Contacts of the helix formed by residues 114 - 143 (chain B) in PDB entry 1TKP
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 ASP 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ASN* 4.8 11.2 + - - +
8A ARG* 3.8 26.1 - - + +
113B TYR* 1.3 75.3 - - - +
115B ILE* 1.3 65.9 + - + +
116B ARG* 3.1 22.2 + - - +
117B THR* 3.1 23.0 + - - -
118B SER* 2.8 23.6 + - - -
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Residues in contact with ILE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 5.1 1.0 - - - +
51B HIS* 5.0 3.4 - - + +
55B VAL* 3.1 41.7 - - + -
56B GLU 4.8 11.4 - - - +
59B GLU* 5.2 8.5 - - - +
63B LEU* 3.9 17.0 - - + -
67B LEU* 4.5 7.0 - - + -
114B ASP* 1.3 75.6 - - + +
116B ARG* 1.3 68.3 + - + +
118B SER* 3.3 9.4 + - - -
119B LEU* 2.9 54.7 + - + +
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 3.1 9.9 + - - +
115B ILE* 1.3 85.1 - - + +
117B THR* 1.3 56.9 + - - +
119B LEU* 3.6 1.3 + - + -
120B ALA* 3.0 29.5 + - - +
169B TYR 4.2 5.9 + - - -
170B LEU* 3.1 62.4 + - + +
171B GLU 4.8 4.2 + - - -
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Residues in contact with THR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 3.6 28.5 - - + -
114B ASP* 3.1 27.9 + - - -
116B ARG* 1.3 73.9 - - - +
118B SER* 1.3 68.5 + - - +
120B ALA* 3.3 5.5 + - - +
121B ASN* 2.8 40.1 + - - +
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B HIS* 3.2 42.2 + - - -
108B GLU* 3.6 11.4 - - - -
112B VAL* 5.7 0.2 - - - +
113B TYR* 3.0 22.9 + - - +
114B ASP 2.8 22.0 + - - -
115B ILE* 3.5 13.6 - - - +
117B THR* 1.3 77.9 - - - +
119B LEU* 1.3 61.2 + - - +
121B ASN* 3.4 1.4 + - - +
122B ASP* 3.1 17.3 + - - -
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B HIS* 5.2 0.2 - - - +
63B LEU* 3.9 17.9 - - + -
66B PHE* 6.2 0.2 - - + -
67B LEU* 4.4 19.5 - - + -
115B ILE* 2.9 46.2 + - + +
116B ARG* 3.8 4.9 - - + +
118B SER* 1.3 74.9 - - - +
120B ALA* 1.4 53.1 + - - +
122B ASP* 3.2 15.5 + - - +
123B MET* 2.8 34.1 + - - +
166B ILE* 3.6 17.8 - - + +
169B TYR* 3.8 29.6 - - + -
170B LEU* 4.1 17.9 - - + -
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG 3.0 19.0 + - - +
117B THR* 3.8 5.2 - - - +
119B LEU* 1.4 71.6 - - - +
121B ASN* 1.3 68.3 + - - +
123B MET* 3.2 11.9 + - + +
124B ALA* 3.0 22.5 + - - +
170B LEU* 3.7 17.4 - - + +
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Residues in contact with ASN 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 3.8 10.3 - - - +
108B GLU* 2.6 43.4 + - + +
113B TYR* 5.1 2.0 - - - -
117B THR* 2.8 33.7 + - - +
118B SER 3.5 2.7 - - - +
120B ALA* 1.3 74.2 - - - +
122B ASP* 1.3 61.3 + - - +
124B ALA* 3.3 8.1 + - - +
125B ILE* 3.2 25.1 + - - +
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 4.3 2.0 - - + +
47B GLN* 2.8 32.2 + - - +
48B LEU* 3.9 23.7 - - + +
51B HIS* 2.4 33.8 + - - +
67B LEU* 4.2 5.4 - - - +
118B SER 3.1 9.1 + - - +
119B LEU* 3.2 11.3 + - - +
121B ASN* 1.3 71.1 - - - +
123B MET* 1.3 66.2 + - - +
125B ILE* 3.3 9.8 - - - +
126B TYR* 2.9 28.7 + - + -
166B ILE* 3.7 15.5 - - + -
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Residues in contact with MET 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU 2.8 15.1 + - - +
120B ALA* 3.2 12.8 + - + +
122B ASP* 1.3 76.3 - - - +
124B ALA* 1.3 63.3 + - - +
126B TYR* 3.2 9.6 + - - +
127B GLY* 3.0 20.4 + - - -
163B ALA* 4.3 15.0 - - + +
166B ILE* 3.9 10.5 - - + -
167B GLU* 4.1 39.0 - - + +
170B LEU* 3.8 20.9 - - + -
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASP* 6.2 0.2 - - - +
120B ALA 3.0 11.9 + - - +
121B ASN* 3.4 11.9 - - - +
123B MET* 1.3 76.2 - - - +
