Contacts of the helix formed by residues 130 - 153 (chain A) in PDB entry 2P3Z
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 GLY 130 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER 3.1 18.1 + - - +
128A GLY 3.2 1.2 + - - -
129A SER* 1.3 80.0 - - - +
131A GLY* 1.3 67.4 + - - -
132A LEU 3.8 0.3 + - - -
133A VAL 4.4 0.2 + - - -
134A MET* 3.5 20.3 + - - +
281A HIS 4.9 3.6 - - - -
282A HIS 5.1 0.2 - - - -
283A GLY* 4.1 9.9 - - - -
305A TRP 4.9 0.7 - - - -
127B SER 4.2 0.9 - - - -
128B GLY* 3.3 16.9 + - - -
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Residues in contact with GLY 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLY* 1.3 74.6 - - - -
132A LEU* 1.3 55.6 + - - -
134A MET* 2.9 5.3 + - - +
135A ASN* 2.8 43.5 + - - +
281A HIS 4.8 7.1 + - - -
305A TRP* 4.8 2.6 + - - +
125B TYR 4.6 4.0 - - - -
126B TYR* 3.2 22.9 - - - -
128B GLY* 3.8 4.0 - - - -
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Residues in contact with LEU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.5 10.3 - - + -
88A ALA* 3.5 42.8 - - + +
91A MET* 3.8 36.8 - - + -
92A GLY 4.5 1.1 - - - +
95A ILE* 4.7 5.6 - - + -
130A GLY 3.8 0.4 + - - -
131A GLY* 1.3 69.5 - - - -
133A VAL* 1.3 65.2 + - + +
135A ASN* 3.3 11.4 + - - +
136A THR* 3.0 28.1 + - - +
126B TYR* 2.7 29.9 + - + +
132B LEU* 3.9 27.6 - - + -
133B VAL* 4.2 13.7 - - + -
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Residues in contact with VAL 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 4.0 20.6 - - + -
123A THR* 4.0 22.0 - - + +
126A TYR* 3.7 41.3 - - + +
127A SER* 3.5 31.9 - - - +
130A GLY 4.4 0.6 + - - -
131A GLY 3.1 1.2 + - - -
132A LEU* 1.3 76.3 - - + +
134A MET* 1.3 64.1 + - - +
136A THR* 3.1 4.3 + - - -
137A ILE* 3.0 26.7 + - + +
132B LEU* 4.2 13.7 - - + -
133B VAL* 6.2 0.9 - - + -
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Residues in contact with MET 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU* 3.6 29.4 - - + -
123A THR* 5.6 0.2 - - - +
127A SER* 4.2 20.6 + - - +
129A SER 4.2 0.9 - - - -
130A GLY* 3.5 29.0 + - - +
131A GLY 2.9 9.0 + - - +
133A VAL* 1.3 82.1 - - - +
135A ASN* 1.3 52.8 + - - +
137A ILE* 3.3 10.0 + - + +
138A SER* 2.7 37.9 + - - -
283A GLY* 4.5 2.7 - - - -
284A THR* 3.8 26.2 - - + -
305A TRP 3.3 17.7 - - - +
306A CYS 3.8 6.1 - - - +
307A GLY* 3.7 22.2 - - - +
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Residues in contact with ASN 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 5.3 0.4 - - - +
86A SER* 3.5 8.5 + - - +
87A THR* 3.0 37.6 + - - +
88A ALA* 5.1 0.2 - - - -
131A GLY* 2.8 32.9 + - - +
132A LEU* 3.4 10.1 - - - +
134A MET* 1.3 72.1 - - - +
136A THR* 1.3 57.9 + - - +
138A SER* 4.1 0.2 - - - -
139A CYS* 3.0 24.6 + - - +
304A GLY 3.3 16.4 - - - +
305A TRP* 3.2 43.0 - - - +
125B TYR 5.2 5.5 + - - -
126B TYR* 5.3 4.0 - - - +
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.9 12.1 - - + -
88A ALA* 3.5 6.1 - - - +
92A GLY* 3.4 28.5 - - - +
95A ILE* 3.9 25.2 - - + +
96A VAL* 3.5 29.4 - - + -
100A LEU* 4.6 1.8 - - + -
132A LEU* 3.0 14.3 + - - +
133A VAL 3.4 8.7 - - - -
134A MET 3.1 0.4 - - - -
135A ASN* 1.3 75.2 - - - +
137A ILE* 1.3 65.3 + - - +
139A CYS* 3.2 4.2 + - - +
140A VAL* 3.1 22.0 + - - +
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Residues in contact with ILE 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 4.2 16.6 - - + -
116A HIS* 4.2 9.4 - - + +
119A MET* 3.7 41.7 - - + +
120A LEU* 4.2 20.4 - - + -
