Contacts of the helix formed by residues 159 - 180 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A GLN* 3.6 5.0 + - - +
157A LEU 3.7 4.2 + - - +
158A GLY* 1.3 70.3 - - - -
160A VAL* 1.3 61.3 + - - +
161A ALA* 3.3 11.8 + - - +
162A LEU* 3.1 32.1 + - - +
163A ALA* 3.2 18.9 + - - +
57B GLN* 4.7 0.2 + - - -
159B SER* 4.7 3.9 - - - -
156D ARG 3.5 6.7 - - - -
157D LEU 3.0 21.8 + - - -
158D GLY* 3.4 7.4 - - - -
159D SER 4.7 3.4 - - - -
163D ALA* 6.5 0.2 - - - -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.6 5.8 - - + -
148A THR* 3.6 33.2 - - - +
149A TYR* 4.2 23.8 - - + -
157A LEU* 4.2 11.9 - - + -
158A GLY 4.3 2.5 - - - +
159A SER* 1.3 71.7 - - - +
161A ALA* 1.3 64.4 + - - +
163A ALA* 3.6 7.5 - - - +
164A VAL* 3.0 35.7 + - - +
57B GLN* 5.3 1.1 - - - +
154D ASN* 5.7 4.3 - - - +
156D ARG* 3.3 38.8 + - + +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ALA* 3.1 36.4 - - - +
56A VAL* 3.6 26.1 - - + +
57A GLN* 3.4 29.8 - - + +
159A SER* 3.5 0.7 - - - +
160A VAL* 1.3 82.6 - - + +
162A LEU* 1.3 57.7 + - - +
164A VAL* 3.6 2.9 + - - +
165A GLY 2.9 21.8 + - - -
156D ARG 4.9 0.6 + - - -
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Residues in contact with LEU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.3 3.1 - - + -
53A ALA* 3.8 16.4 - - + +
159A SER* 3.1 25.5 + - - +
161A ALA* 1.3 75.0 - - - +
163A ALA* 1.3 55.6 + - - +
166A PHE* 2.7 83.7 + - + +
162B LEU* 3.9 18.2 - - + -
162D LEU* 3.9 26.5 - - + -
163D ALA* 6.3 2.2 - - - +
166D PHE* 3.9 19.7 - - + -
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Residues in contact with ALA 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A CYS* 3.9 6.6 - - - -
148A THR* 4.1 12.3 - - + -
159A SER 3.2 11.9 + - - +
160A VAL* 3.6 8.1 - - - +
162A LEU* 1.3 80.1 - - - +
164A VAL* 1.3 57.5 + - - +
166A PHE* 3.3 6.7 + - - +
167A SER* 2.9 28.2 + - - -
54B THR* 4.7 3.5 + - - +
57B GLN* 3.8 34.1 - - + +
162B LEU* 6.3 1.8 - - - -
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.6 26.7 - - + -
56A VAL* 4.5 8.5 - - + -
141A PHE* 3.5 15.4 - - + -
144A CYS* 4.4 3.8 - - - +
145A ILE* 3.9 25.1 - - + +
148A THR* 3.6 21.1 - - - +
149A TYR* 4.1 14.8 - - + +
160A VAL 3.0 21.8 + - - +
161A ALA* 3.8 4.7 - - - +
163A ALA* 1.3 73.7 - - - +
165A GLY* 1.3 64.6 + - - +
167A SER* 3.1 10.4 + - - -
168A LEU 3.0 17.8 + - - -
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Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY* 3.1 37.8 - - - -
52A LEU* 4.2 7.2 - - - +
53A ALA* 4.1 6.1 - - - -
161A ALA 2.9 16.6 + - - -
162A LEU 3.5 2.7 - - - -
164A VAL* 1.3 77.7 - - - +
166A PHE* 1.3 57.5 + - - +
168A LEU* 3.0 3.1 + - - +
169A THR 2.9 22.0 + - - -
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.2 20.2 - - + -
50A LEU* 4.3 9.9 - - + -
162A LEU* 2.7 57.9 + - + +
163A ALA* 3.8 5.6 - - - +
165A GLY* 1.3 69.6 - - - -
167A SER* 1.3 60.7 - - - +
169A THR* 3.4 10.7 - - - -
170A LEU* 2.9 27.7 + - - +
50B LEU* 3.7 38.5 - - + +
53B ALA* 6.1 2.7 - - + -
54B THR* 4.4 4.5 - - - +
162B LEU* 3.9 27.4 - - + -
166B PHE* 4.1 15.0 - + - -
166D PHE* 4.1 15.9 - + - -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 2.6 40.5 + - - +
141A PHE* 3.3 20.5 - - - -
144A CYS* 4.0 12.8 - - - -
163A ALA 2.9 14.4 + - - -
164A VAL 3.1 11.4 + - - -
166A PHE* 1.3 75.2 - - - +
168A LEU* 1.3 58.6 + - - +
170A LEU* 3.2 3.5 + - - +
171A GLY 3.0 23.0 + - - -
54B THR* 3.6 16.1 + - - +
