Contacts of the helix formed by residues 110 - 139 (chain B) in PDB entry 1UMN
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 110 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG 4.6 1.8 - - - -
108B ASN 4.2 6.3 - - - +
109B VAL* 1.3 77.0 - - - +
111B ILE* 1.3 64.1 + - - +
112B GLU* 3.5 7.2 + - - +
113B GLU* 2.9 49.7 + - - +
114B GLN* 2.9 22.2 + - - +
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET* 3.6 36.3 - - + -
51B ARG 3.4 25.4 + - - +
52B GLY* 4.1 4.9 - - - +
53B ARG 3.9 11.2 - - - +
54B GLY* 4.0 21.1 - - - +
58B TRP* 4.3 9.4 - - + -
109B VAL 3.8 0.6 + - - -
110B THR* 1.3 72.9 - - - +
112B GLU* 1.3 63.7 + - + +
114B GLN* 3.1 9.3 + - - +
115B LEU* 3.0 36.0 + - + +
53J ARG* 3.7 31.2 - - - +
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Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B THR* 3.2 7.6 + - - +
111B ILE* 1.3 78.8 - - + +
113B GLU* 1.3 62.0 + - + +
115B LEU* 3.4 3.1 + - - +
116B ALA* 3.0 27.9 + - - +
166B LEU* 3.8 29.1 - - + +
53J ARG* 2.8 47.5 + - - +
1174J EPE 5.4 0.5 - - - -
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASN 4.5 0.9 - - - +
109B VAL* 3.5 21.4 - - + +
110B THR* 2.9 53.1 + - - +
112B GLU* 1.3 78.1 - - + +
114B GLN* 1.3 58.7 + - - +
116B ALA* 3.2 8.4 + - - +
117B ARG* 2.9 27.9 + - - +
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLN* 5.6 1.0 - - - +
46B VAL* 3.6 41.6 - - + +
49B TYR* 4.4 22.6 + - - +
50B MET* 4.5 11.4 - - + +
106B ASP 4.2 8.5 + - - -
109B VAL* 3.6 30.2 + - + +
110B THR 2.9 22.1 + - - +
111B ILE* 3.1 11.2 + - - +
113B GLU* 1.3 79.1 - - - +
115B LEU* 1.3 65.7 + - + +
117B ARG* 3.1 10.9 + - - +
118B VAL* 3.1 25.7 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 5.5 0.2 - - + -
50B MET* 4.7 4.7 - - + -
58B TRP* 3.7 52.7 - - + +
62B MET* 4.5 10.8 - - + -
111B ILE* 3.0 29.3 + - + +
112B GLU 3.8 3.8 - - - +
114B GLN* 1.3 79.1 - - + +
116B ALA* 1.3 66.9 + - - +
118B VAL* 3.1 8.3 + - + +
119B VAL* 2.9 27.6 + - - +
162B LEU* 4.0 16.8 - - + +
165B GLU* 3.9 18.6 - - + -
166B LEU* 4.1 20.0 - - + -
53J ARG* 5.3 1.1 - - - +
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B GLU 3.0 18.7 + - - +
113B GLU* 3.5 8.5 - - - +
115B LEU* 1.3 76.5 - - - +
117B ARG* 1.3 62.3 + - - +
119B VAL* 3.4 6.4 + - - +
120B GLU* 3.1 29.4 + - + +
163B GLN* 5.7 0.2 - - - +
166B LEU* 4.0 15.0 - - + +
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Residues in contact with ARG 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.8 31.9 - - + +
46B VAL* 4.9 6.7 - - + -
100B LEU* 4.9 6.7 - - - +
101B LYS* 3.1 32.3 + - - +
103B VAL* 6.4 0.2 - - - +
113B GLU 2.9 12.7 + - - +
114B GLN* 3.1 16.1 + - - +
116B ALA* 1.3 75.5 - - - +
118B VAL* 1.3 65.2 + - - +
120B GLU* 2.9 40.9 + - - +
121B VAL* 3.0 34.6 + - - +
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 6.1 0.9 - - + -
43B LEU* 3.9 14.1 - - + -
46B VAL* 4.2 14.6 - - + -
62B MET* 3.9 25.4 - - + -
65B TYR* 4.2 7.2 - - + -
114B GLN 3.1 15.3 + - - +
115B LEU* 3.1 9.6 + - - +
117B ARG* 1.3 76.5 - - + +
119B VAL* 1.3 57.4 + - - +
121B VAL* 3.1 8.8 + - - +
122B PHE* 2.8 62.0 + - + -
162B LEU* 3.9 11.7 - - + -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU 2.9 19.7 + - - +
116B ALA* 3.6 10.5 - - - +
118B VAL* 1.3 76.9 - - - +
120B GLU* 1.3 58.6 + - + +
122B PHE* 3.2 6.9 + - - +
123B ARG* 2.8 56.4 + - + +
159B ILE* 4.5 7.6 - - + +
162B LEU* 3.5 31.9 - - + -
163B GLN* 3.6 33.7 - - + +
166B LEU* 4.5 2.2 - - + -
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 5.4 0.4 - - - +
116B ALA* 3.1 22.8 + - + +
117B ARG* 2.9 41.5 + - - +
