Contacts of the helix formed by residues 120 - 147 (chain D) in PDB entry 3E5X
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 120 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ARG* 2.9 33.3 + - - +
116C PHE* 5.6 2.0 - - + +
117C ARG* 2.8 57.1 + - - +
116D PHE 3.5 12.4 + - - +
118D THR 4.2 0.6 - - - -
119D ASP* 1.3 72.5 - - - +
121D ASP* 1.4 61.3 + - - +
123D ILE* 3.1 40.8 + - + +
124D PHE* 3.7 8.3 - - + -
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Residues in contact with ASP 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C ARG* 3.0 32.8 + - - -
24D LYS* 6.4 0.4 - - + -
119D ASP* 3.1 16.4 - - - +
120D GLU* 1.4 78.6 - - - +
122D MET* 1.3 67.4 + - + +
124D PHE* 3.2 17.9 + - - +
125D GLU* 3.2 18.3 + - + +
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Residues in contact with MET 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 4.2 7.9 - - - -
24D LYS* 3.6 39.7 - - + -
25D LEU* 3.9 24.5 - - + -
28D TYR* 3.8 18.2 - - + -
115D VAL* 3.9 22.4 - - + -
116D PHE* 4.0 6.5 - - + -
119D ASP* 3.2 33.9 + - - +
121D ASP* 1.3 79.6 - - + +
123D ILE* 1.3 64.5 + - - +
125D GLU* 3.4 18.0 + - + +
126D ILE* 3.1 28.0 + - + +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C PHE* 3.8 25.1 - - + -
123C ILE* 3.5 35.9 - - + -
127C PHE* 4.2 1.1 - - - -
116D PHE* 3.7 34.0 - - + +
120D GLU* 3.1 32.3 + - + +
122D MET* 1.3 78.4 - - - +
124D PHE* 1.3 61.1 + - + +
126D ILE* 3.3 3.6 + - - +
127D PHE* 2.9 58.7 + - + -
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 4.0 4.0 - - + -
88C TYR* 3.2 23.5 + - - +
109C GLU* 3.7 21.1 - - + +
112C LEU* 4.1 9.4 - - + -
113C ARG* 3.7 56.8 - - + +
116C PHE* 3.8 30.1 - + - -
120D GLU* 3.7 21.1 - - + -
121D ASP* 3.2 8.7 + - - +
123D ILE* 1.3 78.3 - - + +
125D GLU* 1.3 63.5 + - - +
127D PHE* 3.3 20.0 + + - +
128D LYS* 3.0 35.0 + - - +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D PHE* 3.5 25.8 - - - -
21D PRO 5.0 1.2 - - - +
22D ILE* 3.6 35.1 - - + +
24D LYS* 5.9 1.3 - - + -
121D ASP* 3.2 17.7 + - + +
122D MET* 3.8 25.4 - - + +
124D PHE* 1.3 74.4 - - - +
126D ILE* 1.3 62.7 + - - +
128D LYS* 2.8 35.8 + - - +
129D ASN* 3.1 17.8 + - - +
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Residues in contact with ILE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C PHE* 3.5 23.3 - - + -
22D ILE* 3.9 11.2 - - + -
25D LEU* 4.8 15.9 - - + -
53D MET* 4.0 23.1 - - + -
83D LEU* 3.9 19.5 - - + -
112D LEU* 4.4 9.2 - - + -
116D PHE* 3.8 27.1 - - + -
122D MET* 3.1 18.0 + - + +
123D ILE 3.7 3.8 - - - +
125D GLU* 1.3 72.2 - - + +
127D PHE* 1.3 65.2 + - - +
129D ASN* 3.1 3.0 + - + +
130D TYR* 2.9 38.6 + - + -
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Residues in contact with PHE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C MET* 3.7 20.2 - - + -
87C LEU* 4.2 2.5 - - + -
88C TYR* 4.4 7.9 - - + -
112C LEU* 4.5 1.3 - - + -
116C PHE* 3.7 25.8 - + - -
123C ILE* 4.3 3.8 - - - -
126C ILE* 3.5 26.7 - - + -
127C PHE* 3.4 29.8 - + - -
130C TYR* 3.7 26.3 - + + +
