Contacts of the helix formed by residues 119 - 147 (chain A) in PDB entry 3EUP
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 HIS 119 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.6 26.7 - - + +
54A GLU* 3.2 45.4 + - + +
58A ILE* 4.9 0.6 - - - +
115A ALA* 2.8 27.4 + - + +
116A ASP 5.2 0.2 + - - -
118A THR* 1.3 85.1 + - - +
120A ASP* 1.3 65.8 + - - +
121A ALA* 3.5 12.5 - - - +
122A LEU* 3.2 37.8 + - + +
123A ARG* 3.0 18.7 + - - +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A HIS* 1.3 71.8 - - - +
121A ALA* 1.3 64.6 + - - +
123A ARG* 3.2 12.7 + - - +
124A LYS* 2.9 61.1 + - + +
178B LYS* 6.0 2.4 - - - -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLU* 4.3 9.0 - - - +
58A ILE* 4.5 12.1 - - + -
119A HIS* 3.4 17.0 - - - +
120A ASP* 1.3 79.3 - - - +
122A LEU* 1.3 62.7 + - - +
124A LYS* 3.3 10.0 + - - +
125A LYS* 3.1 25.8 + - + +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.6 9.4 - - + -
54A GLU 5.5 0.2 - - - +
57A ALA* 4.5 21.1 - - + +
58A ILE* 4.0 25.4 - - + -
61A PHE* 4.2 21.1 - - + -
111A THR* 3.9 23.4 - - + +
115A ALA* 3.7 15.3 - - + -
119A HIS* 3.2 35.6 - - + +
121A ALA* 1.3 76.4 - - - +
123A ARG* 1.3 65.0 + - - +
125A LYS* 3.3 11.4 + - + +
126A ALA* 3.0 21.7 + - - +
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A THR* 5.5 1.8 - - + +
115A ALA* 3.6 12.5 - - - +
116A ASP* 3.7 25.6 - - + +
119A HIS 3.0 13.8 + - - +
120A ASP* 3.6 14.8 + - - +
122A LEU* 1.3 75.8 - - - +
124A LYS* 1.3 100.2 + - - +
126A ALA* 3.0 7.2 + - - +
127A GLY* 2.9 22.6 + - - -
175B ARG 3.4 13.5 - - - +
176B ALA* 2.8 40.6 + - - +
177B THR* 3.7 16.2 + - - +
178B LYS* 3.9 32.5 - - - +
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Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ASP* 2.9 45.1 + - + +
121A ALA* 3.6 8.3 - - - +
122A LEU 3.2 0.2 - - - -
123A ARG* 1.3 103.5 - - - +
125A LYS* 1.3 62.3 + - - +
127A GLY* 3.3 0.9 + - - -
128A GLU* 2.9 34.6 + - + +
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 3.6 25.8 - - + +
61A PHE* 3.9 22.4 - - + -
62A ASP* 2.7 43.2 + - - -
121A ALA* 3.1 17.5 + - + +
122A LEU* 3.6 16.6 - - + +
123A ARG 3.2 0.4 - - - -
124A LYS* 1.3 75.2 - - - +
126A ALA* 1.3 57.8 + - - +
128A GLU* 3.4 19.6 + - - +
129A ALA* 2.9 27.9 + - - +
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Residues in contact with ALA 126 (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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61A PHE* 4.3 7.8 - - + -
108A LEU* 4.6 6.5 - - + +
111A THR* 4.5 5.8 - - + -
112A THR* 3.4 35.9 - - - +
122A LEU 3.0 13.3 + - - +
123A ARG* 3.0 9.2 + - - +
125A LYS* 1.3 78.9 - - - +
127A GLY* 1.3 55.9 + - - +
129A ALA* 3.2 8.6 + - - +
130A ILE* 3.0 32.2 + - - +
176B ALA* 4.3 5.4 - - + -
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Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ARG* 2.9 15.6 + - - -
124A LYS 3.7 2.9 - - - -
126A ALA* 1.3 73.7 - - - +
128A GLU* 1.3 64.3 + - - +
130A ILE* 3.3 2.4 + - - +
131A LEU* 2.9 34.6 + - - +
176B ALA* 3.3 24.8 + - - -
177B THR* 4.3 7.2 - - - -
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Residues in contact with GLU 128 (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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124A LYS* 2.9 26.3 + - + +
125A LYS* 3.7 21.4 - - - +
127A GLY* 1.3 73.7 - - - +
129A ALA* 1.3 57.2 + - - +
131A LEU* 3.3 5.7 + - - +
132A SER* 2.8 36.9 + - - +
135A LYS* 5.6 0.2 + - - -
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Residues in contact with ALA 129 (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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61A PHE* 4.1 11.2 - - + -
65A TRP* 3.5 40.5 + - + +
