Contacts of the helix formed by residues 113 - 139 (chain A) in PDB entry 2QQY
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 MSE 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A VAL* 4.3 13.5 - - + -
8A LEU* 3.5 31.2 - - + -
62A LYS* 6.2 0.7 - - - -
66A LEU* 3.8 27.6 - - + -
108A ALA* 2.9 14.0 + - + +
109A ALA* 4.8 1.0 - - - +
111A LEU* 3.4 35.0 - - + +
112A ASN* 1.3 74.4 - - - +
114A THR* 1.3 58.1 + - - +
115A GLU 3.5 1.6 - - - -
116A LEU* 3.2 22.7 + - + -
117A VAL* 2.9 31.6 + - - +
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Residues in contact with THR 114 (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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112A ASN 3.2 9.3 + - - -
113A MSE 1.3 72.1 - - - +
115A GLU* 1.3 65.8 + - - +
117A VAL* 3.3 6.4 + - - +
118A VAL* 3.0 31.4 + - + +
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 2.8 32.3 + - - -
62A LYS* 2.6 30.9 + - - -
113A MSE 3.5 0.2 - - - -
114A THR* 1.3 78.8 - - - +
116A LEU* 1.3 62.5 + - - +
118A VAL* 3.5 9.1 + - - +
119A LYS* 3.0 26.7 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.0 29.8 - - + -
12A LEU* 4.8 9.2 - - + -
58A TYR* 3.5 31.9 - - + +
59A LEU* 6.1 0.2 - - + -
62A LYS* 4.5 24.2 - - + +
108A ALA* 3.7 22.0 - - + -
113A MSE 3.2 23.0 + - + +
115A GLU* 1.3 82.9 + - - +
117A VAL* 1.3 60.0 + - - +
119A LYS 3.3 0.9 + - - -
120A LEU* 2.8 51.6 + - + +
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Residues in contact with VAL 117 (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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105A LYS* 4.0 18.8 - - + +
108A ALA* 3.7 5.6 - - + +
109A ALA* 3.5 39.9 - - + +
113A MSE 2.9 19.1 + - - +
114A THR* 3.6 9.4 - - - +
116A LEU* 1.3 75.5 - - - +
118A VAL* 1.3 59.6 + - + +
120A LEU* 3.2 2.3 + - - +
121A GLU* 2.8 53.4 + - - +
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Residues in contact with VAL 118 (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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114A THR* 3.0 26.1 + - + +
115A GLU* 3.7 11.9 - - + +
117A VAL* 1.3 77.4 - - + +
119A LYS* 1.3 59.8 + - + +
121A GLU* 3.5 14.1 + - - +
122A ASP* 3.0 42.5 + - - +
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Residues in contact with LYS 119 (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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54A GLY 5.5 2.0 + - - -
55A HIS* 4.9 7.5 - - - -
58A TYR* 3.4 63.9 - - + +
115A GLU* 3.0 20.0 + - - +
116A LEU 3.9 1.3 - - - +
118A VAL* 1.3 80.5 - - + +
120A LEU* 1.3 57.7 + - - +
122A ASP* 3.3 10.8 + - + +
123A MSE 2.9 47.8 + - + +
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Residues in contact with LEU 120 (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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12A LEU* 5.1 3.1 - - + -
101A TYR* 3.6 36.1 - - + +
104A ARG* 3.5 40.6 - - + +
105A LYS* 3.6 23.8 - - + +
108A ALA* 3.9 3.4 - - + -
116A LEU* 2.8 48.4 + - + +
117A VAL 3.8 2.7 - - - +
119A LYS* 1.3 69.4 - - - +
121A GLU* 1.3 59.8 + - - +
123A MSE 3.7 14.9 - - + +
124A ILE* 2.8 37.6 + - + +
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Residues in contact with GLU 121 (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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105A LYS* 3.8 26.5 - - + +
117A VAL* 2.8 41.3 + - - +
118A VAL* 3.6 14.0 - - - +
120A LEU* 1.3 72.9 - - - +
122A ASP* 1.3 59.4 + - - +
124A ILE* 3.5 8.3 + - - +
125A ALA* 2.9 28.3 + - - +
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Residues in contact with ASP 122 (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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118A VAL* 3.0 35.1 + - - +
