Contacts of the helix formed by residues 125 - 155 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 1.3 75.0 - - + +
126B LYS* 1.3 66.3 + - - +
127B PRO* 3.6 17.0 - - + +
128B LYS* 2.7 61.7 + - - +
129B GLN 3.0 7.8 + - - -
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Residues in contact with LYS 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU 3.1 5.3 + - - -
125B GLU* 1.3 69.6 - - - +
127B PRO* 1.3 68.3 - - + +
129B GLN* 3.2 16.9 + - - +
130B VAL* 3.1 27.1 + - + +
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Residues in contact with PRO 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLU* 3.0 19.3 - - + +
126B LYS* 1.3 96.9 - - + +
128B LYS* 1.3 58.5 + - - +
130B VAL* 3.3 8.4 + - + +
131B GLU* 2.9 30.0 + - - +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 4.6 22.9 - - + +
125B GLU* 2.7 49.4 + - + +
127B PRO* 1.3 77.9 - - - +
129B GLN* 1.3 57.8 + - - +
131B GLU* 3.5 17.0 + - + +
132B MSE 3.0 32.6 + - + +
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Residues in contact with GLN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.7 34.9 - - + +
122B GLY* 3.4 37.6 + - - -
124B LEU* 2.5 46.3 + - + +
125B GLU 3.0 4.0 + - - -
126B LYS* 3.3 21.5 - - - +
128B LYS* 1.3 76.0 - - - +
130B VAL* 1.3 60.0 + - + +
132B MSE 3.5 0.2 + - - -
133B GLY* 2.8 25.3 + - - -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LYS* 3.1 13.8 + - + +
127B PRO* 3.3 9.8 + - + +
129B GLN* 1.3 74.1 - - + +
131B GLU* 1.3 62.3 + - - +
133B GLY* 3.6 2.3 - - - +
134B LYS* 2.8 31.2 + - + +
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PRO* 2.9 17.3 + - - +
128B LYS* 3.5 18.5 - - + +
130B VAL* 1.3 79.0 - - - +
132B MSE 1.3 60.3 + - - +
134B LYS* 3.2 8.3 - - - +
135B LYS* 3.1 20.1 + - - +
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Residues in contact with MSE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ASP* 4.0 27.1 - - + +
118B ASP* 5.6 5.8 - - - +
119B LEU* 3.6 29.2 - - + -
124B LEU* 6.3 3.8 - - + -
128B LYS* 3.0 22.3 + - + +
131B GLU* 1.3 72.3 - - - +
133B GLY* 1.3 53.8 + - - +
134B LYS 2.9 1.3 - - - -
135B LYS* 2.7 28.5 + - + -
136B LEU* 2.7 60.5 + - + +
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Residues in contact with GLY 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 4.5 9.8 - - - +
129B GLN 2.8 17.6 + - - -
130B VAL* 3.3 3.1 + - - -
132B MSE 1.3 76.5 - - - +
134B LYS* 1.3 59.3 + - - +
136B LEU* 4.0 9.4 - - - +
137B GLU* 3.2 24.4 + - - +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 2.8 15.5 + - + +
131B GLU* 3.2 12.6 - - - +
133B GLY* 1.3 78.1 - - - +
135B LYS* 1.3 63.1 + - - +
137B GLU* 3.2 26.7 + - - +
138B LYS* 3.2 19.9 + - + +
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Residues in contact with LYS 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLU 3.1 8.8 + - - +
132B MSE 2.7 33.6 + - - +
134B LYS* 1.3 74.1 - - - +
136B LEU* 1.3 65.5 + - + +
138B LYS* 3.3 16.9 + - + +
139B LYS* 3.2 43.1 + - + +
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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
----------------------------------------------------------
112B ASN* 4.6 19.7 - - + +