108A LEU* 4.5 5.2 - - + -
125A LYS 2.9 14.7 + - - +
126A ALA* 3.2 10.1 + - - +
128A GLU* 1.3 77.5 - - - +
130A ILE* 1.3 62.1 + - - +
132A SER* 3.8 5.3 - - - -
133A TRP* 3.0 24.6 + - - +
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Residues in contact with ILE 130 (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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108A LEU* 3.5 39.5 - - + -
126A ALA 3.0 17.2 + - - +
127A GLY* 3.6 4.9 - - - +
129A ALA* 1.3 76.6 - - - +
131A LEU* 1.3 60.3 + - - +
133A TRP* 3.4 5.5 + - + +
134A LYS* 2.9 25.8 + - - +
161A PHE* 4.4 17.3 - - + -
164A ILE* 3.7 29.6 - - + +
172B LEU* 5.2 2.9 - - + -
173B ILE* 4.3 16.4 - - + -
176B ALA* 4.1 13.0 - - + -
177B THR* 4.0 20.9 - - + -
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLY* 2.9 23.6 + - - +
128A GLU* 4.0 4.7 - - - +
130A ILE* 1.3 73.8 - - - +
132A SER* 1.3 59.6 + - - +
134A LYS* 3.3 8.0 + - + +
135A LYS* 2.9 50.1 + - - +
161A PHE* 3.8 25.8 - - + -
177B THR* 4.2 12.3 - - + -
182B TYR* 3.8 41.1 - - + +
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A TRP* 6.1 0.7 - - - -
69A LYS* 5.9 6.7 - - - -
128A GLU* 2.8 24.3 + - - +
129A ALA* 3.8 5.4 - - - -
131A LEU* 1.3 69.9 - - - +
133A TRP* 1.3 64.9 + - - +
135A LYS* 3.4 15.4 + - - +
136A ASN* 3.1 33.4 + - - +
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Residues in contact with TRP 133 (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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65A TRP* 3.8 28.3 - + + -
72A LEU* 3.9 13.5 - - + +
89A TYR* 3.0 46.9 + + - -
108A LEU* 3.9 15.3 - - + -
129A ALA 3.0 17.0 + - - +
130A ILE* 3.6 4.3 - - + +
132A SER* 1.3 74.4 - - - +
134A LYS* 1.3 63.5 + - - +
136A ASN* 3.2 12.5 + - + +
137A LEU* 3.0 31.9 + - + +
163A MET 5.6 0.4 - - - -
164A ILE* 3.8 39.0 - - + -
167A VAL* 4.1 17.9 - - + -
168A GLU* 3.5 31.2 - - - -
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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
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130A ILE 2.9 18.0 + - - +
131A LEU* 3.5 11.4 - - + +
133A TRP* 1.3 75.9 - - - +
135A LYS* 1.3 68.6 + - + +
137A LEU* 3.1 7.8 + - - +
138A VAL* 2.9 41.7 + - + +
157A THR* 2.9 52.2 + - - +
160A ALA* 4.1 8.5 - - + -
161A PHE* 3.6 29.9 - - + -
164A ILE* 3.7 16.7 - - + +
182B TYR* 6.4 0.2 - - - -
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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 LEU* 2.9 48.5 + - - +
132A SER* 3.7 14.7 + - - +
133A TRP 3.2 0.4 - - - -
134A LYS* 1.3 81.2 - - + +
136A ASN* 1.3 66.2 + - - +
138A VAL* 2.6 30.0 - - + +
139A THR* 3.0 13.9 + - - -
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Residues in contact with ASN 136 (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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72A LEU* 6.5 1.8 - - + -
132A SER* 3.1 23.2 + - - +
133A TRP* 3.4 13.8 - - + +
135A LYS* 1.3 79.2 - - - +
137A LEU* 1.3 63.6 + - + +
139A THR* 3.2 10.0 + - - +
140A ILE* 3.1 30.3 + - + +
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Residues in contact with LEU 137 (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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72A LEU* 6.2 0.7 - - + -
85A MET 5.8 0.2 - - - +
86A LEU* 4.1 9.6 - - + +
89A TYR* 3.2 26.7 - - + +
133A TRP* 3.0 24.5 + - + +
134A LYS 3.1 6.3 + - - +
136A ASN* 1.3 78.1 - - + +
138A VAL* 1.3 57.5 + - - +
140A ILE* 3.1 14.3 + - + +
141A ILE* 2.8 38.1 + - + +
160A ALA* 3.4 33.7 - - + +
163A MET* 3.7 31.9 - - + -
164A ILE* 3.8 21.5 - - + -
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Residues in contact with VAL 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 44.2 + - + +
