Contacts of the helix formed by residues 125 - 156 (chain A) in PDB entry 1T7S
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 GLU 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 1.3 99.2 - - + +
126A LYS* 1.3 65.8 + - - +
127A PRO* 3.3 10.8 - - + -
128A LYS* 3.0 33.1 + - + +
129A GLN* 3.1 9.1 + - - +
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU 3.9 0.2 - - - -
125A GLU* 1.3 71.5 - - - +
127A PRO* 1.3 70.0 - - + +
129A GLN* 3.1 26.0 + - + +
130A VAL* 3.1 28.6 + - + +
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Residues in contact with PRO 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 3.3 11.9 - - + -
126A LYS* 1.3 95.3 - - + +
128A LYS* 1.3 61.3 + - + +
130A VAL* 3.5 9.2 + - + +
131A GLU* 3.2 32.3 + - - +
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Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU 5.0 1.3 - - - +
125A GLU* 3.0 27.3 + - + +
127A PRO* 1.3 79.1 - - + +
129A GLN* 1.3 60.9 + - + +
131A GLU* 3.5 12.9 + - + +
132A MSE 3.0 37.7 + - + +
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Residues in contact with GLN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.2 41.7 + - + +
122A GLY* 3.0 41.3 - - - +
123A PHE 3.5 5.4 + - - +
124A LEU 3.5 12.6 + - - +
125A GLU 3.1 13.4 + - - +
126A LYS* 3.1 18.3 + - + +
128A LYS* 1.3 76.2 - - + +
130A VAL* 1.3 60.3 + - + +
132A MSE 3.0 6.6 + - - +
133A GLY* 2.8 26.7 + - - -
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LYS* 3.1 28.4 + - + +
127A PRO* 3.7 9.4 - - + +
129A GLN* 1.3 76.8 - - + +
131A GLU* 1.3 62.9 + - + +
133A GLY* 3.4 2.5 + - - +
134A LYS* 3.1 40.1 + - + +
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Residues in contact with GLU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PRO* 3.2 18.3 + - - +
128A LYS* 3.7 14.2 - - - +
130A VAL* 1.3 74.9 - - + +
132A MSE 1.3 64.5 + - + +
134A LYS* 3.1 22.4 - - - +
135A LYS* 3.1 23.2 + - - +
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Residues in contact with MSE 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASP* 4.8 13.0 - - + +
119A LEU* 4.5 11.4 - - + -
128A LYS* 3.0 28.8 + - + +
129A GLN* 3.0 13.5 + - - +
131A GLU* 1.3 73.5 - - - +
133A GLY* 1.3 67.0 + - - +
134A LYS 3.0 1.4 + - - -
135A LYS* 3.0 20.6 + - + +
136A LEU* 2.9 55.1 + - + +
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Residues in contact with GLY 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.8 20.5 - - - +
129A GLN 2.8 17.4 + - - -
130A VAL* 3.9 2.2 - - - -
132A MSE 1.3 72.7 - - - +
134A LYS* 1.3 53.6 + - - +
136A LEU* 3.5 4.6 - - - +
137A GLU* 2.6 41.1 + - - +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.1 33.5 + - + +
131A GLU* 3.1 15.7 - - - +
132A MSE 3.0 0.2 - - - -
133A GLY* 1.3 76.6 - - - +
135A LYS* 1.3 66.1 + - + +
137A GLU* 3.1 18.6 + - - +
138A LYS* 2.9 23.6 + - - +
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Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A GLU* 3.3 22.2 - - - +
132A MSE 3.0 21.4 + - + +
134A LYS* 1.3 78.4 - - + +
136A LEU* 1.3 59.5 + - + +
138A LYS* 3.1 14.0 + - - +
139A LYS* 2.9 38.9 + - - +
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Residues in contact with LEU 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 4.5 11.7 - - + +
115A ASP* 3.8 42.2 - - + +
116A VAL* 3.8 28.7 - - + +
119A LEU* 4.3 15.0 - - + -
132A MSE 2.9 31.8 + - + +
133A GLY* 3.5 7.9 - - - +
135A LYS* 1.3 75.5 - - + +
137A GLU* 1.3 60.2 + - - +
139A LYS* 2.8 24.8 + - + +
140A VAL* 2.8 35.2 + - + +
