Contacts of the helix formed by residues 159 - 180 (chain B) in PDB entry 4NEF
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 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A PRO 5.0 5.6 - - - +
159A THR* 3.8 16.2 - - + -
162A LEU* 5.9 1.6 - - + -
157B PRO 2.8 12.5 + - - -
158B GLY* 1.4 79.0 - - - +
160B PRO* 1.4 58.6 - - - +
161B ALA 3.5 1.8 - - - -
162B LEU* 4.2 10.5 - - + +
163B SER* 2.9 37.7 + - - -
57C GLN* 4.1 2.7 + - - -
161C ALA* 5.7 1.9 + - - +
162C LEU* 3.8 28.2 + - + +
159D THR* 3.7 22.7 - - + -
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Residues in contact with PRO 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 5.6 2.5 - - + -
148B SER* 3.7 39.0 - - - +
149B THR* 5.1 3.6 - - + -
157B PRO* 4.3 8.1 - - + -
158B GLY 3.6 9.4 - - - +
159B THR* 1.4 87.4 - - - +
161B ALA* 1.3 53.8 + - - +
163B SER* 3.7 0.3 - - - -
164B ILE* 2.8 45.6 + - + +
57C GLN* 4.8 0.9 - - - +
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Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLY* 3.3 33.6 - - - +
56B VAL* 3.9 15.8 - - + +
57B GLN* 3.7 33.2 - - + +
159B THR 3.5 0.6 - - - -
160B PRO* 1.3 78.5 - - - +
162B LEU* 1.3 57.8 + - + +
164B ILE* 3.9 1.8 - - - +
165B GLY 2.8 25.1 + - - -
159D THR* 5.6 1.3 - - - +
163D SER* 5.0 2.7 - - - +
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 5.7 0.2 - - + -
50B LEU* 6.0 1.3 - - + -
53B GLY* 5.2 6.1 - - - +
159B THR* 3.6 9.2 + - + -
160B PRO 3.4 0.4 - - - -
161B ALA* 1.3 78.2 - - + +
163B SER* 1.4 53.0 + - - +
165B GLY* 3.3 1.5 + - - -
166B PHE* 2.8 47.7 + - + -
162C LEU* 3.7 25.4 - - + -
159D THR* 3.8 27.6 - - + +
162D LEU* 3.9 30.1 - - + -
163D SER* 4.2 17.0 - - - +
166D PHE* 3.7 33.2 - - + -
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B CYS* 3.8 6.6 - - - -
148B SER* 4.0 2.7 - - - -
159B THR* 2.9 30.1 + - - -
160B PRO 3.7 2.5 - - - -
162B LEU* 1.4 75.4 - - - +
164B ILE* 1.4 57.4 + - - +
166B PHE* 3.3 3.9 + - - +
167B SER* 3.0 28.1 + - - -
53C GLY 5.4 0.6 + - - -
54C THR* 4.6 3.8 + - - +
57C GLN* 3.0 40.3 + - - +
161C ALA* 5.0 2.4 - - - +
162C LEU* 4.2 15.5 - - - +
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 3.7 21.8 - - + -
56B VAL* 4.3 22.0 - - + -
141B LEU* 4.0 3.3 - - + +
144B CYS* 4.3 1.6 - - - -
145B ILE* 3.7 54.3 - - + +
148B SER* 4.0 17.7 - - - +
149B THR* 4.2 15.5 - - + -
160B PRO* 2.8 27.2 + - + +
161B ALA* 3.9 3.8 - - - +
163B SER* 1.4 70.4 - - - +
165B GLY* 1.3 60.8 + - - +
167B SER* 3.3 9.3 + - - -
168B VAL* 3.2 23.1 + - - +
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Residues in contact with GLY 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B GLY* 3.2 34.0 - - - -
50B LEU* 5.6 0.4 - - - -
52B ILE* 4.6 2.9 - - - -
53B GLY* 3.8 10.7 - - - -
161B ALA 2.8 17.7 + - - -
162B LEU* 3.6 1.8 - - - -
164B ILE* 1.3 76.7 - - - +
166B PHE* 1.4 56.2 + - - +
168B VAL* 3.2 3.6 + - - +
169B ALA 3.1 21.3 + - - -
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Residues in contact with PHE 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B MET* 3.8 27.1 - - + -
49B GLY 6.2 0.7 - - - -
50B LEU* 4.3 12.1 - - + -
162B LEU* 2.8 37.1 + - + +
163B SER* 4.0 3.6 - - - +
165B GLY* 1.4 69.5 - - - +
