Contacts of the helix formed by residues 105 - 136 (chain A) in PDB entry 1XL4
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 ILE 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ASP 4.7 5.2 - - - +
74A VAL* 2.7 48.7 + - + +
75A ILE 4.4 0.2 - - - -
76A GLU* 3.3 50.3 - - + +
103A ILE* 4.9 1.1 - - + -
104A PRO* 1.3 92.8 - - - +
106A GLY* 1.3 68.4 + - - +
109A ALA* 3.4 2.5 - - - +
110A ASN* 4.5 0.7 - - - +
101B LYS* 5.1 8.5 - - - +
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ILE* 1.3 74.7 - - - +
107A PRO* 1.3 75.3 - - - +
108A LEU 2.9 6.3 + - - -
109A ALA 3.1 10.6 + - - -
110A ASN* 3.0 22.1 + - - +
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Residues in contact with PRO 107 (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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106A GLY* 1.3 82.2 - - - +
108A LEU* 1.3 60.4 + - + +
110A ASN* 3.9 1.3 - - - +
111A THR* 2.6 35.0 + - - +
79B ARG* 5.0 10.8 - - - +
84B THR* 4.8 16.6 - - + +
88B PHE* 4.2 15.1 - - + -
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A CYS* 3.9 41.2 - - + +
74A VAL* 5.0 5.2 - - + -
106A GLY 2.9 1.4 + - - -
107A PRO* 1.3 77.6 - - + +
109A ALA* 1.3 67.2 + - - +
111A THR* 3.1 16.0 + - - +
112A LEU* 3.3 17.5 + - - +
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 3.5 17.5 - - + -
71A CYS* 5.7 0.2 - - - -
74A VAL* 3.5 25.2 - - + +
75A ILE* 5.3 0.4 - - + -
104A PRO* 3.8 5.8 - - + -
105A ILE 3.4 37.8 + - - +
106A GLY 3.1 2.2 + - - +
108A LEU* 1.3 77.9 - - - +
110A ASN* 1.3 58.3 + - - +
112A LEU* 3.3 2.4 + - - -
113A VAL* 3.1 31.9 + - - +
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 3.9 19.7 - - - +
105A ILE* 4.1 1.2 - - - +
106A GLY 3.0 36.9 + - - +
107A PRO 4.0 0.2 - - - +
109A ALA* 1.3 74.8 - - - +
111A THR* 1.3 59.5 + - - +
112A LEU 3.3 0.2 - - - -
113A VAL* 3.7 8.9 - - - +
114A THR* 3.0 28.8 + - - -
88B PHE* 3.1 42.7 - - + +
92B GLN* 3.8 20.3 + - - -
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PRO* 2.6 23.6 + - - +
108A LEU* 3.1 8.3 + - - +
110A ASN* 1.3 76.2 - - - +
112A LEU* 1.3 67.1 + - + +
114A THR* 3.7 7.2 + - - +
115A LEU* 3.3 23.5 + - + +
88B PHE* 3.9 12.8 - - + -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.9 14.1 - - + -
67A ALA* 3.6 39.0 - - + +
68A TYR* 3.3 44.4 - - + +
71A CYS* 4.2 12.1 - - - -
108A LEU 3.3 9.2 + - - +
109A ALA 3.3 1.7 + - - +
111A THR* 1.3 80.1 - - + +
113A VAL* 1.3 54.3 + - - +
115A LEU* 3.1 12.8 + - + +
116A GLU* 2.6 37.9 + - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 3.5 14.8 - - - +
89A PHE* 4.1 3.8 - - + -
93A THR* 3.8 17.0 - - + +
104A PRO* 3.5 27.4 - - + -
109A ALA 3.1 16.2 + - - +
110A ASN* 3.7 10.1 - - - +
112A LEU* 1.3 75.8 - - - +
114A THR* 1.3 59.1 + - - +
116A GLU* 3.2 0.9 + - - +
117A ALA* 2.8 30.5 + - - +
91B VAL* 5.0 3.8 - - + -
92B GLN* 5.0 8.5 - - + +
97B ILE* 3.9 16.4 - - + -
99B TYR* 3.7 19.1 - - + +
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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
----------------------------------------------------------
110A ASN 3.0 17.5 + - - -
111A THR* 3.8 8.5 - - - +
113A VAL* 1.3 78.4 - - - +
115A LEU* 1.3 63.1 + - - +
117A ALA* 3.4 0.5 - - - +
118A LEU 3.3 10.2 + - - -
57B TYR* 3.0 45.0 + - + +
58B LEU* 4.2 14.4 - - + -
87B PHE* 4.4 5.2 - - + -
88B PHE* 3.7 12.2 - - - -
91B VAL* 3.4 35.5 - - + +
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Residues in contact with LEU 115 (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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64A PHE* 4.8 7.6 - - + -