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Residues in contact with GLU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLY 2.6 22.2 + - - +
134A LYS* 3.6 22.3 + - - +
136A LEU* 1.3 73.4 - - - +
138A LYS* 1.3 60.4 + - - +
140A VAL* 3.1 17.5 - - + +
141A LYS* 2.9 53.9 + - - +
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Residues in contact with LYS 138 (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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134A LYS 2.9 13.5 + - - +
135A LYS* 3.1 14.6 - - - +
137A GLU* 1.3 77.8 - - - +
139A LYS* 1.3 58.6 + - + +
141A LYS* 3.4 9.5 + - - +
142A TYR* 3.0 28.8 + - + +
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Residues in contact with LYS 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A LEU* 5.0 12.1 - - - +
112A ASN* 3.9 30.4 - - - +
115A ASP* 5.1 4.9 + - - -
135A LYS* 2.9 22.9 + - - +
136A LEU* 2.8 20.6 + - + +
138A LYS* 1.3 75.5 - - + +
140A VAL* 1.3 66.6 + - - +
142A TYR* 3.1 12.0 + - + +
143A PHE* 2.9 22.3 + - - +
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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
----------------------------------------------------------
112A ASN* 4.1 22.4 + - + +
116A VAL* 5.3 10.3 - - + -
136A LEU* 2.8 21.1 + - + +
137A GLU* 3.1 26.0 - - + +
139A LYS* 1.3 70.9 - - - +
141A LYS* 1.3 80.2 + - + +
143A PHE* 3.0 12.9 - - - +
144A ASN* 2.9 21.7 + - - +
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 2.9 58.0 + - + +
138A LYS* 3.5 7.2 - - - +
139A LYS 3.2 0.4 - - - -
140A VAL* 1.3 86.8 - - + +
142A TYR* 1.3 63.3 + - - +
144A ASN* 3.0 19.3 + - - +
145A GLU* 3.1 18.7 + - + +
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Residues in contact with TYR 142 (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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138A LYS* 3.0 16.0 + - + +
139A LYS* 3.4 13.2 - - + +
141A LYS* 1.3 74.6 - - - +
143A PHE* 1.3 66.2 + - - +
145A GLU* 2.9 24.9 + - + +
146A GLU* 3.0 47.0 + - + +
149A ARG* 6.3 0.2 - - - -
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Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 2.9 55.4 - - + +
108A ALA* 3.8 17.7 - - + -
109A TYR* 3.7 28.0 - + + -
112A ASN* 5.0 5.8 - - - +
139A LYS 2.9 12.6 + - - +
140A VAL* 3.0 17.9 - - - +
142A TYR* 1.3 80.2 - - - +
144A ASN* 1.3 60.5 + - + +
146A GLU* 3.0 8.9 + - - +
147A ALA* 2.9 40.5 + - + +
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Residues in contact with ASN 144 (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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140A VAL 2.9 11.0 + - - +
141A LYS* 3.2 14.1 - - - +
143A PHE* 1.3 81.3 - - + +
145A GLU* 1.3 74.2 + - - +
147A ALA* 4.0 4.7 - - - +
148A GLU* 3.1 47.6 + - - +
114B ARG* 3.2 29.7 - - - +
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Residues in contact with GLU 145 (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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141A LYS* 3.4 15.7 - - + +
142A TYR* 2.9 18.8 + - + +
144A ASN* 1.3 88.2 - - - +
146A GLU* 1.3 69.1 + - - +
148A GLU* 3.5 10.1 + - - +
149A ARG* 3.0 37.2 + - - +
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Residues in contact with GLU 146 (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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101A ASN* 5.1 1.7 + - - -
105A LEU* 4.0 16.5 - - + +
142A TYR* 3.0 54.3 + - + +
143A PHE* 3.4 8.1 - - - +
145A GLU* 1.3 75.1 - - - +
147A ALA* 1.3 66.1 + - - +
149A ARG* 2.6 42.4 + - - +
150A HIS* 3.0 35.9 + - + -
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.1 22.8 - - + +