115B ASP* 3.8 31.2 - - + +
116B VAL* 4.5 20.6 - - + +
119B LEU* 4.8 6.5 - - + -
132B MSE 2.7 70.7 + - + +
133B GLY* 4.0 8.5 - - - +
135B LYS* 1.3 73.9 - - + +
137B GLU* 1.3 58.4 + - - +
139B LYS* 3.0 14.0 + - + +
140B VAL* 2.8 33.6 + - + +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY 3.2 16.3 + - - +
134B LYS* 3.2 19.6 + - - +
136B LEU* 1.3 80.1 - - - +
138B LYS* 1.3 59.8 + - - +
140B VAL* 4.0 7.1 - - - +
141B LYS* 3.1 59.1 + - + +
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Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LYS* 3.2 19.3 + - + +
135B LYS* 3.5 14.8 - - + +
136B LEU 3.1 0.6 - - - -
137B GLU* 1.3 76.9 - - - +
139B LYS* 1.3 59.8 + - + +
141B LYS* 3.8 5.1 - - - +
142B TYR* 2.9 31.1 + - - +
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Residues in contact with LYS 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN* 3.7 30.9 + - - +
115B ASP* 5.9 0.8 + - - -
135B LYS* 3.2 46.7 - - + +
136B LEU* 3.2 14.7 - - + +
138B LYS* 1.3 75.6 - - + +
140B VAL* 1.3 59.7 + - - +
142B TYR* 3.3 13.0 + - + +
143B PHE* 2.9 29.5 + - - +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ASN* 4.4 18.6 - - + +
116B VAL* 5.3 9.4 - - + -
136B LEU* 2.8 28.4 + - + +
137B GLU* 4.0 7.6 - - + +
138B LYS 3.4 0.2 - - - -
139B LYS* 1.3 72.8 - - - +
141B LYS* 1.3 66.0 + - + +
143B PHE* 3.3 10.1 + - - +
144B ASN* 3.2 18.0 + - - +
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 3.1 50.2 + - + +
138B LYS* 3.8 5.6 - - - +
140B VAL* 1.3 75.3 - - + +
142B TYR* 1.3 67.2 + - - +
144B ASN* 2.9 24.6 + - - +
145B GLU* 3.2 14.5 + - - +
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Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS* 2.9 19.1 + - - +
139B LYS* 3.5 13.5 - - + +
141B LYS* 1.3 74.9 - - - +
143B PHE* 1.3 61.2 + - - +
145B GLU* 2.9 29.8 + - + +
146B GLU* 2.9 66.8 + - + +
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Residues in contact with PHE 143 (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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105B LEU* 3.1 59.5 - - + -
108B ALA* 3.6 21.1 - - + -
109B TYR* 3.8 22.7 - + + -
112B ASN* 5.0 7.2 - - - +
139B LYS 2.9 13.9 + - - +
140B VAL* 3.3 13.9 - - - +
142B TYR* 1.3 80.4 - - - +
144B ASN* 1.3 59.6 + - - +
146B GLU* 3.7 5.5 - - - +
147B ALA* 2.9 38.4 + - + +
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Residues in contact with ASN 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL 3.2 8.6 + - - +
141B LYS* 2.9 16.7 + - - +
143B PHE* 1.3 82.7 - - - +
145B GLU* 1.3 56.5 + - + +
147B ALA* 4.0 3.7 - - - +
148B GLU* 3.0 45.9 + - - +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B LYS* 3.2 12.5 + - - +
142B TYR* 2.9 30.7 + - + +
144B ASN* 1.3 76.2 - - + +
146B GLU* 1.3 68.4 + - - +
148B GLU* 3.0 9.6 + - - +
149B ARG* 3.0 21.8 + - - +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 5.6 2.1 + - - -
105B LEU* 4.4 15.3 - - + -
142B TYR* 2.9 60.1 + - + +
143B PHE* 3.7 9.0 - - - +
145B GLU* 1.3 72.9 - - - +
147B ALA* 1.3 66.6 + - - +
149B ARG* 3.0 51.3 + - - +
150B HIS* 3.1 17.2 + - + -
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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
