Contacts of the helix formed by residues 118 - 142 (chain B) in PDB entry 1LK3
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 SER 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ASP* 2.5 32.7 + - - -
60B LEU 5.7 1.6 - - - -
63B GLN* 6.0 0.9 - - - -
64B ALA* 4.2 7.2 - - - -
67B GLU* 3.0 23.9 + - - -
117B LYS* 1.3 73.4 - - - +
119B LYS* 1.3 62.8 + - - +
120B ALA 3.0 8.7 + - - -
121B VAL* 3.1 12.8 + - - +
122B GLU* 2.9 29.5 + - - +
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 5.0 2.3 + - - +
117B LYS 3.9 2.0 + - - -
118B SER* 1.3 73.1 + - - +
120B ALA* 1.3 64.5 + - - +
122B GLU* 3.4 7.8 + - + +
123B GLN* 3.1 23.1 + - + +
125L ALA 5.4 5.2 - - - +
126L THR* 3.5 44.9 + - - +
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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
----------------------------------------------------------
51B SER* 4.2 13.9 - - - +
52B LEU* 4.4 9.8 - - + +
55B ASP* 3.3 38.2 + - + +
118B SER* 3.0 0.8 + - - -
119B LYS* 1.3 81.4 - - - +
121B VAL* 1.3 60.1 - - - +
123B GLN* 3.4 9.5 + - - +
124B VAL* 3.3 24.8 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.3 4.9 - - + -
55B ASP* 4.2 1.1 - - - +
64B ALA* 3.7 26.0 - - + +
67B GLU* 3.3 38.6 - - + +
68B MET* 4.1 25.4 - - + +
71B PHE* 5.5 0.2 - - + -
118B SER* 3.1 14.0 + - - +
120B ALA* 1.3 71.2 - - - +
122B GLU* 1.3 67.0 + - - +
123B GLN 3.0 2.0 - - - -
124B VAL* 2.8 18.7 + - - +
125B LYS* 2.9 34.2 + - + +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 4.6 5.2 - - - +
117B LYS* 4.2 36.7 + - + +
118B SER 2.9 23.6 + - - +
119B LYS* 3.4 7.8 + - - +
121B VAL* 1.3 77.4 - - - +
123B GLN* 1.3 56.7 + - - +
125B LYS* 3.4 29.8 + - - +
126B ASN* 2.9 44.5 + - - +
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LYS* 3.1 14.3 + - + +
120B ALA* 3.4 13.5 - - - +
121B VAL 3.0 0.8 - - - -
122B GLU* 1.3 79.1 - - - +
124B VAL* 1.3 57.2 + - + +
126B ASN* 4.7 11.7 - - - +
127B ALA* 3.1 27.3 + - + +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.5 38.7 - - + +
48B LEU* 4.3 11.0 - - + -
52B LEU* 4.3 24.7 - - + -
68B MET* 4.5 8.1 - - - -
71B PHE* 4.4 17.7 - - + -
120B ALA 3.3 14.3 + - - +
121B VAL* 2.8 11.2 + - - +
123B GLN* 1.3 76.7 - - + +
125B LYS* 1.3 60.4 + - + +
127B ALA* 3.1 6.3 + - - +
128B PHE* 2.8 28.6 + - - +
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Residues in contact with LYS 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B GLU* 4.9 11.0 + - - +
70B GLN* 5.3 5.9 + - - -
71B PHE* 4.0 35.4 - - + -
117B LYS* 6.2 0.8 - - - +
121B VAL* 2.9 33.5 + - + +
122B GLU* 3.8 31.2 + - - +
124B VAL* 1.3 79.1 - - + +
126B ASN* 1.3 57.7 + - - +
128B PHE* 3.4 4.6 + - - +
129B ASN* 3.0 36.3 + - - +
57I TYR* 3.4 31.8 + - + +
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B GLU* 2.9 32.0 + - - +
123B GLN* 4.1 12.5 - - - +
125B LYS* 1.3 75.9 - - - +
127B ALA* 1.3 63.9 + - - +
129B ASN* 3.7 13.6 - - - +
130B LYS* 3.2 24.1 + - - +
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Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.8 16.8 - - + +
123B GLN* 3.1 25.4 + - + +
124B VAL* 3.4 6.3 - - - +
126B ASN* 1.3 74.0 - - - +
128B PHE* 1.3 67.0 + - - +
130B LYS* 3.5 7.4 + - - +
131B LEU* 3.1 28.6 + - + +
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.7 12.8 - - + +