143A PHE* 2.9 31.0 + - + +
144A ASN* 4.0 7.4 - - - +
146A GLU* 1.3 72.4 - - - +
148A GLU* 1.3 62.7 + - + +
150A HIS* 3.4 3.7 + - - +
151A LEU* 3.1 23.3 + - - +
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Residues in contact with GLU 148 (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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144A ASN* 3.1 35.3 + - - +
145A GLU* 3.9 9.5 - - - +
147A ALA* 1.3 78.1 - - + +
149A ARG* 1.3 61.6 + - - +
151A LEU* 3.3 11.3 + - + +
152A GLU* 2.9 36.0 + - - +
114B ARG* 2.5 33.6 + - - +
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Residues in contact with ARG 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLU* 3.0 23.6 + - - +
146A GLU* 2.6 50.4 + - - +
148A GLU* 1.3 74.7 - - - +
150A HIS* 1.3 74.6 + - + +
152A GLU* 3.1 11.7 + - + +
153A THR* 3.0 26.3 + - - +
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Residues in contact with HIS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 4.3 13.4 - + - -
98A GLU* 3.4 26.5 + - - +
101A ASN* 2.7 45.0 + - - +
105A LEU* 4.3 9.4 - - + +
146A GLU* 3.0 48.9 + - + +
147A ALA* 3.8 7.0 - - - +
149A ARG* 1.3 83.2 + - + +
151A LEU* 1.3 60.0 + - - +
153A THR* 3.0 11.5 + - - -
154A LEU* 3.0 31.3 + - + +
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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
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147A ALA 3.1 17.8 + - - +
148A GLU* 3.7 10.1 - - + +
150A HIS* 1.3 73.4 - - - +
152A GLU* 1.3 66.9 + - - +
154A LEU* 3.4 19.8 + - + +
155A ASP* 3.1 46.3 + - - +
121B ARG* 3.8 21.5 - - - +
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Residues in contact with GLU 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS 5.2 4.6 - - - +
148A GLU* 2.9 20.2 + - - +
149A ARG* 3.2 14.6 - - - +
151A LEU* 1.3 78.3 - - - +
153A THR* 1.3 62.0 + - - +
155A ASP* 3.4 6.3 + - - +
156A GLY* 3.2 19.2 + - - -
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Residues in contact with THR 153 (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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79A MSE 5.0 17.8 - - + -
82A LYS 5.7 3.8 - - - -
84A ALA* 5.4 0.9 - - - +
94A LEU* 5.3 4.7 - - + -
98A GLU* 3.7 23.2 + - + +
149A ARG* 3.0 17.4 + - - +
150A HIS* 3.0 14.3 + - - -
152A GLU* 1.3 74.5 - - - +
154A LEU* 1.3 68.1 + - - +
156A GLY 3.1 13.3 + - - -
157A MSE 3.5 20.7 + - + +
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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
----------------------------------------------------------
95A MSE 3.5 34.1 - - + -
98A GLU* 3.7 24.9 - - + +
150A HIS* 3.0 19.1 + - + +
151A LEU* 3.4 21.1 + - + +
153A THR* 1.3 76.6 - - - +
155A ASP* 1.3 65.3 + - - +
157A MSE 3.5 19.8 + - - +
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Residues in contact with ASP 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 25.0 + - - +
152A GLU* 3.8 6.7 - - - +
153A THR 3.1 1.0 - - - -
154A LEU* 1.3 80.4 - - - +
156A GLY* 1.3 56.7 + - - +
157A MSE 3.3 3.3 + - - +
158A ASN* 5.1 3.5 + - - -
121B ARG* 2.5 48.1 + - - -
123B PHE* 3.9 23.9 - - + -
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Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS 4.4 4.2 - - - +
83A ASN* 3.4 26.0 - - - +
84A ALA* 2.6 34.7 + - - +
152A GLU 3.2 10.1 + - - -
153A THR 3.1 8.6 + - - -
155A ASP* 1.3 76.4 - - - +
157A MSE 1.3 54.4 + - - +
158A ASN* 3.9 2.0 - - - -
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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