119A LYS* 3.7 12.9 - - + +
121A GLU* 1.3 76.8 - - - +
123A MSE 1.3 59.9 + - + +
125A ALA* 3.3 8.1 + - - +
126A ASP* 2.8 30.7 + - - +
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Residues in contact with MSE 123 (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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55A HIS* 3.6 48.5 - - + +
58A TYR* 4.1 15.5 - - + -
59A LEU* 4.6 3.8 - - + -
101A TYR* 3.9 31.6 - - + -
119A LYS* 2.9 50.4 + - + +
120A LEU* 3.7 31.6 - - + +
122A ASP* 1.3 69.3 - - - +
124A ILE* 1.3 60.6 + - - +
126A ASP* 3.7 5.2 - - - +
127A GLU* 2.8 38.0 + - - +
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Residues in contact with ILE 124 (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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98A ILE* 4.0 13.6 - - + +
101A TYR* 3.5 25.6 - - + +
102A GLU* 3.5 53.2 - - - +
105A LYS* 4.2 14.8 - - + -
120A LEU 2.8 22.7 + - - +
121A GLU* 3.6 6.3 - - - +
123A MSE 1.3 75.4 - - - +
125A ALA* 1.4 54.4 + - - +
127A GLU* 3.3 4.5 + - - +
128A THR* 2.8 47.1 + - - +
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Residues in contact with ALA 125 (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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121A GLU 2.9 20.1 + - - +
122A ASP* 3.6 9.9 - - - +
124A ILE* 1.4 73.1 - - - +
126A ASP* 1.3 59.0 + - - +
128A THR* 3.3 4.7 + - - -
129A ASN* 2.9 38.3 + - - +
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Residues in contact with ASP 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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51A ASP* 2.5 34.7 - - - +
55A HIS* 3.0 22.3 - - + +
122A ASP 2.8 17.0 + - - +
123A MSE 3.7 6.3 - - - +
125A ALA* 1.3 78.2 - - - +
127A GLU* 1.3 64.9 + - - +
129A ASN* 3.3 15.6 + - - +
130A HIS* 3.2 27.4 + - - -
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Residues in contact with GLU 127 (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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51A ASP* 4.0 0.2 - - - +
52A GLU* 3.2 24.7 - - - +
55A HIS* 2.9 30.2 - - + -
94A GLU* 2.5 36.7 - - - +
97A THR* 3.8 26.1 - - + +
98A ILE* 3.6 21.4 - - + +
101A TYR* 4.4 5.6 - - + -
123A MSE 2.8 26.1 + - - +
126A ASP* 1.3 79.4 - - - +
128A THR* 1.3 60.9 + - - +
130A HIS* 3.2 2.0 + - - -
131A MSE 2.9 30.0 + - - +
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Residues in contact with THR 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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98A ILE* 3.6 19.7 - - - +
124A ILE* 2.8 33.9 + - - +
125A ALA* 3.6 5.8 - - - -
127A GLU* 1.3 73.7 - - - +
129A ASN* 1.3 68.2 + - - +
131A MSE 3.8 10.4 - - + +
132A GLU* 2.9 48.1 + - + +
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Residues in contact with ASN 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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125A ALA* 2.9 22.9 + - - +
126A ASP* 3.3 18.9 + - - +
128A THR* 1.3 77.1 - - - +
130A HIS* 1.3 67.6 + - + +
132A GLU* 3.5 11.7 + - - +
133A GLU* 3.1 23.4 + - - +
136A ARG* 4.3 3.3 + - - -
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Residues in contact with HIS 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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44A PHE* 4.9 4.4 - + - -
48A GLU* 3.2 37.4 + - - +
51A ASP* 2.5 36.3 + - + -
52A GLU* 3.8 13.8 + - - -
94A GLU* 3.5 22.9 + - + +
126A ASP* 3.2 20.8 + - - -
127A GLU* 3.2 5.1 + - - +
129A ASN* 1.3 81.2 - - + +
131A MSE 1.3 58.1 + - - +
133A GLU* 3.3 7.7 + - + +
134A LEU* 3.0 32.8 + - - +
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Residues in contact with MSE 131 (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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91A ARG* 3.6 58.1 - - + +
