.3 58.2 + - - +
171C GLY* 3.1 2.9 + - - -
172C HIS* 2.8 51.5 + - + -
183C MET* 3.6 32.8 - - + +
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Residues in contact with THR 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 6.2 0.2 - - + -
45C ALA* 2.8 41.6 + - + +
46C LEU* 3.9 17.7 - - + +
49C GLY* 3.2 15.4 - - - -
165C GLY 2.9 8.8 + - - -
166C PHE* 3.4 18.9 - - - -
168C LEU* 1.3 76.5 - - - +
170C LEU* 1.3 51.7 + - - +
172C HIS* 3.1 4.2 + - - +
173C LEU* 2.8 40.9 + - + +
50D LEU* 3.7 19.3 - - + -
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLN* 4.0 23.1 - - + +
166C PHE 2.9 14.5 + - - +
167C SER* 3.3 9.0 - - - +
169C THR* 1.3 76.8 - - - +
171C GLY* 1.3 61.5 - - - +
173C LEU* 3.2 9.0 + - + +
174C PHE* 3.1 22.8 + - + +
26D PHE* 4.0 39.0 - - + +
47D ALA* 3.6 32.3 - - + +
50D LEU* 4.0 5.8 - - + +
51D ALA* 3.8 29.4 - - + +
54D THR* 4.6 3.1 - - + +
55D LEU* 6.5 0.2 - - + -
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Residues in contact with GLY 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C LEU* 3.5 15.1 - - - +
140C GLN* 3.8 11.8 + - - -
167C SER 3.0 11.3 + - - -
168C LEU 3.1 4.7 + - - -
170C LEU* 1.3 75.5 - - - +
172C HIS* 1.3 52.3 + - - +
175C GLY* 2.8 33.3 + - - -
181C ALA* 4.0 2.0 - - - +
183C MET* 3.7 20.9 - - - -
26D PHE* 4.9 2.5 - - - -
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Residues in contact with HIS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C TYR* 5.1 0.4 - - - -
41C VAL* 3.8 1.3 - - - +
44C VAL* 4.3 1.3 - - + -
45C ALA* 3.5 20.6 - - + -
48C PHE* 3.4 44.2 - + + +
168C LEU* 2.8 50.7 + - + -
169C THR 3.1 7.9 + - - +
171C GLY* 1.3 74.3 - - - +
173C LEU* 1.3 65.9 + - - +
174C PHE 3.0 3.6 + - - -
176C MET* 3.0 43.8 + - + +
180C GLY 4.5 1.8 - - - -
181C ALA* 3.9 29.3 + - + -
182C GLY 5.0 3.6 + - - -
183C MET* 3.9 10.7 - - + -
187C ARG* 5.3 0.4 + - - -
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL* 3.8 14.3 - - + +
42C LEU* 4.0 19.5 - - + -
45C ALA* 3.6 18.4 - - + -
169C THR* 2.8 35.1 + - + +
170C LEU* 3.2 10.3 + - - +
172C HIS* 1.3 72.3 - - - +
174C PHE* 1.3 61.0 + - - +
177C TYR* 4.5 9.7 - - - -
30D ALA* 4.0 12.6 - - + +
43D GLN* 3.9 30.5 - - + +
46D LEU* 4.0 11.7 - - + +
47D ALA* 3.6 43.7 - - + +
50D LEU* 4.5 2.2 - - + -
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Residues in contact with PHE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 3.6 27.8 - - + -
137C LEU* 3.3 17.5 - - + -
170C LEU* 3.1 14.7 + - + +
171C GLY 4.1 0.2 - - - +
172C HIS 3.0 0.4 - - - -
173C LEU* 1.3 80.2 - - - +
175C GLY* 1.3 75.3 + - - +
176C MET 3.6 1.0 + - - -
177C TYR* 4.0 10.2 + - - -
178C TYR* 3.4 43.4 - + - -
25D PHE* 3.4 39.9 - + - -
26D PHE* 3.8 25.1 - + + +
29D GLY* 3.5 37.7 - - - +
30D ALA* 3.8 7.6 - - + +
104D LEU* 3.9 6.7 - - + -
107D VAL* 6.4 0.2 - - + -