167B SER* 1.3 57.9 + - - +
169B ALA* 3.6 8.2 - - + +
170B LEU* 2.9 27.7 + - - +
46C MET* 5.1 1.3 - - + -
50C LEU* 3.7 40.8 - - + +
54C THR* 4.2 5.6 - - - +
162C LEU* 3.6 37.0 - - + -
166C PHE* 4.3 17.5 - + - -
166D PHE* 4.1 30.3 - + - -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 2.9 31.8 + - - -
141B LEU* 3.3 24.2 - - - +
144B CYS* 3.8 8.2 - - - +
163B SER 3.0 12.5 + - - -
164B ILE 3.3 11.0 - - - -
165B GLY 3.2 0.4 - - - -
166B PHE* 1.3 73.4 - - - +
168B VAL* 1.3 60.2 + - - +
170B LEU* 3.3 2.6 + - - +
171B GLY 3.0 23.2 + - - -
54C THR* 3.7 22.6 + - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 5.0 3.1 - - + -
48B PHE* 3.7 24.5 - - + +
49B GLY* 4.1 1.6 - - - -
52B ILE* 3.8 29.6 - - + -
141B LEU* 3.6 24.7 - - + -
164B ILE 3.2 14.0 + - - +
165B GLY 3.2 8.0 + - - +
167B SER* 1.3 75.8 - - - +
169B ALA* 1.4 59.7 + - - +
171B GLY* 3.3 2.9 + - - -
172B HIS* 2.9 48.7 + - + +
183B MET* 4.0 10.3 - - + +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ALA* 3.4 38.9 - - + +
46B MET* 4.6 7.2 - - - +
49B GLY* 3.9 4.0 - - - -
165B GLY 3.1 13.3 + - - +
166B PHE* 3.6 14.8 - - + +
167B SER 3.3 0.2 - - - -
168B VAL* 1.4 76.3 - - - +
170B LEU* 1.4 56.8 + - - +
172B HIS 3.2 1.9 + - - -
173B LEU* 3.0 28.6 + - + +
50C LEU* 3.9 15.5 - - + -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B GLN* 3.5 23.8 - - + +
166B PHE 2.9 18.5 + - - +
167B SER 3.5 4.0 - - - +
168B VAL 3.3 0.2 - - - -
169B ALA* 1.4 70.6 - - - +
171B GLY* 1.3 66.2 + - - +
173B LEU* 3.3 19.9 + - + +
174B LEU* 3.7 6.4 + - - +
26C PHE* 3.8 32.2 - - + +
30C SER* 5.0 1.0 + - - +
47C ALA* 3.3 32.3 - - + +
50C LEU* 4.1 7.8 - - + +
51C GLY* 3.7 26.2 - - - +
54C THR* 3.8 15.5 - - + +
55C LEU* 5.9 2.9 - - + -
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Residues in contact with GLY 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU* 3.5 9.3 - - - +
140B GLN* 4.3 1.5 - - - +
167B SER 3.0 12.5 + - - -
168B VAL 3.3 4.2 + - - -
170B LEU* 1.3 75.2 - - - +
172B HIS* 1.3 49.9 - - - +
174B LEU 3.4 0.5 + - - -
175B GLY* 2.8 34.0 + - - -
181B CYS* 3.7 8.3 - - - -
183B MET* 3.7 17.9 - - - -
26C PHE* 3.9 14.8 - - - -
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Residues in contact with HIS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B PHE* 5.5 1.2 - - - -
44B ILE* 4.7 0.2 - - - +
45B ALA* 3.6 20.2 - - - -
48B PHE* 3.4 49.8 - + + +
168B VAL* 2.9 41.5 + - + +
169B ALA* 3.2 8.0 + - - +
171B GLY* 1.3 72.1 - - - +
173B LEU* 1.4 62.2 + - - +
174B LEU 3.1 2.2 - - - -
176B ILE* 3.1 44.4 + - + +
180B GLY 4.3 1.7 + - - -
181B CYS* 3.5 42.0 - - + +
182B SER 4.8 4.5 + - - -
183B MET* 4.3 3.7 - - - -
187B ARG* 5.0 0.7 - - - -
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL* 4.0 11.5 - - + +
42B LEU* 3.9 23.8 - - + -
45B ALA* 4.0 7.4 - - + -
169B ALA 3.0 16.9 + - - +
170B LEU* 3.3 12.0 + - + +
172B HIS* 1.4 74.6 - - - +
174B LEU* 1.4 56.4 + - - +
177B HIS* 3.5 21.7 + - - -
30C SER* 3.3 21.7 + - - +
43C GLN* 3.6 34.9 - - + +
46C MET* 3.9 11.4 - - + +
47C ALA* 3.5 37.2 - - + +
50C LEU* 4.6 9.6 - - + -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 4.3 4.5 - - + -
137B LEU* 3.8 12.3 - - + -
170B LEU 3.7 1.0 + - - -