94A GLU* 4.1 8.7 + - + -
95A TYR* 4.0 20.6 - - + -
98A ILE* 4.0 20.6 - - + -
127A GLU 2.9 17.2 + - - +
128A THR* 3.3 10.3 + - + +
130A HIS* 1.3 76.9 - - - +
132A GLU* 1.3 68.7 + - + +
134A LEU* 3.3 12.7 + - - +
135A ASP* 3.0 32.3 + - - +
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Residues in contact with GLU 132 (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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128A THR* 2.9 38.8 + - + +
129A ASN* 3.8 11.0 - - - +
131A MSE 1.3 85.2 - - + +
133A GLU* 1.3 57.2 + - - +
135A ASP* 3.4 12.6 + - - +
136A ARG* 3.1 50.4 + - - +
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Residues in contact with GLU 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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44A PHE* 4.1 25.6 - - + -
129A ASN 3.1 17.0 + - - +
130A HIS* 3.6 8.3 - - + +
131A MSE 3.3 0.2 - - - -
132A GLU* 1.3 73.6 - - - +
134A LEU* 1.3 58.9 + - - +
136A ARG* 2.9 39.8 + - - +
137A LEU* 2.9 49.6 + - + +
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Residues in contact with LEU 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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26A TYR* 4.4 5.8 - - - +
44A PHE* 3.7 27.8 - - + -
45A PHE* 5.3 0.2 - - + -
48A GLU* 5.1 2.5 - - - +
87A LEU* 3.8 32.8 - - + +
90A ALA* 3.8 16.4 - - + +
91A ARG* 3.6 39.7 - - + +
94A GLU* 4.1 10.5 - - + -
130A HIS 3.0 18.6 + - - +
131A MSE 3.3 7.8 + - - +
133A GLU* 1.3 74.1 - - - +
135A ASP* 1.3 58.3 + - - +
137A LEU* 3.3 7.4 + - + +
138A LEU* 2.8 36.6 + - + +
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Residues in contact with ASP 135 (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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91A ARG* 2.8 48.0 + - - +
131A MSE 3.0 19.8 + - - +
132A GLU* 3.5 15.5 - - - +
133A GLU 3.2 0.2 - - - -
134A LEU* 1.3 76.0 - - - +
136A ARG* 1.3 56.1 + - - +
138A LEU* 4.4 5.0 - - - +
139A ASN* 2.8 47.7 + - - +
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Residues in contact with ARG 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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129A ASN* 4.3 3.2 + - - +
132A GLU* 3.1 36.1 + - - +
133A GLU* 2.9 60.2 + - - +
135A ASP* 1.3 76.7 - - + +
137A LEU* 1.3 65.3 + - + +
138A LEU 3.4 0.3 + - - -
139A ASN* 3.5 16.8 + - - +
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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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40A VAL* 6.2 3.4 - - + -
41A LEU* 4.3 18.2 - - + -
44A PHE* 4.0 37.7 - - + -
84A ARG* 5.4 0.2 + - - -
87A LEU* 4.5 16.8 - - + +
133A GLU* 2.9 35.1 + - + +
134A LEU* 3.6 14.1 - - + +
136A ARG* 1.3 78.3 - - + +
138A LEU* 1.3 60.6 + - - +
139A ASN 4.4 2.6 - - - +
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Residues in contact with LEU 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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84A ARG* 2.8 52.1 + - - +
87A LEU* 3.6 46.4 - - + +
88A GLU* 3.9 25.4 - - + -
91A ARG* 4.4 14.4 - - + -
134A LEU 2.8 29.3 + - - +
135A ASP* 3.8 8.1 - - - +
137A LEU* 1.3 72.9 - - - +
139A ASN* 1.3 69.9 + - - +
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Residues in contact with ASN 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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84A ARG* 5.3 3.9 + - - +
135A ASP* 2.8 39.8 + - - +
136A ARG* 3.5 14.2 + - - +
137A LEU 4.4 2.6 - - - +
138A LEU* 1.3 91.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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