Contacts of the helix formed by residues 127 - 156 (chain B) in PDB entry 2RS9
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 127 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 3.3 45.1 - - + +
4A GLY* 4.3 1.8 - - - +
123B ASN* 4.2 4.9 - - + +
124B ALA* 3.5 18.6 + - + +
126B ASP* 1.3 81.3 - - - +
128B ILE* 1.3 63.9 + - - +
129B PHE* 3.6 15.5 + - + +
130B TYR* 3.2 27.6 + - - +
131B ARG* 3.4 20.6 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B GLY* 6.4 1.6 - - - -
67B ILE* 4.4 15.9 - - + -
127B THR* 1.3 71.6 - - - +
129B PHE* 1.3 89.8 + - + +
131B ARG* 3.3 5.9 + - - +
132B ALA* 2.9 28.2 + - + +
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Residues in contact with PHE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG 5.8 2.0 - - - -
5A ALY 3.5 60.6 - - + +
67B ILE* 3.7 36.3 - - + -
68B PHE* 4.0 1.0 - - - -
119B CYS* 3.2 14.3 - - - -
123B ASN* 5.3 1.8 - - + -
127B THR* 3.3 14.1 - - + +
128B ILE* 1.3 93.7 - - + +
130B TYR* 1.3 65.0 + - - +
132B ALA* 3.4 7.5 + - - +
133B ALA 3.2 17.7 + - - -
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Residues in contact with TYR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B CYS* 4.4 0.4 - - - -
120B LEU* 3.6 24.4 - - + +
123B ASN* 3.3 35.7 + - - +
124B ALA 3.5 8.7 - - - +
125B LYS* 3.5 41.2 - - + +
126B ASP* 4.0 2.0 - - - -
127B THR* 3.2 23.1 + - - +
128B ILE 3.4 0.2 - - - -
129B PHE* 1.3 76.2 - - - +
131B ARG* 1.3 73.3 + - + +
133B ALA* 3.2 7.3 + - - +
134B VAL* 3.2 34.0 + - + +
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B THR 3.4 12.2 + - - +
128B ILE* 3.3 6.9 + - - +
130B TYR* 1.3 87.1 - - + +
132B ALA* 1.3 58.8 + - - +
134B VAL* 3.3 27.5 + - - +
135B ARG* 2.9 27.6 + - - +
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Residues in contact with ALA 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS 5.6 0.2 - - - +
63B ASP* 5.5 1.6 - - - +
67B ILE* 3.5 27.8 - - + -
68B PHE* 3.6 18.7 - - + -
128B ILE* 2.9 18.8 + - + +
129B PHE 3.6 5.2 - - - +
130B TYR 3.3 0.2 - - - -
131B ARG* 1.3 77.0 - - - +
133B ALA* 1.3 55.8 + - - +
135B ARG* 3.3 9.0 + - - +
136B LEU* 3.2 23.4 + - - +
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Residues in contact with ALA 133 (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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68B PHE* 3.5 9.8 - - + -
116B VAL* 3.6 21.8 - - + +
119B CYS* 3.6 31.9 - - + -
120B LEU* 4.0 8.5 - - + -
129B PHE 3.2 8.2 + - - +
130B TYR 3.2 9.1 + - - +
132B ALA* 1.3 72.5 - - - +
134B VAL* 1.3 63.2 + - - +
136B LEU* 3.3 7.7 + - - +
137B ARG* 3.0 23.0 + - - +
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Residues in contact with VAL 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 4.4 13.2 - - + -
130B TYR* 3.2 28.6 + - + +
131B ARG* 3.3 35.4 + - - +
133B ALA* 1.3 74.0 - - - +
135B ARG* 1.3 60.5 + - - +
137B ARG* 3.3 31.0 + - - +
138B GLU* 3.3 29.8 + - + +
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS 4.6 8.7 - - - +
131B ARG* 2.9 13.8 + - + +
132B ALA* 3.4 13.5 - - - +
133B ALA 3.3 0.2 - - - -
134B VAL* 1.3 75.0 - - - +
136B LEU* 1.3 57.8 + - - +
138B GLU* 3.3 23.1 + - - +
139B GLN* 2.9 76.1 + - - +
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU 4.3 4.9 - - - +
62B LYS* 3.6 41.3 - - + +
63B ASP* 4.2 5.4 - - + +
68B PHE* 3.3 42.4 - - + -
90B PHE* 4.1 11.2 - - + -
112B PHE* 3.5 30.4 - - + -
115B ILE* 5.1 3.4 - - + -
116B VAL* 4.0 11.4 - - + -