125B ILE* 1.3 62.7 + - + +
127B GLY* 3.1 11.1 + - - -
128B ASP* 3.2 22.9 + - - +
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Residues in contact with ILE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.9 2.9 - - + -
44B LEU* 3.6 35.4 - - + -
47B GLN* 3.4 39.9 - - + +
105B VAL* 4.0 32.5 - - + -
106B ASP* 3.5 25.4 - - + +
107B VAL* 5.1 0.4 - - - -
121B ASN 3.2 10.0 + - - +
122B ASP* 3.3 10.1 - - - +
124B ALA* 1.3 72.3 - - + +
126B TYR* 1.3 67.7 + - - +
127B GLY 3.1 0.3 + - - -
128B ASP* 3.1 4.2 + - - +
129B ILE* 2.9 27.0 + - + +
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Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.7 33.0 - - + -
48B LEU* 3.3 25.1 - - + +
70B ALA* 3.6 8.7 + - - +
74B ALA* 5.7 0.2 - - - +
122B ASP 2.9 31.5 + - - -
123B MET* 3.2 8.7 + - - +
125B ILE* 1.3 75.2 - - - +
127B GLY* 1.3 58.5 + - - +
129B ILE* 3.2 6.0 + - - +
130B ILE* 2.7 36.0 + - + +
159B LEU* 3.5 43.7 - - + -
162B ASP* 3.3 24.3 + - + +
163B ALA* 3.7 20.4 - - + -
166B ILE* 3.6 26.2 - - + -
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B MET 3.0 13.6 + - - -
124B ALA* 3.1 4.2 + - - -
125B ILE 3.1 0.4 - - - -
126B TYR* 1.3 76.5 - - - +
128B ASP* 1.3 63.9 + - - +
130B ILE* 3.1 10.8 + - - +
131B GLU* 3.1 31.8 + - - +
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Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ASN* 5.5 1.6 - - - +
104B SER* 5.1 6.0 + - - +
105B VAL* 3.9 26.4 - - + +
106B ASP* 5.3 2.6 + - - +
124B ALA* 3.5 16.9 - - - +
125B ILE 3.1 5.8 + - - +
127B GLY* 1.3 76.1 - - - +
129B ILE* 1.4 64.7 + - - +
131B GLU* 3.5 11.0 + - - +
132B ALA* 3.1 25.9 + - - +
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 5.7 3.8 - - - +
40B ASN* 3.8 39.5 - - + +
41B VAL* 3.8 26.9 - - + -
44B LEU* 4.1 10.8 - - + -
105B VAL* 4.1 5.4 - - + -
125B ILE* 2.9 29.0 + - + +
126B TYR* 3.6 4.0 - - - +
128B ASP* 1.4 75.8 - - - +
130B ILE* 1.3 63.0 + - - +
132B ALA* 3.8 5.1 - - - +
133B THR* 2.7 36.0 + - - +
159B LEU* 3.7 31.4 - - + -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B TYR* 2.7 31.6 + - + +
127B GLY* 3.1 8.5 + - - +
129B ILE* 1.3 75.8 - - - +
131B GLU* 1.3 59.2 + - + +
133B THR* 3.2 2.6 + - - -
134B ARG* 3.0 61.5 + - - +
156B LEU* 3.7 17.5 - - + +
159B LEU* 4.4 9.0 - - + +
160B GLU* 3.6 28.3 - - + +
163B ALA* 3.6 30.5 - - + -
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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 GLY 3.1 21.3 + - - +
128B ASP* 4.1 9.8 - - - +
129B ILE 3.3 0.2 - - - -
130B ILE* 1.3 73.2 - - + +
132B ALA* 1.3 66.9 + - - +
133B THR 3.1 1.5 + - - -
134B ARG* 3.3 26.7 + - - +
135B GLU* 3.0 32.5 + - - +
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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
----------------------------------------------------------
37B ASP* 4.1 14.8 - - - +
40B ASN* 5.3 7.0 - - - +
128B ASP 3.1 16.3 + - - +
129B ILE* 3.8 7.4 - - - +
131B GLU* 1.3 77.4 - - - +
133B THR* 1.3 58.5 + - - +
135B GLU* 2.9 19.1 + - - +
136B HIS* 2.9 40.2 + - + -
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Residues in contact with THR 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ASP* 4.0 9.9 + - - -
129B ILE* 2.7 34.9 + - - +
130B ILE 3.5 4.7 - - - -
131B GLU 3.1 0.6 - - - -
132B ALA* 1.3 73.4 - - - +
134B ARG* 1.3 58.8 + - - +
136B HIS* 3.3 8.2 + - - +
137B THR* 2.3 41.2 + - + +
152B LEU* 3.8 35.9 - - + +
156B LEU* 3.8 21.7 - - + +
159B LEU* 4.7 5.1 - - + +
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 3.0 33.8 + - - +
131B GLU* 3.4 24.4 + - - +
133B THR* 1.3 74.7 - - - +
