Contacts of the helix formed by residues 132 - 159 (chain A) in PDB entry 2PPL
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 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ALA* 1.3 80.7 - - - +
133A TYR* 1.3 66.3 + - - +
134A THR* 3.9 7.6 + - - -
135A GLN* 3.1 26.6 + - + +
136A ALA* 2.9 18.0 + - - +
267A ASP* 3.6 25.6 - - - +
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Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ALA 3.7 1.0 + - - -
132A THR* 1.3 71.3 - - - +
134A THR* 1.3 67.4 + - + +
136A ALA* 3.2 6.1 + - - +
137A ALA* 2.9 32.1 + - + +
172A LEU* 4.0 12.6 - - + +
196A VAL* 3.2 24.6 - - + +
198A ALA* 2.6 48.3 + - + +
199A SER* 3.9 8.7 - - - -
233A PHE* 5.6 1.1 - + - -
266A LEU* 3.8 42.4 - - + +
267A ASP* 2.8 22.4 + - - +
270A TRP* 3.8 43.9 - + + -
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Residues in contact with THR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.7 20.1 - - + +
44A ILE* 3.7 21.1 - - - +
132A THR* 3.3 8.3 + - - -
133A TYR* 1.3 80.9 - - + +
135A GLN* 1.3 65.0 + - - +
137A ALA* 3.5 6.5 + - - +
138A ASN* 2.8 33.8 + - - -
199A SER* 4.2 16.6 - - - +
266A LEU* 5.9 2.7 - - + -
267A ASP* 4.5 1.9 + - - +
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Residues in contact with GLN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.5 21.4 - - + +
45A LEU 2.9 24.1 + - - +
46A PRO* 3.8 1.4 - - - +
47A TRP* 3.4 40.0 + - + +
131A ALA* 3.7 11.2 - - + -
132A THR* 3.1 23.7 + - + +
134A THR* 1.3 76.4 + - - +
136A ALA* 1.3 59.4 + - - +
138A ASN* 3.2 2.1 + - - +
139A ASN* 2.8 57.4 + - - +
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Residues in contact with ALA 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP* 3.8 4.5 - - - -
128A GLY 3.9 12.1 - - - +
129A SER* 3.7 28.5 - - - +
131A ALA* 3.8 1.9 - - + +
132A THR 2.9 18.3 + - - +
133A TYR 3.5 4.3 - - - +
135A GLN* 1.3 76.4 - - - +
137A ALA* 1.3 61.6 + - - +
139A ASN* 3.2 12.6 + - - +
140A VAL* 3.3 15.2 + - - +
172A LEU* 3.9 11.2 - - + -
270A TRP* 3.9 12.8 - - - +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 4.5 6.2 + - - +
133A TYR* 2.9 22.4 + - + +
134A THR* 3.7 10.1 - - - +
135A GLN 3.2 0.4 - - - -
136A ALA* 1.3 77.4 - - - +
138A ASN* 1.3 58.9 + - - +
140A VAL* 3.2 22.0 - - - +
141A ARG* 4.6 1.4 + - - +
172A LEU* 4.2 8.3 - - + +
199A SER* 4.3 14.1 - - - -
200A PHE* 3.6 34.6 - - + -
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP* 3.7 15.8 + - - +
40A ARG* 3.1 28.4 + - - +
42A LEU 5.3 0.4 + - - -
44A ILE* 3.5 50.4 - - + +
46A PRO* 3.6 13.6 - - + +
134A THR* 2.8 24.6 + - - +
135A GLN* 3.7 7.4 - - - +
137A ALA* 1.3 75.5 - - - +
139A ASN* 1.3 62.6 + - - +
140A VAL 3.0 6.9 + - - -
141A ARG* 3.0 30.5 + - - +
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Residues in contact with ASN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 4.2 5.4 - - - -
47A TRP* 2.8 56.7 + - - -
52A ILE* 4.0 8.9 - - + +
125A TRP* 4.5 4.7 - - + -
128A GLY* 2.8 27.9 + - - +
131A ALA* 4.3 0.4 - - - +
135A GLN* 2.8 42.0 + - - +
136A ALA 3.2 7.6 + - - +
138A ASN* 1.3 71.3 - - - +
140A VAL* 1.3 60.6 + - - +
141A ARG 3.2 0.4 - - - -
142A VAL* 3.3 6.7 + - - +
143A VAL* 3.3 25.2 + - - +
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A TRP* 3.9 3.8 - - + -
136A ALA 3.3 10.8 + - - +
137A ALA 3.2 19.3 - - - +
138A ASN 3.0 0.2 - - - -
139A ASN* 1.3 75.5 - - - +
141A ARG* 1.3 58.8 + - + +
143A VAL* 4.1 2.2 - - - +
144A GLY* 2.9 28.4 + - - -
172A LEU* 3.7 28.9 - - + +
175A HIS* 3.7 31.0 - - + +
176A VAL* 3.7 27.3 - - + +
179A GLU* 4.0 10.0 - - + +
200A PHE* 4.5 6.3 - - + -
207A VAL 5.4 0.2 - - - +