171B GLY 3.4 5.5 + - - +
172B HIS 3.1 0.2 - - - -
173B LEU* 1.4 77.3 - - - +
175B GLY* 1.3 63.8 + - - +
176B ILE 3.3 3.1 + - - -
177B HIS* 3.5 13.6 + - - -
178B TYR* 3.3 42.2 - - + +
25C PHE* 3.7 35.9 - - + +
26C PHE* 3.7 31.0 - - + +
29C GLY* 3.5 36.6 - - - +
30C SER* 3.8 8.5 - - - +
104C LEU* 4.4 2.0 - - + -
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Residues in contact with GLY 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B VAL* 4.6 2.0 - - - -
137B LEU* 3.6 23.7 - - - +
171B GLY 2.8 20.7 + - - -
174B LEU* 1.3 71.3 - - - +
176B ILE* 1.4 63.2 + - - +
178B TYR* 3.2 7.5 + - - +
179B THR* 3.0 24.4 + - - -
181B CYS* 3.2 13.4 + - - -
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Residues in contact with ILE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL* 3.7 47.8 - - + +
44B ILE* 3.7 35.9 - - + -
45B ALA 4.1 0.2 - - - +
122B SER* 4.4 6.1 + - - -
172B HIS* 3.1 38.3 + - + +
174B LEU 3.3 0.2 - - - -
175B GLY* 1.4 73.5 - - - +
177B HIS* 1.3 62.8 + - + +
178B TYR 4.4 0.2 - - - -
180B GLY* 3.1 43.0 + - - +
181B CYS* 3.6 0.6 - - - +
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Residues in contact with HIS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B VAL* 3.6 33.9 - - + +
122B SER* 3.4 14.2 - - - +
123B ASN* 2.8 27.1 + - - +
125B THR* 4.5 0.7 + - - -
173B LEU 3.5 25.5 + - - -
174B LEU* 3.6 12.8 - - - +
175B GLY 3.3 0.8 - - - -
176B ILE* 1.3 75.3 - - - +
178B TYR* 1.3 59.5 + - + +
29C GLY 4.5 3.1 - - - -
30C SER* 4.8 5.4 + - - -
33C ASN* 3.4 59.6 + - + +
35C PRO* 4.4 10.9 - - - +
37C ALA* 4.3 8.2 - - + +
39C PRO* 5.2 0.4 - - + -
43C GLN* 4.5 7.1 + - - -
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 3.6 4.7 - - - +
122B SER* 2.8 29.8 + - - +
125B THR* 3.8 35.2 - - + +
130B ALA* 5.2 0.7 - - - -
133B VAL* 3.9 31.2 - - + -
174B LEU* 3.3 40.2 - - + -
175B GLY* 3.2 4.5 + - - +
177B HIS* 1.3 79.2 - - - +
179B THR* 1.3 63.9 + - + +
180B GLY 3.8 0.2 - - - -
33C ASN* 3.1 29.8 + - - -
104C LEU* 3.4 14.2 - - - +
107C ILE* 3.6 28.0 - - + -
108C THR* 2.7 28.3 + - - -
109C PRO* 4.5 4.0 - - + -
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Residues in contact with THR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASN* 3.3 11.6 - - - +
120B ALA 3.1 35.4 + - - -
121B LEU* 4.4 3.6 - - + -
130B ALA* 3.6 30.5 - - + +
133B VAL* 5.7 1.7 - - + +
134B GLU* 2.6 30.7 + - + +
137B LEU* 5.0 0.5 - - - +
175B GLY* 3.0 6.8 + - - -
178B TYR* 1.3 80.7 - - + +
180B GLY* 1.3 58.3 + - - +
181B CYS 3.1 7.0 + - - -
182B SER 5.0 0.4 - - - -
203B VAL* 4.4 3.4 - - + -
204B PHE* 3.6 25.1 - - + -
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 5.6 1.7 - - - +
48B PHE* 5.7 0.9 - - - -
118B VAL 5.7 1.3 - - - -
119B ASN* 3.8 4.2 - - - +
120B ALA 4.0 2.2 + - - -
122B SER* 5.1 1.0 - - - -
172B HIS* 4.3 3.3 + - - -
176B ILE* 3.1 39.3 + - - +
178B TYR 3.8 0.2 - - - -
179B THR* 1.3 76.6 - - - +
181B CYS* 1.4 68.8 + - - +
187B ARG* 4.6 7.4 + - - -
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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
------------------------------------------------------------
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