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Residues in contact with LEU 168 (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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23A TYR* 3.2 30.3 - - + +
45A ALA 4.9 0.2 - - - -
48A PHE* 3.5 29.2 - - + +
49A GLY* 4.3 0.4 - - - -
52A LEU* 3.5 20.6 - - + -
141A PHE* 3.9 17.4 - - + -
164A VAL 3.0 12.2 + - - +
165A GLY 3.3 9.2 - - - +
167A SER* 1.3 76.7 - - - +
169A THR* 1.3 57.7 + - - +
171A GLY* 3.1 2.9 + - - -
172A HIS* 2.8 51.8 + - + -
183A MET* 3.6 31.6 - - + -
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Residues in contact with THR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 6.2 0.2 - - + -
45A ALA* 2.8 40.7 + - + +
46A LEU* 3.9 17.6 - - + +
49A GLY* 3.2 15.9 - - - -
165A GLY 2.9 8.4 + - - -
166A PHE* 3.4 18.7 - - - -
167A SER 3.2 0.2 - - - -
168A LEU* 1.3 75.5 - - - +
170A LEU* 1.3 52.5 + - - +
172A HIS* 3.1 4.0 + - - +
173A LEU* 2.8 41.5 + - + +
50B LEU* 3.7 19.3 - - + -
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Residues in contact with LEU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 4.0 23.6 - - + +
166A PHE 2.9 14.0 + - - +
167A SER* 3.3 9.9 - - - +
169A THR* 1.3 77.1 - - - +
171A GLY* 1.3 62.5 + - - +
173A LEU* 3.2 8.4 + - + +
174A PHE* 3.1 22.3 + - + +
26B PHE* 4.0 39.0 - - + +
47B ALA* 3.6 32.3 - - + +
50B LEU* 4.0 6.3 - - + +
51B ALA* 3.8 29.4 - - + +
54B THR* 4.6 3.8 - - + +
55B LEU* 6.5 0.4 - - + -
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Residues in contact with GLY 171 (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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137A LEU* 3.5 16.3 - - - +
140A GLN* 3.8 12.2 + - - -
167A SER 3.0 11.1 + - - -
168A LEU 3.1 5.3 + - - -
170A LEU* 1.3 76.2 - - - +
172A HIS* 1.3 52.5 + - - +
175A GLY* 2.8 32.9 + - - -
181A ALA* 4.0 2.3 - - - +
183A MET* 3.7 21.1 - - - -
26B PHE* 4.9 2.0 - - - -
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Residues in contact with HIS 172 (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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23A TYR* 5.1 0.9 - - - -
41A VAL* 3.8 1.6 - - - +
44A VAL* 4.3 1.6 - - + -
45A ALA* 3.5 20.4 - - + -
48A PHE* 3.4 43.2 - + + -
168A LEU* 2.8 52.4 + - + -
169A THR 3.1 7.7 + - - +
171A GLY* 1.3 73.6 - - - +
173A LEU* 1.3 68.1 + - - +
174A PHE 3.0 3.0 + - - -
176A MET* 3.0 43.2 + - + +
180A GLY 4.5 1.8 - - - -
181A ALA* 3.9 30.4 + - + -
182A GLY 5.0 3.1 + - - -
183A MET* 3.9 10.3 - - + -
187A ARG* 5.3 0.2 + - - -
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Residues in contact with LEU 173 (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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41A VAL* 3.8 14.1 - - + +
42A LEU* 4.0 20.0 - - + -
45A ALA* 3.6 18.1 - - + +
169A THR* 2.8 34.8 + - + +
170A LEU* 3.2 10.5 + - - +
172A HIS* 1.3 71.7 - - - +
174A PHE* 1.3 60.2 + - - +
177A TYR* 4.5 9.7 - - - -
30B ALA* 4.0 12.7 - - + +
43B GLN* 3.9 29.1 - - + +
46B LEU* 4.0 10.5 - - + +
47B ALA* 3.6 44.9 - - + +
50B LEU* 4.5 2.2 - - + -
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Residues in contact with PHE 174 (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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133A VAL* 3.6 28.5 - - + -
137A LEU* 3.3 16.6 - - + -
170A LEU* 3.1 14.5 + - + +
171A GLY 4.1 0.4 - - - +
172A HIS 3.0 0.2 - - - -