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A CYS 5.1 0.8 + - - -
28A PHE* 3.6 48.3 - - + +
29A SER 2.6 35.2 + - - +
34A TRP* 3.3 65.0 - - + +
40A ARG* 5.4 1.3 - - - +
44A ILE 4.6 4.2 + - - -
46A PRO* 4.4 12.0 - - + +
137A ALA 5.2 1.3 - - - +
138A ASN* 3.0 23.3 + - - +
140A VAL* 1.3 78.4 - - + +
142A VAL* 1.3 57.1 + - - +
144A GLY* 4.0 0.7 - - - -
145A ALA* 3.1 26.7 + - - +
179A GLU* 3.4 25.5 - - - +
183A LYS* 5.0 0.9 + - - -
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 4.0 10.3 - - + -
25A LEU* 4.0 13.5 - - + -
28A PHE* 4.1 9.9 - - + -
46A PRO* 3.4 34.5 - - + -
47A TRP 3.6 10.5 - - - +
49A PRO* 4.4 11.2 - - + -
52A ILE* 3.8 17.3 - - + -
139A ASN 3.3 7.4 + - - +
141A ARG* 1.3 73.6 - - - +
143A VAL* 1.3 61.6 + - - +
145A ALA* 3.2 7.7 + - - +
146A GLN* 2.9 50.0 + - - +
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 3.8 22.7 - - + -
54A THR* 3.9 8.1 - - + +
123A VAL* 4.1 17.5 - - + -
125A TRP* 3.7 44.6 - - + -
139A ASN 3.3 17.0 + - - +
140A VAL 4.1 2.7 - - - +
142A VAL* 1.3 76.2 - - - +
144A GLY* 1.3 57.4 + - - +
146A GLN* 3.2 9.0 + - - +
147A VAL* 2.9 27.5 + - - +
176A VAL* 3.8 21.5 - - + -
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Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL 2.9 16.0 + - - -
143A VAL* 1.3 74.6 - - - +
145A ALA* 1.3 63.5 + - - +
147A VAL* 3.3 1.5 + - - -
148A ALA* 3.0 19.6 + - - +
176A VAL* 3.6 27.7 - - - +
179A GLU* 3.8 9.2 - - - -
180A ALA* 3.5 16.1 - - - +
183A LYS* 5.5 0.2 - - - -
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.9 21.2 - - + +
28A PHE* 4.0 20.2 - - + -
141A ARG 3.1 16.7 + - - +
142A VAL* 3.3 9.2 - - - +
144A GLY* 1.3 74.1 - - - +
146A GLN* 1.3 57.9 + - - +
148A ALA* 3.4 7.6 + - - +
149A GLN* 2.8 27.5 + - - +
179A GLU* 4.9 1.0 - - - +
183A LYS* 4.4 18.7 - - + +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.7 20.1 - - + +
49A PRO* 3.8 30.1 + - - +
52A ILE* 4.7 0.2 - - - +
54A THR* 2.6 38.3 + - + +
56A PHE* 3.7 15.2 - - + -
72A LEU* 3.7 26.8 - - + +
142A VAL* 2.9 23.4 + - - +
143A VAL* 3.2 18.8 + - - +
145A ALA* 1.3 73.5 - - - +
147A VAL* 1.3 64.4 + - - +
149A GLN* 3.2 4.1 + - - +
150A MET* 2.9 19.2 + - - +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 4.0 22.4 - - + -
91A PHE* 4.4 13.0 - - + -
93A ILE* 4.5 4.7 - - + -
123A VAL* 4.1 22.0 - - + -
143A VAL 2.9 19.1 + - - +
144A GLY 3.3 6.3 + - - +
146A GLN* 1.3 74.0 - - - +
148A ALA* 1.3 62.3 + - - +
150A MET* 3.1 4.9 + - - +
151A LEU* 3.0 25.1 + - + +
167A LEU* 4.2 23.3 - - + -
176A VAL* 4.5 10.5 - - + -
180A ALA* 3.6 19.7 - - + -
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A GLY 3.0 13.9 + - - +
145A ALA* 3.5 10.5 - - - +
147A VAL* 1.3 77.9 - - - +
149A GLN* 1.3 56.8 + - - +
151A LEU* 3.1 5.9 + - - +
152A ASP* 2.9 28.3 + - - +
180A ALA* 3.8 6.0 - - - +
183A LYS* 3.8 24.9 - - + -
184A THR* 3.7 23.5 + - - +
483A NA 4.4 4.5 - - - -
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Residues in contact with GLN 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLU 5.0 0.2 - - - +
24A ASP* 3.6 37.3 + - + +
25A LEU* 3.4 21.1 - - + +
72A LEU* 3.5 33.3 + - + +
145A ALA 2.8 15.0 + - - +
146A GLN 3.2 8.9 + - - +
148A ALA* 1.3 76.2 - - - +
150A MET* 1.3 56.3 + - - +
152A ASP* 3.3 8.2 + - + +
153A ILE* 2.9 43.4 + - + +
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Residues in contact with MET 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PHE* 3.6 41.1 - - + -
70A LEU* 3.9 24.7 - - + +
71A LEU 4.5 2.0 - - - +
72A LEU* 3.6 25.3 - - + +
78A ILE* 4.0 25.4 - - - -
91A PHE* 4.0 23.8 - - + -
121A ILE* 5.5 2.2 - - + -
146A GLN 2.9 13.7 + - - +