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Residues in contact with GLY 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C VAL* 4.6 1.6 - - - -
137C LEU* 4.1 13.5 - - - -
171C GLY 2.8 21.9 + - - -
174C PHE* 1.3 83.1 - - - +
176C MET* 1.3 64.8 + - - +
177C TYR 3.2 3.4 - - - -
178C TYR* 2.8 18.0 + - - +
179C THR* 2.9 13.2 + - - -
180C GLY 3.4 0.5 + - - -
181C ALA* 3.7 6.6 + - - -
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Residues in contact with MET 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C SER* 5.8 1.3 - - - -
40C HIS* 3.8 27.4 - - + +
41C VAL* 3.9 33.2 - - + +
44C VAL* 3.3 44.9 - - + -
120C THR 5.2 0.3 - - - +
172C HIS* 3.0 37.1 + - + +
174C PHE 3.6 0.2 - - - -
175C GLY* 1.3 70.6 - - - +
177C TYR* 1.3 60.8 + - - +
180C GLY* 2.9 44.6 + - - +
181C ALA* 3.9 1.6 - - - +
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Residues in contact with TYR 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PRO 3.6 9.9 - - - -
37C GLY* 2.6 50.0 + - - -
38C PRO* 3.6 2.6 - - - +
41C VAL* 3.6 11.7 - - + -
122C HIS* 3.3 30.9 + - + +
173C LEU 4.5 10.5 - - - -
174C PHE 4.3 12.8 - - - +
175C GLY 3.2 1.0 - - - -
176C MET* 1.3 77.4 - - - +
178C TYR* 1.3 64.6 + + + +
29D GLY 5.5 7.4 - - - -
30D ALA* 5.2 3.1 - - - -
32D LEU 5.2 4.7 - - - -
33D ARG* 4.3 25.8 + - - -
43D GLN* 3.3 18.8 + - - -
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Residues in contact with TYR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C THR 4.4 0.7 - - - -
121C LEU* 3.5 1.6 - - - +
122C HIS* 2.9 31.8 + - - +
125C VAL* 3.9 22.2 - - + +
133C VAL* 4.1 19.1 - - + -
174C PHE* 3.4 50.6 - + - -
175C GLY 2.8 6.2 + - - +
176C MET 4.2 0.2 - - - -
177C TYR* 1.3 87.2 - + + +
179C THR* 1.3 72.4 + - + +
180C GLY 3.8 0.2 - - - -
29D GLY 4.7 4.7 - - - -
32D LEU* 3.6 11.1 - - + +
104D LEU* 3.6 15.6 - - + +
107D VAL* 3.7 21.5 - - + -
108D THR* 3.5 28.9 + - - -
109D PRO* 4.0 5.6 - - + -
112D VAL* 5.8 2.9 - - + -
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Residues in contact with THR 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C ASN* 3.5 1.4 - - - +
120C THR 3.0 20.3 + - - +
121C LEU* 3.2 22.4 - - + -
125C VAL* 5.0 0.2 - - + -
130C ALA* 3.5 28.5 - - + +
133C VAL* 4.5 3.3 - - + +
134C GLU* 2.6 27.8 + - + +
137C LEU* 4.3 4.2 - - - +
175C GLY 2.9 6.4 + - - -
178C TYR* 1.3 83.3 - - + +
180C GLY* 1.3 60.0 + - - +
181C ALA* 2.9 10.1 + - - -
204C TYR* 2.9 28.9 + - - -
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Residues in contact with GLY 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE* 6.0 0.5 - - - -
119C ASN* 3.3 7.1 - - - +
120C THR 3.6 7.2 + - - -
172C HIS* 4.5 2.6 - - - -
175C GLY 3.4 0.2 + - - -
176C MET* 2.9 38.9 + - - +
179C THR* 1.3 76.3 - - - +
181C ALA* 1.3 73.4 + - - +
187C ARG* 4.7 5.7 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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