119B VAL* 1.3 77.8 - - + +
121B VAL* 1.3 63.9 + - - +
123B ARG* 3.3 9.8 + - - +
124B TYR* 3.1 22.3 + - - +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.8 33.0 - - + +
42B ILE* 4.0 24.9 - - + -
43B LEU* 5.7 2.9 - - + -
100B LEU* 4.3 13.0 - - + -
117B ARG* 3.0 41.4 + - - +
118B VAL* 3.5 9.4 - - - +
120B GLU* 1.3 77.2 - - - +
122B PHE* 1.3 75.3 + - + +
124B TYR* 3.2 9.4 + - - +
125B LEU* 3.0 23.4 + - + +
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 4.2 17.3 - - + -
65B TYR* 3.8 31.2 - + + -
69B ILE* 4.5 9.4 - - + -
118B VAL* 2.8 42.0 + - + +
119B VAL* 3.8 2.7 - - - +
121B VAL* 1.3 83.9 - - + +
123B ARG* 1.3 56.2 + - - +
125B LEU* 3.3 5.0 + - + +
126B ALA* 2.9 30.0 + - - +
155B ILE* 3.5 35.1 - - + +
158B HIS* 3.8 25.6 - + + -
159B ILE* 3.7 18.6 - - + -
162B LEU* 3.7 21.3 - - + -
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 2.8 38.6 + - + +
120B GLU* 3.7 8.7 - - - +
121B VAL 3.3 0.2 - - - -
122B PHE* 1.3 73.8 - - - +
124B TYR* 1.3 64.4 + - - +
126B ALA* 3.3 3.9 + - - +
127B ALA* 3.0 23.4 + - - +
159B ILE* 3.8 20.9 - - + +
163B GLN* 3.4 26.7 + - - +
170B PRO 2.9 29.1 + - - -
171B LYS* 3.1 27.2 + - - +
172B LEU* 4.0 9.4 + - - +
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B GLN* 3.8 4.3 + - - -
35B ASP* 2.8 44.2 + - + -
99B GLN* 3.4 44.2 + - + +
100B LEU* 3.7 30.5 - - + -
120B GLU 3.1 14.3 + - - +
121B VAL 3.4 7.6 - - - +
123B ARG* 1.3 77.7 - - - +
125B LEU* 1.3 62.5 + - + +
127B ALA* 3.1 9.3 + - + +
128B LEU* 2.8 41.8 + - + +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ASP* 4.2 29.4 - - + +
36B LEU* 4.1 19.7 - - + -
39B ALA* 4.1 15.0 - - + -
69B ILE* 3.8 28.3 - - + -
100B LEU* 4.9 0.4 - - + -
121B VAL* 3.0 25.0 + - + +
122B PHE* 3.3 16.8 + - + +
124B TYR* 1.3 82.8 - - + +
126B ALA* 1.3 58.1 + - - +
128B LEU* 3.1 7.9 + - + +
129B PHE* 2.8 51.7 + - + -
155B ILE* 4.4 6.5 - - + -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B PHE 2.9 17.8 + - - +
123B ARG* 3.6 8.3 - - - +
125B LEU* 1.3 76.2 - - - +
127B ALA* 1.3 58.8 + - - +
129B PHE* 3.3 5.5 + - - +
130B GLN* 2.9 27.2 + - - +
152B LYS* 3.8 11.5 - - + +
155B ILE* 3.8 18.5 - - + +
156B GLU* 4.2 22.2 - - + +
159B ILE* 4.4 3.6 - - + -
172B LEU* 6.0 0.9 - - + -
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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
----------------------------------------------------------
123B ARG 3.0 13.1 + - - +
124B TYR* 3.1 11.4 + - + +
126B ALA* 1.3 73.7 - - - +
128B LEU* 1.3 66.6 + - - +
130B GLN* 3.2 8.9 + - - +
131B LYS* 3.0 21.5 + - - +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.7 5.8 - - + -
28B VAL* 4.0 18.3 - - + +
31B GLN* 3.8 23.3 - - + -
32B ALA* 3.6 28.9 - - + -
35B ASP* 3.5 28.3 - - + +
124B TYR* 2.8 26.5 + - + +
125B LEU* 3.4 11.7 - - + +
127B ALA* 1.3 77.4 - - - +
129B PHE* 1.3 70.2 + - + +
131B LYS* 3.0 11.6 + - + +
132B GLY* 2.9 24.4 + - - -
148B PHE* 4.9 0.8 - - + -
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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
----------------------------------------------------------
32B ALA* 4.8 0.4 - - + -
36B LEU* 4.1 24.9 - - + -
72B TYR* 4.4 4.7 - + - -
76B MET* 3.8 24.7 - - + -
125B LEU* 2.8 34.0 + - + +
126B ALA* 3.6 6.1 - - - +
128B LEU* 1.3 91.1 - - + +
130B GLN* 1.3 57.0 + - - +
132B GLY 3.3 0.2 + - - -
133B PHE* 2.9 28.2 + - - +
148B PHE* 3.5 41.5 - + + +
151B ALA* 3.5 20.6 - - + -
152B LYS* 3.6 28.7 - - + -
155B ILE* 4.0 17.3 - - + -
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Residues in contact with GLN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ALA 2.9 13.6 + - - +