71B PHE* 3.7 29.2 - + + -
75B GLU* 4.5 4.0 - - + -
76B VAL* 4.0 22.9 - - + -
79B GLN* 3.7 27.1 - - - -
124B VAL 2.8 16.7 + - - +
125B LYS 3.6 2.0 - - - +
127B ALA* 1.3 75.5 - - - +
129B ASN* 1.3 82.5 + - - +
131B LEU* 3.0 17.4 + - - +
132B GLN* 3.1 13.3 + - - +
135B GLY* 3.4 35.2 - - - -
136B ILE* 3.8 15.5 - - + -
139B ALA* 4.2 8.3 - - + -
50I TYR* 4.6 4.9 - - - -
57I TYR* 4.0 3.1 - + - -
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Residues in contact with ASN 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LYS* 3.0 20.2 + - - +
126B ASN* 3.7 16.2 - - - +
127B ALA 3.4 0.2 - - - -
128B PHE* 1.3 83.8 - - - +
130B LYS* 1.3 57.9 + - - +
132B GLN* 3.0 23.6 + - - +
50I TYR* 4.6 0.8 + - - -
57I TYR* 2.7 35.6 + - - -
58I THR 3.4 17.0 - - - +
59I ASN* 3.3 43.8 + - - +
60I TYR 5.1 0.7 + - - +
93M GLY* 4.4 0.5 - - - -
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASN 3.2 14.6 + - - +
127B ALA* 3.6 8.1 - - - +
129B ASN* 1.3 80.7 - - - +
131B LEU* 1.3 57.8 + - + +
62I GLU* 4.7 17.7 + - - +
1M ASP* 2.9 33.9 + - - +
92M ASN* 4.6 0.9 - - - +
93M GLY* 2.9 49.2 + - - +
94M PRO* 3.8 3.4 - - + +
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Residues in contact with LEU 131 (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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45B ASN* 5.5 2.7 - - + +
47B LEU* 4.4 11.0 - - + -
127B ALA* 3.1 23.9 + - + +
128B PHE* 3.0 7.6 + - - +
130B LYS* 1.3 77.9 - - + +
132B GLN* 1.3 63.5 + - - +
134B LYS* 3.1 31.4 + - + +
135B GLY* 3.3 24.6 + - - +
138B LYS* 3.9 28.7 - - + -
91M TRP 2.9 21.8 - - - +
92M ASN* 3.9 2.2 - - - +
93M GLY 4.2 0.7 - - - -
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Residues in contact with GLN 132 (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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128B PHE* 3.1 8.3 + - - +
129B ASN* 3.0 13.9 + - - +
131B LEU* 1.3 79.2 - - - +
133B GLU* 1.3 65.4 + - - +
135B GLY* 2.9 19.8 + - - -
136B ILE* 3.3 10.2 + - - +
47I TRP* 3.9 12.0 - - - -
50I TYR* 4.1 8.7 - - - -
59I ASN* 3.6 21.3 + - - +
104I ASN* 3.6 28.0 + - - +
90M SER 3.4 15.0 - - - +
92M ASN 3.5 4.5 - - - +
93M GLY* 3.4 30.0 - - - +
95M LEU* 3.6 26.4 + - + +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLN* 4.8 0.7 - - - +
131B LEU 3.3 0.2 + - - -
132B GLN* 1.3 78.6 - - - +
134B LYS* 1.3 65.7 + - - +
136B ILE* 3.1 28.3 + - + +
137B TYR* 3.4 12.6 - - - -
102I GLY 3.2 19.3 - - - +
104I ASN* 2.8 45.3 + - - +
105I TRP* 3.8 1.8 - - - -
31M ARG* 2.7 33.5 + - - +
90M SER* 2.8 37.5 + - - +
91M TRP* 3.8 13.0 - - + -
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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
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39B MET* 3.7 7.3 - - + +
42B GLN* 2.9 40.8 - - - +
131B LEU* 3.1 27.5 + - + +
133B GLU* 1.3 77.1 - - - +
135B GLY* 1.3 56.7 + - - +
137B TYR* 3.2 3.6 + - - +
138B LYS* 2.9 36.4 + - + +
91M TRP* 3.2 53.8 + - + +
92M ASN* 4.5 6.9 + - - +
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Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 4.5 0.7 - - - +
128B PHE* 3.4 16.4 - - - -
131B LEU* 3.3 33.5 + - - +
132B GLN 2.9 8.4 + - - -
134B LYS* 1.3 77.1 - - - +
136B ILE* 1.3 58.5 + - - +
138B LYS* 3.9 1.9 - - - +
139B ALA* 2.9 32.7 + - - +