132B ALA 3.2 13.1 + - - +
133B ALA 3.3 8.5 + - - +
135B ARG* 1.3 73.5 - - - +
137B ARG* 1.3 62.3 + - - +
140B GLY* 3.1 23.2 + - - +
141B GLY 3.4 5.0 + - - -
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 4.8 3.4 - - - -
113B ASN* 5.6 5.8 - - - +
116B VAL* 4.0 25.1 - - + +
120B LEU* 5.0 9.8 - - - +
133B ALA 3.0 13.9 + - - +
134B VAL* 3.3 32.5 + - - +
136B LEU* 1.3 75.3 - - - +
138B GLU* 1.3 80.0 + - - +
141B GLY* 3.8 12.3 - - - -
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 3.3 23.4 + - + +
135B ARG* 3.8 24.2 + - - +
136B LEU 3.2 0.2 - - - -
137B ARG* 1.3 100.9 + - + +
139B GLN* 1.3 67.4 + - + +
140B GLY 3.6 0.2 - - - -
141B GLY* 3.3 9.2 + - - -
142B ALA* 3.5 10.7 + - - +
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Residues in contact with GLN 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 3.8 33.3 + - + +
135B ARG* 2.9 67.9 + - - +
138B GLU* 1.3 74.6 - - + +
140B GLY* 1.3 59.5 + - - +
142B ALA* 3.5 20.4 + - - +
143B VAL* 3.7 8.5 - - - +
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 3.5 28.3 - - - +
62B LYS* 3.9 8.8 - - - +
112B PHE* 4.3 5.4 - - - -
136B LEU 3.1 14.3 + - - -
139B GLN* 1.3 73.7 - - - +
141B GLY* 1.3 62.6 + - - +
142B ALA 3.3 0.9 - - - -
143B VAL* 3.2 19.0 + - - +
144B LEU* 3.2 15.4 + - - +
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Residues in contact with GLY 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 4.5 2.2 - - - -
136B LEU 3.4 6.5 + - - -
137B ARG 3.8 12.3 - - - -
138B GLU 3.3 8.0 + - - -
139B GLN 3.3 1.8 - - - -
140B GLY* 1.3 76.7 - - - +
142B ALA* 1.3 58.5 + - - +
144B LEU* 3.7 10.1 + - - +
145B ARG* 3.3 40.0 + - - -
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Residues in contact with ALA 142 (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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138B GLU 3.5 7.8 + - - +
139B GLN* 3.5 13.1 + - - +
140B GLY 3.3 0.2 - - - -
141B GLY* 1.3 74.4 - - - +
143B VAL* 1.3 64.2 + - + +
145B ARG* 3.0 18.5 + - - +
146B GLN* 3.0 20.1 + - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 4.1 6.1 - - + -
58B GLN* 3.6 24.2 - - + +
59B LEU* 3.7 23.1 - - + -
62B LYS* 3.9 25.1 - - + -
139B GLN 3.7 6.7 - - - +
140B GLY* 3.2 24.8 + - - +
142B ALA* 1.3 76.6 - - + +
144B LEU* 1.3 57.4 + - - +
146B GLN* 3.2 29.9 - - - +
147B ALA* 3.1 25.5 - - - +
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Residues in contact with LEU 144 (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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55B THR* 4.6 0.7 - - + -
59B LEU* 4.1 14.8 - - + -
105B PHE* 3.3 15.5 - - + -
108B PHE* 3.7 37.0 - - + +
109B GLU* 4.1 35.9 - - + +
112B PHE* 3.6 37.7 - - + -
113B ASN* 5.0 1.8 - - - +
140B GLY 3.2 13.3 + - - +
141B GLY* 4.0 9.0 - - - +
142B ALA 3.3 0.2 - - - -
143B VAL* 1.3 77.4 - - - +
145B ARG* 1.3 58.5 + - - +
148B ARG* 3.0 31.4 + - - +
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Residues in contact with ARG 145 (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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109B GLU* 4.9 15.8 + - - -
141B GLY* 3.3 30.3 + - - +
142B ALA* 3.0 12.4 + - - +
144B LEU* 1.3 74.5 - - - +
146B GLN* 1.3 65.3 + - - +
147B ALA 3.1 2.8 + - - -
148B ARG* 3.4 27.7 + - - +
149B ARG* 3.5 14.6 + - - +
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Residues in contact with GLN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLN* 4.7 15.2 - - - +