127B ALA* 3.2 11.4 + - - +
129B PHE* 1.3 77.0 - - - +
131B LYS* 1.3 59.8 + - - +
133B PHE* 3.2 14.7 + - - -
134B ASP* 2.9 57.8 + - - +
152B LYS* 3.5 32.2 - - + +
140L GLY 5.2 7.2 + - - +
142L SER* 4.8 4.7 + - - -
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Residues in contact with LYS 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 5.7 4.9 - - + -
28B VAL* 4.5 6.7 - - + -
127B ALA 3.0 11.6 + - - +
128B LEU* 3.0 15.6 + - + +
130B GLN* 1.3 78.9 - - - +
132B GLY* 1.3 56.3 + - - +
134B ASP* 3.2 8.4 + - - +
135B VAL* 2.9 38.6 + - + +
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Residues in contact with GLY 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.6 20.2 - - - +
128B LEU 2.9 12.1 + - - -
129B PHE 3.3 1.5 + - - -
130B GLN 3.3 0.2 - - - -
131B LYS* 1.3 76.3 - - - +
133B PHE* 1.3 53.3 + - - +
135B VAL* 4.0 0.5 - - - +
136B SER* 2.8 36.9 + - - -
148B PHE* 3.4 32.0 - - - -
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Residues in contact with PHE 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B PHE 2.9 14.1 + - - +
130B GLN* 3.3 21.3 - - - +
132B GLY* 1.3 77.2 - - - +
134B ASP* 1.3 78.2 + - - +
136B SER* 3.1 1.9 + - - -
137B ASP* 3.0 26.6 + - - +
145B ASN* 2.9 63.7 + - - +
148B PHE* 3.8 8.2 - - + -
149B ASN* 3.8 20.0 - - + +
152B LYS* 6.0 2.0 - - + -
140L GLY 6.0 0.9 - - - -
142L SER* 3.3 37.7 - - - -
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Residues in contact with ASP 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B GLN* 2.9 45.7 + - - +
131B LYS* 3.2 7.7 + - - +
133B PHE* 1.3 86.4 - - - +
135B VAL* 1.3 58.4 + - + +
137B ASP* 3.6 4.5 - - - +
138B GLU* 3.0 29.5 + - - +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LEU* 4.8 13.9 - - + +
23B ALA 4.6 2.9 - - - +
24B ASP* 3.3 42.2 - - - +
25B SER* 3.5 5.6 - - - +
28B VAL* 4.5 10.8 - - + -
131B LYS* 2.9 22.9 + - + +
132B GLY 4.0 2.7 - - - +
134B ASP* 1.3 77.8 - - + +
136B SER* 1.3 62.6 + - - +
138B GLU* 3.3 6.3 + - - +
139B GLU* 3.1 31.4 + - + +
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Residues in contact with SER 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.2 21.3 + - - -
132B GLY 2.8 22.9 + - - -
133B PHE 3.1 5.5 + - - -
135B VAL* 1.3 77.3 - - - +
137B ASP* 1.3 55.2 + - - +
139B GLU 3.4 0.6 + - - +
140B GLY 2.9 7.3 + - - -
141B ASP* 2.6 48.2 + - - -
144B THR* 3.8 9.6 - - - -
145B ASN* 3.0 26.7 - - - -
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Residues in contact with ASP 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B PHE* 3.0 34.2 + - + +
134B ASP* 3.6 6.5 - - - +
136B SER* 1.3 79.0 + - - +
138B GLU* 1.3 62.4 + - - +
140B GLY* 3.0 13.5 + - - -
141B ASP 5.7 0.2 - - - -
142B SER* 6.1 0.6 - - - +
145B ASN* 3.4 19.4 + - - +
----------------------------------------------------------
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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 ASP 3.0 17.3 + - - +
135B VAL* 3.7 7.0 - - - +
137B ASP* 1.3 77.8 - - - +
139B GLU* 1.3 62.5 + - + +
140B GLY 3.2 0.6 + - - -
----------------------------------------------------------
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ALA 3.6 6.1 - - - +
24B ASP* 3.0 29.2 - - - +
25B SER* 2.8 35.6 + - - +
135B VAL* 3.1 18.9 + - + +
136B SER 3.4 3.6 + - - +
138B GLU* 1.3 82.7 - - + +
140B GLY* 1.3 62.6 + - - +
141B ASP* 3.5 4.6 + - + +
----------------------------------------------------------
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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