123D ILE* 2.9 33.7 + - + -
124D PHE* 3.3 30.9 + + - +
126D ILE* 1.3 76.1 - - - +
128D LYS* 1.3 55.9 + - - +
130D TYR* 3.3 2.8 + - - +
131D LEU* 2.9 31.8 + - - +
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C TYR* 3.4 41.0 + - + -
109C GLU* 5.0 3.0 + - - -
9D ASP* 2.8 33.6 + - - +
11D CYS* 3.5 15.9 - - - -
20D PHE* 3.5 34.3 - - + -
124D PHE* 3.0 18.3 + - - +
125D GLU* 2.8 33.5 + - - +
127D PHE* 1.3 73.3 - - - +
129D ASN* 1.3 57.3 + - - +
131D LEU* 4.4 0.9 - - - -
132D THR* 2.8 35.7 + - - -
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Residues in contact with ASN 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 3.5 14.8 + - - +
20D PHE* 2.9 31.8 + - + +
22D ILE* 3.9 11.2 - - + +
83D LEU* 3.8 34.4 + - + +
85D GLY* 5.6 0.7 - - - -
125D GLU 3.1 12.7 + - - +
126D ILE* 3.1 9.1 + - - +
128D LYS* 1.3 74.9 - - - +
130D TYR* 1.4 67.5 + - - +
132D THR* 3.5 2.8 + - - -
133D LYS* 3.2 53.8 + - - +
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Residues in contact with TYR 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C PHE* 3.6 43.3 + + + +
130C TYR* 3.5 34.3 - + + -
131C LEU* 4.0 19.4 - - - +
134C VAL* 3.8 6.6 - - + +
53D MET* 3.2 17.8 - - + +
85D GLY* 2.8 26.2 + - - -
87D LEU* 4.5 2.4 - - - +
88D TYR* 5.7 0.2 - - - -
126D ILE* 2.9 34.4 + - + -
127D PHE 3.7 3.8 - - - +
129D ASN* 1.4 78.5 + - - +
131D LEU* 1.3 57.3 + - - +
133D LYS* 3.2 8.8 + - + +
134D VAL* 3.0 30.3 + - - +
503D 3C4 3.6 28.7 - - + -
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C GLY 3.6 25.6 - - - +
86C LYS* 4.4 1.8 - - - -
87C LEU 4.1 0.9 - - - +
88C TYR* 3.4 49.1 - - + +
90C THR* 3.7 18.2 - - + -
130C TYR* 4.0 11.3 - - + +
502C 3C4 3.7 30.5 - - + -
11D CYS* 4.0 7.0 - - + -
127D PHE 2.9 20.5 + - - +
128D LYS* 3.8 4.5 - - - +
130D TYR* 1.3 70.6 - - - +
132D THR* 1.3 58.7 + - - +
134D VAL* 4.4 1.3 - - - +
135D ALA* 2.9 30.7 + - - +
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Residues in contact with THR 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D CYS* 3.3 36.9 + - - +
12D GLY 4.4 2.2 - - - +
13D ALA* 3.9 14.9 + - + +
19D PHE* 3.8 27.4 - - + -
20D PHE* 3.6 21.7 - - + +
128D LYS 2.8 22.1 + - - -
129D ASN 3.6 5.2 - - - -
130D TYR 3.3 0.2 - - - -
131D LEU* 1.3 75.6 - - - +
133D LYS* 1.3 63.0 + - - +
135D ALA* 3.9 2.3 - - - +
136D TYR* 3.1 22.2 + - - +
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Residues in contact with LYS 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C VAL* 3.6 18.4 - - + -
19D PHE* 3.7 36.6 - - + -
76D TYR* 4.3 7.0 - - + -
83D LEU 2.8 23.9 + - - -
85D GLY* 3.7 4.4 - - - +
129D ASN* 3.2 32.6 + - - +
130D TYR* 3.2 9.0 + - - +
132D THR* 1.3 74.7 - - - +
134D VAL* 1.3 66.6 + - - +
136D TYR* 3.3 3.3 + - - +
137D TYR* 3.0 36.5 + - + -
503D 3C4 2.6 48.8 + - + +
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Residues in contact with VAL 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR* 6.2 0.4 - - + -
130C TYR* 3.9 19.7 - - + +
133C LYS* 3.8 29.2 - - + -