135A LYS* 2.6 43.1 - - + +
137A LEU* 1.3 75.2 - - - +
139A THR* 1.3 57.1 + - - +
141A ILE* 3.2 1.3 + - - +
142A LYS* 2.9 46.5 + - - +
156A VAL* 3.6 28.7 - - + +
157A THR* 4.5 3.1 - - - +
160A ALA* 3.7 7.9 - - + -
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Residues in contact with THR 139 (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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135A LYS 3.0 16.0 + - - -
136A ASN* 3.2 14.8 + - - +
138A VAL* 1.3 75.2 - - - +
140A ILE* 1.3 63.0 + - + +
142A LYS* 3.6 6.9 + - - +
143A LYS* 3.2 47.6 + - + +
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Residues in contact with ILE 140 (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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72A LEU* 5.7 4.0 - - + -
76A VAL* 4.4 17.3 - - + -
82A TYR* 3.9 7.1 - - + +
85A MET* 3.0 51.8 - - + +
86A LEU* 3.5 32.3 - - + -
136A ASN* 3.1 20.2 + - + +
137A LEU* 3.5 12.8 - - + +
139A THR* 1.3 74.9 - - + +
141A ILE* 1.3 66.6 + - - +
143A LYS* 3.3 11.4 + - + +
144A GLY* 3.0 18.7 + - - -
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Residues in contact with ILE 141 (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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86A LEU* 3.9 21.5 - - + -
137A LEU* 2.8 34.2 + - + +
138A VAL 3.8 3.6 - - - +
140A ILE* 1.3 72.3 - - - +
142A LYS* 1.3 57.4 + - - +
144A GLY* 2.9 4.2 + - - -
145A ILE* 2.8 30.9 + - + +
150A PHE* 3.5 17.5 - - + -
154A THR* 4.4 8.3 - - + -
156A VAL* 3.8 44.4 - - + +
159A ILE* 4.0 20.6 - - + -
160A ALA* 4.2 7.9 - - + -
163A MET* 4.5 3.4 - - - -
197A ILE* 4.3 10.5 - - + -
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Residues in contact with LYS 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 VAL* 2.9 34.5 + - - +
139A THR* 3.9 6.1 - - - +
141A ILE* 1.3 72.4 - - - +
143A LYS* 1.3 62.9 + - - +
145A ILE* 3.3 12.6 + - + +
146A GLN* 3.1 27.2 + - - +
156A VAL* 4.5 25.1 - - + +
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Residues in contact with LYS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.5 33.7 - - + +
85A MET* 5.8 0.7 - - + -
139A THR* 3.2 36.8 + - - +
140A ILE* 3.5 11.5 - - + +
142A LYS* 1.3 73.7 - - - +
144A GLY* 1.3 53.7 + - - +
146A GLN* 3.2 25.8 - - - +
147A ALA* 2.7 36.7 + - - +
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Residues in contact with GLY 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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82A TYR* 3.7 19.4 - - - -
140A ILE 3.0 7.3 + - - -
141A ILE 2.9 7.8 + - - -
143A LYS* 1.3 76.2 - - - +
145A ILE* 1.3 59.7 + - - +
147A ALA 3.4 0.5 + - - -
148A LYS 3.2 2.3 + - - -
149A GLU* 2.8 32.2 + - - +
150A PHE* 3.1 24.9 + - - -
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 2.8 17.8 + - + +
142A LYS* 3.5 12.6 - - + +
143A LYS 3.2 0.2 - - - -
144A GLY* 1.3 77.3 - - - +
146A GLN* 1.3 57.5 + - + +
148A LYS* 3.0 18.4 + - - -
150A PHE* 3.4 17.8 - - + +
151A ARG 3.1 24.2 - - - +
152A PRO* 3.9 30.3 - - + +
154A THR* 4.0 15.7 - - - +
156A VAL* 4.1 19.3 - - + -
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 5.6 1.0 + - - -
142A LYS* 3.1 13.4 + - - +
143A LYS* 3.2 37.3 - - - +
145A ILE* 1.3 77.7 - - + +
147A ALA* 1.3 60.4 + - - +
148A LYS* 3.2 3.0 + - - +
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Residues in contact with ALA 147 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.6 27.1 - - + -
143A LYS 2.7 17.2 + - - +
144A GLY 4.0 2.2 - - - +
145A ILE 3.2 0.4 - - - -
146A GLN* 1.3 77.4 - - + +
148A LYS* 1.3 67.6 + - - +
149A GLU* 3.1 9.4 + - + +
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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