123A THR* 3.3 30.3 - - + +
133A VAL* 3.0 22.9 + - + +
134A MET* 3.6 17.7 - - + +
136A THR* 1.3 74.4 - - - +
138A SER* 1.3 64.9 + - - +
140A VAL* 3.0 4.9 + - - +
141A ASP* 2.8 20.8 + - - +
307A GLY 4.2 11.4 - - - +
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A MET 2.7 23.1 + - - -
135A ASN 3.5 0.2 - - - -
137A ILE* 1.3 73.9 - - - +
139A CYS* 1.3 63.3 + - - +
141A ASP* 3.2 2.0 + - - +
142A LEU* 2.9 31.1 + - - +
303A VAL 3.4 3.0 + - - -
304A GLY* 3.1 31.4 + - - -
305A TRP 3.6 0.7 - - - -
307A GLY 2.7 28.6 + - - -
308A GLY* 3.3 17.7 - - - +
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Residues in contact with CYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.7 20.2 - - + -
72A VAL* 3.7 16.8 - - + -
84A ALA* 3.2 36.8 - - - +
85A VAL* 3.7 14.8 - - - -
86A SER* 3.7 9.9 - - - -
135A ASN 3.0 16.4 + - - +
136A THR 3.2 9.1 + - - +
138A SER* 1.3 75.3 - - - +
140A VAL* 1.3 57.4 + - - +
142A LEU* 3.5 6.2 + - - -
143A ALA* 3.0 27.5 + - - +
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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
----------------------------------------------------------
72A VAL* 4.0 19.1 - - + -
74A VAL* 5.2 2.0 - - + -
96A VAL* 3.8 25.1 - - + -
100A LEU* 4.4 4.3 - - + -
104A ILE* 3.5 36.1 - - + -
119A MET* 3.6 24.0 - - + -
136A THR 3.1 12.0 + - - +
137A ILE 3.0 7.4 + - - +
139A CYS* 1.3 73.5 - - - +
141A ASP* 1.3 65.7 + - - +
143A ALA* 3.2 3.3 + - - +
144A LEU* 3.0 32.0 + - + +
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Residues in contact with ASP 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 3.5 11.8 - - - +
116A HIS* 3.4 27.1 - - + +
119A MET* 4.1 3.0 - - + +
137A ILE 2.8 15.8 + - - +
138A SER 3.5 7.4 - - - +
140A VAL* 1.3 73.1 - - - +
142A LEU* 1.3 55.6 + - - +
144A LEU* 3.3 11.6 + - - +
145A TRP* 3.1 37.2 + - - -
307A GLY 4.0 4.9 - - - +
308A GLY* 4.2 0.2 - - - -
309A LEU 2.9 27.6 + - - -
310A THR* 2.7 32.4 + - - -
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ALA* 3.3 21.1 - - + -
85A VAL 4.8 5.2 - - - +
138A SER 2.9 23.4 + - - +
139A CYS* 4.8 1.8 - - - -
141A ASP* 1.3 69.4 - - - +
143A ALA* 1.3 66.9 + - - +
145A TRP* 3.3 2.4 + - - +
146A ASP* 2.9 20.6 + - - +
303A VAL* 4.0 11.2 - - + +
304A GLY* 4.3 22.9 - - - +
308A GLY* 4.6 0.2 - - - -
309A LEU* 3.8 28.9 - - + +
334A TYR* 3.9 29.2 - - + +
389A PHE* 3.3 33.3 - - + -
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Residues in contact with ALA 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 3.6 34.8 - - + +
74A VAL* 4.1 13.2 - - + +
82A GLY 3.9 3.1 - - - -
83A PHE* 3.8 17.7 - - - +
84A ALA* 3.6 0.8 - - - +
139A CYS 3.0 18.3 + - - +
140A VAL 3.6 4.5 - - - +
142A LEU* 1.3 77.8 - - - +
144A LEU* 1.3 56.1 + - - +
146A ASP* 3.3 3.1 + - - +
147A LEU* 2.9 29.3 + - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.5 32.1 - - + -
74A VAL* 4.2 17.3 - - + -
104A ILE* 4.5 4.5 - - + -
109A VAL 4.5 4.0 - - - +
112A ILE* 3.7 27.6 - - + +
115A ILE* 3.6 42.6 - - + -
119A MET* 4.7 1.6 - - + -
140A VAL* 3.0 29.1 + - + +
141A ASP* 3.5 10.5 - - - +
142A LEU 3.3 0.2 - - - -
143A ALA* 1.3 73.2 - - - +
145A TRP* 1.4 59.6 + - - +
147A LEU* 3.3 6.6 + - + +
148A PHE* 2.9 30.8 + - - +
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Residues in contact with TRP 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ILE* 3.5 35.0 - - + +
113A LYS* 5.2 11.0 - - + -
141A ASP* 3.1 36.0 + - - -
142A LEU* 3.3 6.9 + - - +
144A LEU* 1.4 74.8 - - - +