----------------------------------------------------------
105B LEU* 4.2 24.1 - - + +
143B PHE* 2.9 30.7 + - + +
144B ASN* 4.0 4.3 - - - +
146B GLU* 1.3 78.1 - - - +
148B GLU* 1.3 64.1 + - - +
149B ARG 2.9 1.4 + - - -
150B HIS* 3.2 4.5 + - - +
151B LEU* 3.1 22.5 + - + +
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Residues in contact with GLU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASN* 3.0 35.8 + - - +
145B GLU* 3.0 8.7 + - - +
147B ALA* 1.3 77.5 - - - +
149B ARG* 1.3 64.8 + - - +
151B LEU* 3.2 23.4 - - - +
152B GLU* 3.1 27.7 + - + +
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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
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97B TYR* 4.1 18.2 + - - -
101B ASN* 5.3 1.2 - - - +
145B GLU 3.0 10.2 + - - +
146B GLU* 3.0 36.7 + - - +
147B ALA 2.9 0.4 + - - -
148B GLU* 1.3 74.9 - - - +
150B HIS* 1.3 81.0 + - - +
152B GLU* 2.7 40.1 + - - +
153B THR* 3.1 11.6 + - - +
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Residues in contact with HIS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B TYR* 4.5 2.5 + + - -
98B GLU* 3.2 29.5 - - - +
101B ASN* 2.7 51.1 + - + -
105B LEU* 5.5 9.7 - - + +
146B GLU* 3.1 20.3 + - + -
147B ALA* 3.2 6.7 + - - +
149B ARG* 1.3 114.9 + - + +
151B LEU* 1.3 56.4 - - - +
152B GLU 3.1 0.2 - - - -
153B THR* 3.3 8.5 + - - -
154B LEU* 2.9 37.8 + - + +
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Residues in contact with LEU 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 3.1 12.1 + - + +
148B GLU* 3.2 30.5 - - - +
149B ARG 2.9 0.6 + - - -
150B HIS* 1.3 78.1 - - - +
152B GLU* 1.3 57.6 + - + +
154B LEU* 3.5 12.2 + - + +
155B ASP* 3.0 48.0 + - - +
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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
----------------------------------------------------------
82B LYS* 4.1 32.4 - - + +
148B GLU* 3.1 20.1 + - + +
149B ARG* 2.7 13.7 + - - +
151B LEU* 1.3 75.8 - - + +
153B THR* 1.3 66.2 + - - +
155B ASP* 3.2 14.7 + - - +
156B GLY* 3.3 12.5 + - - -
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Residues in contact with THR 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MSE 4.8 19.1 - - + -
81B GLY 5.2 3.0 + - - +
82B LYS* 3.9 18.6 + - - +
84B ALA* 5.5 3.8 - - + +
94B LEU* 5.4 0.9 - - + -
98B GLU* 4.2 14.4 - - + +
149B ARG* 3.1 14.8 + - - +
150B HIS* 3.3 15.2 + - - -
152B GLU* 1.3 80.4 - - - +
154B LEU* 1.3 61.7 + - - +
156B GLY 3.7 5.9 + - - +
157B MSE 3.6 33.9 - - + +
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B MSE 4.5 20.9 - - + -
98B GLU* 3.3 38.4 - - + +
150B HIS* 2.9 23.9 + - + +
151B LEU* 4.0 13.5 - - + +
153B THR* 1.3 77.9 - - - +
155B ASP* 1.3 62.9 + - - +
156B GLY 3.1 6.6 + - - -
157B MSE 3.9 20.6 + - + +
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Residues in contact with ASP 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.0 35.7 + - - +
152B GLU* 3.2 7.9 + - - +
154B LEU* 1.3 80.0 - - - +
156B GLY* 1.3 55.3 + - - +
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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