173A LEU* 1.3 81.1 - - - +
175A GLY* 1.3 75.3 + - - +
176A MET 3.6 1.4 + - - -
177A TYR* 4.0 10.0 + - - -
178A TYR* 3.4 44.2 - + - -
25B PHE* 3.4 37.2 - + - -
26B PHE* 3.8 25.4 - + + +
29B GLY* 3.5 37.7 - - - +
30B ALA* 3.8 6.7 - - + +
104B LEU* 3.9 7.6 - - + -
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Residues in contact with GLY 175 (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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133A VAL* 4.6 1.6 - - - -
137A LEU* 4.1 12.6 - - - -
171A GLY 2.8 21.9 + - - -
174A PHE* 1.3 82.9 - - - +
176A MET* 1.3 65.0 + - - +
177A TYR 3.1 3.1 - - - -
178A TYR* 2.8 17.9 + - - +
179A THR* 2.9 13.3 + - - -
180A GLY 3.4 0.3 + - - -
181A ALA 3.7 7.1 + - - -
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Residues in contact with MET 176 (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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31A SER* 5.3 1.1 - - - +
40A HIS* 3.8 27.8 - - + +
41A VAL* 3.9 33.9 - - + +
44A VAL* 3.3 44.0 - - + -
120A THR 5.2 0.2 - - - +
172A HIS* 3.0 37.2 + - + +
174A PHE 3.6 0.2 - - - -
175A GLY* 1.3 71.4 - - - +
177A TYR* 1.3 61.3 + - - +
178A TYR 4.2 0.2 - - - -
180A GLY* 2.9 44.1 + - - +
181A ALA* 3.9 1.8 - - - +
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Residues in contact with TYR 177 (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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36A PRO 3.6 10.3 - - - -
37A GLY* 2.6 49.9 + - - -
38A PRO* 3.6 2.9 - - - +
41A VAL* 3.6 11.0 - - + -
122A HIS* 3.3 30.7 + - + +
173A LEU 4.5 10.5 - - - -
174A PHE 4.3 13.7 - - - +
175A GLY 3.0 1.0 + - - -
176A MET* 1.3 77.8 - - - +
178A TYR* 1.3 65.5 + + + +
29B GLY 5.4 6.5 - - - -
30B ALA* 5.2 3.6 - - - -
32B LEU 5.2 4.0 - - - -
33B ARG* 4.3 25.2 + - - -
43B GLN* 3.3 17.9 + - - -
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Residues in contact with TYR 178 (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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120A THR 4.4 0.7 - - - -
121A LEU* 3.5 2.1 - - - +
122A HIS* 2.9 31.0 + - - +
125A VAL* 3.9 21.5 - - + +
133A VAL* 4.1 20.0 - - + -
174A PHE* 3.4 50.4 - + - -
175A GLY 2.8 6.7 + - - +
177A TYR* 1.3 86.3 - + + +
179A THR* 1.3 70.9 + - + +
180A GLY 3.8 0.2 - - - -
29B GLY 4.7 4.3 - - - -
32B LEU* 3.6 11.4 - - + +
104B LEU* 3.6 16.0 - - + +
107B VAL* 3.7 22.7 - - + -
108B THR* 3.5 27.8 + - - -
109B PRO* 4.0 7.2 - - + -
112B VAL* 5.8 2.7 - - + -
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Residues in contact with THR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN* 3.5 0.7 - - - +
120A THR 3.0 20.7 + - - +
121A LEU* 3.2 22.2 - - + -
130A ALA* 3.5 28.9 - - + +
133A VAL* 4.5 3.5 - - + +
134A GLU* 2.6 26.6 + - + +
137A LEU* 4.3 4.3 - - - +
175A GLY 2.9 6.4 + - - -
178A TYR* 1.3 82.0 - - + +
180A GLY* 1.3 59.9 + - - +
181A ALA* 2.9 9.4 + - - -
204A TYR* 2.9 29.7 + - - -
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Residues in contact with GLY 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 6.0 0.3 - - - -
119A ASN* 3.3 7.6 - - - +
120A THR 3.6 7.0 + - - -
172A HIS* 4.5 2.9 - - - -
175A GLY 3.4 0.4 + - - -
176A MET* 2.9 39.6 + - - +
179A THR* 1.3 75.7 - - - +
181A ALA* 1.3 73.7 + - - +
187A ARG* 4.7 5.5 + - - -
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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