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Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 4.8 0.9 - - + -
76B VAL* 4.5 4.7 - - + +
79B GLN* 3.6 35.9 - - + +
80B ALA* 3.6 34.5 - - + +
83B GLN* 3.7 19.1 - - + +
128B PHE* 3.9 17.7 - - + -
132B GLN 3.3 6.5 + - - +
133B GLU* 3.1 27.7 + - + +
135B GLY* 1.3 75.5 - - - +
137B TYR* 1.3 66.7 + - + +
139B ALA* 4.1 1.1 - - - +
140B MET* 3.1 31.0 + - + +
102I GLY* 3.7 13.0 - - - -
104I ASN* 5.2 0.2 - - - +
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Residues in contact with TYR 137 (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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36B PHE* 3.6 43.6 - + - -
37B PHE* 3.8 32.8 - + - +
39B MET* 3.6 24.5 - - + -
83B GLN* 3.6 29.9 + - + +
133B GLU 3.4 13.9 - - - -
134B LYS 3.2 8.2 + - - +
136B ILE* 1.3 82.0 - - + +
138B LYS* 1.3 57.4 + - - +
140B MET* 3.3 2.1 + - - +
141B SER* 2.9 30.7 + - - -
31M ARG* 3.2 22.4 + - - -
91M TRP* 3.6 19.7 - + - -
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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
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39B MET* 3.9 6.8 - - + +
42B GLN* 3.9 22.4 + - - +
44B ASP* 4.8 4.2 - - - +
45B ASN* 3.4 43.2 + - - +
46B LEU* 5.9 0.4 - - - +
47B LEU* 4.3 8.3 - - + -
131B LEU* 3.9 24.7 - - + -
134B LYS* 2.9 30.2 + - - +
135B GLY* 3.9 5.6 - - - +
137B TYR* 1.3 77.7 - - - +
139B ALA* 1.3 62.7 + - - +
141B SER* 3.0 9.1 + - - +
142B GLU* 3.0 48.2 + - + +
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Residues in contact with ALA 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU* 3.4 26.6 - - + +
71B PHE* 5.3 0.2 - - + -
72B TYR* 2.8 36.5 + - + +
76B VAL* 3.9 24.2 - - + -
128B PHE* 4.2 6.3 - - + -
135B GLY 2.9 22.5 + - - +
138B LYS* 1.3 74.2 - - - +
140B MET* 1.3 61.6 + - - +
142B GLU* 3.8 1.9 + - - -
143B PHE 3.5 7.3 + - - -
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Residues in contact with MET 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 2.9 24.2 - - - -
33B VAL* 4.5 4.7 - - + -
37B PHE* 3.5 41.3 - - + -
72B TYR* 4.8 4.3 - - - -
76B VAL* 3.8 21.3 - - + -
77B MET* 4.5 11.2 - - + -
80B ALA* 3.6 21.5 - - + -
91B VAL* 4.1 21.8 - - + -
94B LEU* 3.9 25.8 - - + -
136B ILE 3.1 21.4 + - - +
137B TYR 3.7 0.4 - - - +
138B LYS 3.1 0.2 - - - -
139B ALA* 1.3 76.5 - - - +
141B SER* 1.3 67.1 + - - +
143B PHE* 3.0 7.8 + - - +
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Residues in contact with SER 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B PHE* 3.1 23.2 - - - -
34B LYS* 5.4 2.9 - - - +
37B PHE* 4.0 19.9 - - - +
38B GLN* 4.1 31.6 + - - +
39B MET* 5.0 1.9 - - - +
137B TYR 2.9 15.0 + - - -
138B LYS* 3.0 15.1 + - - +
140B MET* 1.3 76.0 - - - +
142B GLU* 1.3 67.3 + - - +
143B PHE 3.2 0.3 + - - -
144B ASP* 3.3 6.8 - - - +
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.1 22.4 + - + +
47B LEU* 2.9 20.5 + - - +
48B LEU* 2.8 46.0 + - + +
138B LYS* 3.0 36.5 + - + +
139B ALA* 3.9 4.9 - - - +
140B MET 3.2 0.2 - - - -
141B SER* 1.3 85.2 + - - +
143B PHE* 1.3 62.7 + - - +
144B ASP* 3.2 7.0 - - - -
145B ILE* 3.0 29.5 + - + +
146B PHE 3.2 7.4 + - - -
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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