134C VAL* 3.6 22.7 - - + +
137C TYR* 4.3 14.4 - - + -
502C 3C4 3.4 36.1 - - + -
130D TYR 3.0 19.1 + - - +
131D LEU 3.8 4.5 - - - +
133D LYS* 1.3 75.8 - - - +
135D ALA* 1.3 58.3 + - - +
137D TYR* 4.0 1.7 - - - +
138D ALA* 2.9 36.1 + - + +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C THR* 3.8 19.5 - - + +
92C ASN* 3.2 23.8 + - - +
502C 3C4 3.6 26.9 - - - +
11D CYS 4.0 7.9 - - - +
12D GLY* 5.5 1.1 - - - -
13D ALA 6.1 0.2 - - - +
131D LEU 2.9 17.7 + - - +
132D THR 3.9 3.4 - - - +
134D VAL* 1.3 79.5 - - - +
136D TYR* 1.3 60.2 + - - +
138D ALA* 4.7 0.2 - - - -
139D ARG* 3.2 16.1 + - - +
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Residues in contact with TYR 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141C VAL* 6.2 0.7 - - + -
13D ALA* 3.6 26.9 - - + +
14D ILE 3.6 22.9 - - - -
15D ILE 4.2 2.5 - - - -
16D PRO* 3.6 31.4 - - + +
19D PHE* 3.8 23.8 - + + -
132D THR 3.1 17.9 + - - +
133D LYS 3.8 3.1 - - - +
134D VAL 3.2 0.2 - - - -
135D ALA* 1.3 77.0 - - - +
137D TYR* 1.3 89.0 + + - +
139D ARG* 3.6 17.4 + - - +
140D GLN* 2.9 55.1 + - + +
186D ILE* 3.9 16.3 + - - +
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Residues in contact with TYR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C VAL* 4.3 9.6 - - + +
137C TYR* 3.5 25.4 - - + +
138C ALA* 3.7 33.4 - - + +
141C VAL* 3.6 17.8 - - + +
19D PHE* 3.5 21.4 - + - -
75D LEU* 2.7 41.0 + - + +
76D TYR* 3.4 16.7 - + - -
133D LYS* 3.0 34.7 + - + +
134D VAL* 5.3 0.4 - - - -
136D TYR* 1.3 95.3 - + - +
138D ALA* 1.3 63.8 + - - +
140D GLN* 3.3 2.8 + - - -
141D VAL* 3.1 27.5 + - - +
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C LEU* 3.7 34.3 - - + +
92C ASN* 5.7 0.4 - - - +
137C TYR* 3.7 31.4 - - + +
502C 3C4 4.9 2.7 - - + -
134D VAL* 2.9 22.9 + - + +
135D ALA* 4.4 2.9 - - - +
137D TYR* 1.3 75.8 - - - +
139D ARG* 1.3 63.3 + - - +
141D VAL* 3.5 1.9 + - - +
142D ALA* 3.1 23.2 + - - +
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Residues in contact with ARG 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ILE* 4.1 18.5 - - + +
67C PHE* 4.0 15.2 - - + -
92C ASN* 3.4 26.6 + - - +
13D ALA 2.9 27.9 + - - -
14D ILE* 4.0 10.1 + - - +
135D ALA 3.2 20.1 + - - +
136D TYR* 3.6 23.7 - - - +
138D ALA* 1.3 79.1 - - - +
140D GLN* 1.3 59.3 + - - +
142D ALA* 3.2 3.1 + - - +
143D GLU* 2.7 51.5 + - + +
155D ARG* 5.5 2.4 - - - +
159D GLU* 3.8 23.6 + - - -
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Residues in contact with GLN 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C VAL* 3.7 25.2 - - + +
145C ASN* 5.7 0.2 - - - +
136D TYR* 2.9 43.1 + - + +
137D TYR* 3.7 5.8 - - - +
138D ALA 3.3 0.2 - - - -
139D ARG* 1.3 83.0 + - - +
141D VAL* 1.4 60.2 + - - +
143D GLU* 3.7 20.0 + - - +
144D MET* 2.8 59.6 + - - +
152D ARG* 4.5 0.8 - - - +
186D ILE* 3.4 26.1 + - - +
187D THR* 4.0 11.3 + - - +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU 5.8 3.6 - - - +
75C LEU* 6.1 2.2 - - + -
136C TYR* 6.3 0.4 - - + -
137C TYR* 3.6 26.9 - - + +