142B ALA* 3.0 11.4 + - - +
143B VAL* 3.2 47.0 + - - +
145B ARG* 1.3 74.2 - - - +
147B ALA* 1.3 59.8 + - + +
149B ARG* 2.8 40.6 + - - +
150B GLN* 3.9 2.3 - - - +
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Residues in contact with ALA 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 4.6 5.5 - - - +
55B THR* 3.4 34.1 - - + +
105B PHE* 3.8 11.6 - - + -
143B VAL 3.1 19.0 + - - +
145B ARG 3.1 0.6 - - - -
146B GLN* 1.3 82.0 - - + +
148B ARG* 1.3 62.2 + - - +
149B ARG 3.3 1.6 - - - -
150B GLN* 3.3 29.5 + - - +
151B ALA 4.0 1.6 + - - -
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B PHE* 3.6 35.7 - - + -
109B GLU* 5.2 7.2 - - - -
144B LEU 3.0 19.7 + - - +
145B ARG* 3.4 20.4 + - - +
147B ALA* 1.3 75.1 - - - +
149B ARG* 1.3 60.2 + - - +
151B ALA* 3.0 21.9 + - + +
152B GLU* 3.1 37.0 + - + +
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Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ARG 3.5 7.2 + - - +
146B GLN* 2.8 34.1 + - - +
148B ARG* 1.3 83.2 - - - +
150B GLN* 1.3 81.8 + - - +
151B ALA 3.3 0.2 - - - -
152B GLU* 3.9 11.6 - - + +
153B LYS* 3.2 29.8 + - - +
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Residues in contact with GLN 150 (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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51B LEU* 3.8 34.2 + - + +
55B THR* 5.1 2.4 + - - -
146B GLN 3.9 2.7 + - - +
147B ALA* 3.5 25.0 + - - +
148B ARG 3.1 1.0 + - - -
149B ARG* 1.3 111.6 + - - +
151B ALA* 1.3 57.6 + - - +
153B LYS* 3.4 21.6 - - - +
154B MET* 3.7 15.2 - - - +
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Residues in contact with ALA 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PHE* 3.7 35.0 - - + -
51B LEU* 3.7 9.0 - - + +
105B PHE* 5.0 6.1 - - + -
147B ALA 4.9 0.2 - - - +
148B ARG* 3.0 13.6 + - + +
150B GLN* 1.3 76.1 - - - +
152B GLU* 1.3 63.2 + - + +
153B LYS 3.3 1.6 - - - -
154B MET* 3.2 13.1 + - - +
155B GLY* 2.9 25.5 + - - -
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Residues in contact with GLU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ARG* 3.1 50.0 + - + +
149B ARG* 3.7 7.6 + - - +
151B ALA* 1.3 77.2 - - + +
153B LYS* 1.3 60.2 + - - +
154B MET 3.3 1.0 + - - -
155B GLY* 4.0 4.1 - - - +
156B SER* 3.4 28.2 + - - +
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Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ARG 3.2 16.4 + - - +
150B GLN* 3.4 26.2 - - - +
152B GLU* 1.3 75.3 - - - +
154B MET* 1.3 66.6 + - + +
156B SER* 4.6 3.6 + - - -
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Residues in contact with MET 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY* 4.2 5.2 - - - -
48B PHE* 3.7 40.8 - - + +
51B LEU* 4.0 5.6 - - + -
150B GLN 3.7 20.2 - - - +
151B ALA* 3.3 17.9 - - - +
153B LYS* 1.3 84.5 - - + +
155B GLY* 1.3 61.5 + - - +
156B SER* 3.3 4.8 + - - -
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Residues in contact with GLY 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ALA 2.9 15.1 + - - -
152B GLU* 3.4 6.4 + - - -
154B MET* 1.3 75.1 - - - +
156B SER* 1.3 71.9 + - - +
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B GLU* 3.4 18.1 + - - +
153B LYS 5.2 3.6 - - - -
154B MET* 3.3 7.0 - - - +
155B GLY* 1.3 83.3 - - - +
157B GLY* 1.3 66.7 + - - +
158B PRO 4.9 1.7 - - - +
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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