135B GLU* 1.3 64.1 + - + +
137B THR* 3.3 14.0 + - - +
138B GLU* 3.2 28.2 + - - +
156B LEU* 4.0 14.0 - - + +
160B GLU* 3.0 32.5 + - - -
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Residues in contact with GLU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLU* 3.0 21.5 + - + +
132B ALA* 2.9 22.6 + - - +
134B ARG* 1.3 75.5 - - + +
136B HIS* 1.3 66.8 + - + +
138B GLU* 3.0 16.0 + - - +
139B LEU* 2.9 25.2 + - - +
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Residues in contact with HIS 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ALA* 3.3 42.4 + - + +
34B LEU* 5.7 0.2 - - + -
36B ALA* 4.9 5.6 - - + -
37B ASP* 3.0 37.8 + - - +
132B ALA* 2.9 24.7 + - + +
133B THR 3.3 3.8 + - - +
135B GLU* 1.3 81.4 + - + +
137B THR* 1.3 67.3 + - - +
139B LEU* 3.4 10.4 - - + +
140B ALA* 2.9 25.3 + - - +
152B LEU* 3.6 19.6 - - + +
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Residues in contact with THR 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B THR* 2.3 40.6 - - + +
134B ARG* 3.5 11.1 + - - +
135B GLU 3.1 0.2 - - - -
136B HIS* 1.3 78.7 - - - +
138B GLU* 1.3 62.5 + - - +
140B ALA* 3.9 2.5 - - - +
141B GLU* 2.9 27.5 + - - +
149B ALA* 4.0 9.4 - - - +
152B LEU* 3.9 27.6 - - + -
153B ARG* 3.8 22.6 + - + +
156B LEU* 4.8 7.4 - - + -
----------------------------------------------------------
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Residues in contact with GLU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ARG* 3.2 24.3 - - - +
135B GLU* 3.0 11.7 + - - +
137B THR* 1.3 80.9 - - - +
139B LEU* 1.3 57.9 + - - +
141B GLU* 3.3 4.6 + - - -
142B ASN* 2.9 43.8 + - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLN* 3.5 48.7 - - + +
30B CYS* 4.7 2.2 - - - +
33B ALA* 4.3 13.9 - - + -
135B GLU 2.9 12.5 + - - +
136B HIS* 3.4 14.8 - - + +
138B GLU* 1.3 75.3 - - - +
140B ALA* 1.3 64.3 + - - +
142B ASN* 3.0 12.1 + - + +
143B LEU* 2.9 31.8 + - + +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B CYS* 4.4 9.6 - - + -
136B HIS 2.9 18.9 + - - +
137B THR 3.9 0.2 - - - +
139B LEU* 1.3 72.9 - - - +
141B GLU* 1.3 63.6 + - - +
143B LEU 3.2 2.1 + - - +
144B GLY 3.2 2.6 + - - -
145B ASP* 2.9 45.5 + - + +
148B THR* 3.9 17.3 - - + -
149B ALA* 3.7 21.8 - - + +
152B LEU* 4.4 0.4 - - + -
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Residues in contact with GLU 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B THR 2.9 18.0 + - - +
138B GLU* 4.1 4.7 - - - +
140B ALA* 1.3 72.8 - - - +
142B ASN* 1.3 62.8 + - - +
144B GLY* 2.7 20.5 + - - +
145B ASP 4.6 1.1 - - - -
146B HIS* 3.2 40.3 + - + +
149B ALA* 3.3 12.5 - - + +
153B ARG* 2.7 45.1 + - - +
----------------------------------------------------------
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Residues in contact with ASN 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B GLU* 2.9 30.0 + - - +
139B LEU* 3.0 11.6 + - + +
141B GLU* 1.3 81.0 - - - +
143B LEU* 1.3 65.9 + - + +
144B GLY 3.2 0.9 + - - -
----------------------------------------------------------
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Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B MET* 6.0 0.2 - - - -
25B ASP* 6.1 0.2 - - - +
26B ARG* 2.9 54.7 + - + +
29B GLN* 3.3 46.0 - - + +
30B CYS* 3.5 31.2 - - - -
139B LEU* 2.9 29.8 + - + +
140B ALA 3.2 2.7 + - - +
142B ASN* 1.3 79.5 - - + +
144B GLY* 1.3 58.1 + - - +
145B ASP* 3.1 4.1 + - + +
----------------------------------------------------------
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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