147A VAL 3.1 8.7 + - - +
149A GLN* 1.3 76.0 - - - +
151A LEU* 1.3 57.9 + - - +
153A ILE* 3.2 9.7 + - - +
154A LEU* 3.0 33.6 + - + +
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Residues in contact with LEU 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE* 3.5 35.2 - - + -
147A VAL* 3.0 22.3 + - + +
148A ALA* 3.1 7.2 + - - +
150A MET* 1.3 74.6 - - - +
152A ASP* 1.3 57.8 + - - +
154A LEU* 3.5 9.7 + - + +
155A LEU* 3.1 27.7 + - - +
160A TYR 4.6 1.4 - - - +
162A PRO* 5.1 8.5 - - + +
165A VAL* 4.0 17.5 - - + -
167A LEU* 4.5 13.7 - - + -
180A ALA* 5.1 0.9 - - + -
184A THR* 3.7 38.4 - - + +
187A LEU* 4.1 20.0 - - + -
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Residues in contact with ASP 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA 2.9 12.9 + - - +
149A GLN* 3.3 12.1 + - + +
151A LEU* 1.3 74.6 - - - +
153A ILE* 1.3 60.1 + - - +
155A LEU* 3.2 14.8 + - - +
156A THR* 2.8 50.2 + - - -
184A THR* 5.7 0.6 - - - +
483A NA 4.6 5.4 - - - -
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Residues in contact with ILE 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU 5.0 1.3 - - - +
72A LEU* 3.7 44.4 - - + +
75A PRO* 3.7 30.7 - - + -
78A ILE* 3.7 21.8 - - + -
149A GLN* 2.9 31.9 + - + +
150A MET* 3.5 8.5 - - - +
152A ASP* 1.3 75.2 - - - +
154A LEU* 1.3 58.8 + - - +
156A THR* 5.1 0.4 - - - -
157A GLU* 2.9 53.0 + - + +
158A TYR* 3.8 2.5 + - + -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 6.6 0.2 - - + -
78A ILE* 4.1 28.9 - - + -
83A PHE* 3.6 43.3 - - + -
89A THR* 5.6 0.2 - - + -
91A PHE* 4.6 8.1 - - + -
121A ILE* 5.3 1.6 - - + -
150A MET* 3.0 30.1 + - + +
151A LEU* 3.7 22.7 - - + +
152A ASP 3.2 0.2 - - - -
153A ILE* 1.3 77.2 - - - +
155A LEU* 1.3 61.0 + - - +
158A TYR* 3.1 23.0 + - + +
160A TYR* 2.9 45.5 + - + +
165A VAL* 5.4 1.1 - - + -
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Residues in contact with LEU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU 3.1 18.2 + - - +
152A ASP* 3.2 17.4 + - - +
154A LEU* 1.3 77.9 - - - +
156A THR* 1.3 64.0 + - - +
159A SER* 3.1 27.5 + - - -
160A TYR 3.4 10.7 + - - +
161A PRO* 4.2 22.9 - - + -
162A PRO* 4.2 15.0 - - + -
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Residues in contact with THR 156 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASP* 2.8 35.5 + - - -
153A ILE* 5.1 0.4 - - - -
155A LEU* 1.3 80.0 - - - +
157A GLU* 1.3 69.3 + - + +
159A SER* 4.3 5.0 + - - -
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Residues in contact with GLU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 3.4 32.1 - - - +
153A ILE* 2.9 29.8 + - + +
156A THR* 1.3 84.3 - - + +
158A TYR* 1.3 80.2 + - + +
159A SER* 3.7 0.7 - - - -
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Residues in contact with TYR 158 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 2.7 31.4 + - + -
76A SER* 3.3 6.9 - - - -
78A ILE* 3.8 20.4 - - + -
79A GLU* 3.2 49.4 + - + +
85A MET* 3.6 37.6 - - + +
153A ILE* 4.0 8.7 - - + -
154A LEU* 3.1 16.5 + - + +
157A GLU* 1.3 97.3 - - + +
159A SER* 1.3 72.4 + - - +
160A TYR* 3.1 6.6 + - + +
----------------------------------------------------------
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Residues in contact with SER 159 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A LEU* 3.1 21.6 + - - -
156A THR 4.3 4.6 + - - -
157A GLU 3.7 0.7 - - - -
158A TYR* 1.3 80.5 - - - +
160A TYR* 1.3 58.4 + - - +
161A PRO* 3.5 10.2 - - - +
----------------------------------------------------------
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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