146A ASP* 1.3 57.9 + - - +
148A PHE* 3.8 10.1 - + - +
149A GLY* 2.9 26.7 + - - -
156A VAL* 3.9 15.4 - - + +
159A LEU* 4.2 35.4 - - + +
160A LEU* 4.4 19.5 - - + -
309A LEU* 3.7 25.5 - - + +
310A THR* 3.0 31.0 + - - +
389A PHE* 3.9 15.9 - - + -
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Residues in contact with ASP 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY* 3.2 2.5 - - - -
83A PHE* 2.9 35.4 + - - +
142A LEU 2.9 13.2 + - - +
143A ALA 3.4 8.7 - - - +
145A TRP* 1.3 77.5 - - - +
147A LEU* 1.3 58.5 + - - +
150A LYS* 2.9 67.5 + - - +
388A GLY* 3.4 4.9 - - - -
389A PHE* 2.9 41.9 + - + +
390A GLY 4.3 0.3 + - - -
391A VAL* 5.1 1.6 - - - +
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 4.3 3.8 - - + -
74A VAL* 3.4 37.0 - - + +
76A ALA* 4.3 8.1 - - + +
80A GLN* 3.6 26.9 - - + +
81A THR 3.6 14.1 - - - +
82A GLY* 3.7 10.4 - - - +
109A VAL* 3.7 28.9 - - + -
143A ALA 2.9 16.7 + - - +
144A LEU* 3.7 6.3 - - + +
146A ASP* 1.3 74.3 - - - +
148A PHE* 1.3 60.3 + - - +
150A LYS* 3.0 3.6 + - + -
151A VAL* 2.8 45.8 + - + +
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Residues in contact with PHE 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.1 13.2 - - + -
109A VAL* 3.6 32.1 + - + +
110A SER* 3.8 29.6 - - - -
112A ILE* 3.8 19.5 - - + -
144A LEU 2.9 20.9 + - - +
145A TRP* 3.8 12.8 - + - +
147A LEU* 1.3 72.1 - - - +
149A GLY* 1.3 61.5 + - - +
151A VAL* 3.3 4.2 + - + +
152A VAL* 3.0 44.0 + - + +
159A LEU* 4.0 27.1 - - + -
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Residues in contact with GLY 149 (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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145A TRP 2.9 16.4 + - - -
148A PHE* 1.3 76.5 - - - +
150A LYS* 1.3 58.4 + - - +
152A VAL* 4.6 1.6 - - - -
153A GLY* 2.7 26.2 + - - -
154A LEU 3.0 28.6 + - - +
156A VAL* 5.4 0.4 - - - -
159A LEU* 3.8 15.1 - - - +
387A PRO* 3.7 0.7 - - - +
388A GLY* 3.7 7.2 - - - -
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Residues in contact with LYS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN* 3.3 20.3 + - + +
81A THR 3.4 25.9 + - - +
83A PHE* 4.0 8.9 - - - -
146A ASP* 2.9 51.0 + - - +
147A LEU* 3.0 5.6 + - + +
149A GLY* 1.3 78.2 - - - +
151A VAL* 1.3 61.8 + - - +
153A GLY* 3.6 7.6 + - - -
387A PRO* 3.8 32.9 - - + +
390A GLY* 4.8 2.5 - - - +
391A VAL 2.9 27.7 + - - +
392A GLU* 3.8 17.0 + - - +
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A MET* 4.8 4.5 - - - +
6A THR 5.1 1.8 - - - +
7A LEU* 3.9 19.3 - - + -
8A PRO* 3.7 37.9 - - + -
76A ALA* 4.8 0.7 - - + -
78A ASN* 5.2 0.7 - - - +
80A GLN* 3.4 28.3 + - + +
109A VAL* 4.4 8.7 - - + -
147A LEU* 2.8 39.8 + - + +
148A PHE 3.8 4.5 - - - +
150A LYS* 1.3 79.2 - - - +
152A VAL* 1.3 61.5 + - - +
153A GLY 3.5 0.2 + - - -
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A MET* 3.9 37.8 - - + +
7A LEU* 4.5 4.3 - - + -
148A PHE* 3.0 50.7 + - + +
149A GLY* 4.1 4.7 - - - +
151A VAL* 1.3 76.4 - - - +
153A GLY* 1.3 58.2 + - - +
154A LEU* 3.8 31.3 - - + +
159A LEU* 4.5 8.1 - - + -
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Residues in contact with GLY 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLY 2.7 14.7 + - - -
150A LYS 3.6 7.2 + - - -
151A VAL 3.3 2.8 - - - -
152A VAL* 1.3 78.0 - - - +
154A LEU* 1.3 65.6 + - - +
155A PRO* 4.6 1.2 - - - +
387A PRO* 4.3 18.9 - - - +
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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