140C GLN* 3.6 31.6 - - + +
141C VAL* 3.5 20.4 - - + +
144C MET* 4.0 9.4 - - - +
186C ILE 5.9 1.3 - - - +
137D TYR 3.1 20.3 + - - +
138D ALA 3.7 4.5 - - - +
140D GLN* 1.4 72.9 - - - +
142D ALA* 1.3 66.0 + - - +
144D MET* 3.2 5.8 + - - +
145D ASN* 3.1 37.1 + - - +
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Residues in contact with ALA 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 3.3 33.9 - - + -
67C PHE* 3.8 7.4 - - + -
73C LYS* 3.9 17.7 - - + -
74C LEU 5.3 0.7 - - - +
75C LEU* 4.4 4.0 - - + -
138D ALA 3.1 12.6 + - - +
139D ARG 3.7 6.7 - - - +
141D VAL* 1.3 79.7 - - - +
143D GLU* 1.3 61.5 + - - +
145D ASN* 3.2 11.4 + - - +
146D THR* 2.7 23.7 + - - -
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Residues in contact with GLU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE* 3.7 15.7 - - + -
139D ARG* 2.7 39.5 + - + +
140D GLN* 3.8 21.3 + - - +
142D ALA* 1.3 73.7 - - - +
144D MET* 1.3 58.3 + - - +
146D THR* 3.1 1.7 + - - -
147D TYR* 2.8 44.8 + - + +
152D ARG* 3.4 32.3 - - + +
155D ARG* 3.1 30.9 + - - +
159D GLU* 4.3 3.1 - - - +
187D THR* 5.8 1.7 - - - +
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Residues in contact with MET 144 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C VAL* 4.1 22.4 - - - +
144C MET* 3.4 42.9 - - + +
145C ASN* 3.1 31.2 - - - +
140D GLN* 2.8 44.4 + - - +
141D VAL 3.6 0.2 - - - +
143D GLU* 1.3 76.0 - - - +
145D ASN* 1.3 62.4 + - - +
146D THR 3.3 0.8 + - - -
147D TYR 3.9 8.8 - - - +
152D ARG* 3.8 30.6 + - - +
187D THR 4.9 1.6 - - - +
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Residues in contact with ASN 145 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LYS* 3.5 29.5 + - + +
140C GLN* 5.8 0.4 - - - +
144C MET* 3.2 20.2 - - - +
152C ARG* 4.9 0.2 + - - -
185C GLU 5.1 4.9 + - - -
186C ILE 5.8 0.6 + - - -
187C THR 5.1 0.2 - - - -
188C GLY* 3.3 38.3 - - - +
190C HIS* 5.1 11.8 - - - -
141D VAL* 3.1 32.3 + - - +
142D ALA* 3.2 8.6 + - - +
143D GLU 3.2 0.6 - - - -
144D MET* 1.3 75.3 - - - +
146D THR* 1.3 58.4 + - - +
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Residues in contact with THR 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE* 3.7 8.0 - - + -
69C ASP* 5.2 0.4 - - - +
71C SER* 3.4 29.4 - - - +
73C LYS* 3.3 23.7 - - - +
142D ALA 2.7 20.9 + - - -
143D GLU 3.1 0.8 + - - -
145D ASN* 1.3 78.2 - - - +
147D TYR* 1.3 93.2 + - + +
148D ASN 4.3 0.2 + - - -
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Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C PHE* 3.4 29.8 - + - +
68C GLU* 3.9 1.4 + - - -
69C ASP* 3.2 28.0 + - - -
143D GLU* 2.8 22.9 + - + +
144D MET 3.9 7.0 - - - +
146D THR* 1.3 104.3 - - + +
148D ASN* 1.3 64.6 + - - +
149D PRO* 4.0 0.3 - - - +
151D ILE* 3.7 29.6 - - + -
152D ARG* 3.3 27.1 + - + -
155D ARG* 3.6 42.1 + - - -
226D SER 5.5 2.0 - - - -
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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).
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