111A THR* 3.3 17.6 + - + +
112A LEU* 3.1 17.2 + - + +
114A THR* 1.3 78.8 - - - +
116A GLU* 1.3 65.5 + - - +
117A ALA 3.1 0.2 - - - -
118A LEU* 3.1 20.8 + - + +
119A CYS* 3.0 35.3 + - - -
54B THR* 5.2 8.5 - - + -
57B TYR* 5.5 0.7 - - + -
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 3.8 1.4 - - - +
64A PHE* 3.3 34.4 - - + -
68A TYR* 2.9 28.6 + - - -
90A SER* 2.3 42.6 + - - +
93A THR* 3.6 10.2 - - + -
94A MET* 3.6 30.0 - - + +
112A LEU 2.6 20.4 + - - +
113A VAL* 3.7 3.6 - - - +
115A LEU* 1.3 73.3 - - - +
117A ALA* 1.3 61.1 + - - +
119A CYS* 3.7 2.6 - - - +
120A GLY* 3.1 19.2 + - - -
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Residues in contact with ALA 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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93A THR* 5.0 6.7 - - - +
94A MET* 5.2 3.5 - - - +
96A THR* 5.7 1.6 - - - -
113A VAL 2.8 17.3 + - - +
114A THR* 3.4 8.5 - - - +
116A GLU* 1.3 77.5 - - - +
118A LEU* 1.3 61.3 + - - +
120A GLY* 3.6 0.7 + - - -
121A MET* 3.1 22.7 + - - +
57B TYR* 3.8 11.4 - - + +
91B VAL* 4.8 1.1 - - + -
95B ALA* 3.8 25.4 - - + +
97B ILE* 4.0 13.7 - - + -
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Residues in contact with LEU 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 3.3 9.0 + - - +
115A LEU* 3.1 18.9 + - + +
117A ALA* 1.3 76.8 - - - +
119A CYS* 1.3 61.0 + - - +
121A MET* 3.2 28.9 + - + +
122A LEU* 2.8 49.9 + - + +
50B ILE* 5.9 0.2 - - + -
53B ILE* 4.6 6.1 - - + -
54B THR* 3.4 43.1 - - + +
57B TYR* 3.8 37.2 + - + -
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Residues in contact with CYS 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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60A THR* 5.5 4.5 - - + -
64A PHE* 3.9 26.9 - - + -
94A MET* 5.2 6.5 - - - -
115A LEU* 3.0 27.6 + - - -
116A GLU* 3.7 8.1 - - - +
117A ALA 3.3 0.2 - - - -
118A LEU* 1.3 74.1 - - - +
120A GLY* 1.3 55.2 + - - +
122A LEU* 3.3 8.6 + - - +
123A GLY* 2.6 34.0 + - - -
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Residues in contact with GLY 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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94A MET* 3.6 36.9 - - - +
116A GLU 3.1 11.9 + - - -
117A ALA 4.1 0.4 - - - -
119A CYS* 1.3 76.3 - - - +
121A MET* 1.3 57.6 + - - +
123A GLY* 3.6 1.9 - - - -
124A LEU* 2.9 29.3 + - - +
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Residues in contact with MET 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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117A ALA 3.1 15.7 + - - +
118A LEU* 3.3 31.9 - - + +
120A GLY* 1.3 79.7 - - - +
122A LEU* 1.3 78.3 + - + +
124A LEU* 3.3 6.0 + - - +
125A ALA* 3.3 17.1 + - - +
53B ILE* 4.7 6.1 - - + -
57B TYR* 5.7 4.0 - - + -
123B GLY 4.6 3.1 - - - +
124B LEU* 3.7 42.6 - - + +
127B ALA* 3.9 23.6 - - + -
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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
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118A LEU* 2.8 39.6 + - + +
119A CYS* 3.8 8.1 - - - +
121A MET* 1.3 96.1 - - + +
123A GLY* 1.3 57.4 + - - +
125A ALA* 3.2 5.9 + - - +
126A VAL* 2.9 37.0 + - + +
50B ILE* 4.6 24.5 - - + -
53B ILE* 4.3 22.2 - - + -
54B THR* 5.6 0.2 - - - +
127B ALA* 4.9 1.3 - - + -
131B ILE* 4.5 17.3 - - + -
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Residues in contact with GLY 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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119A CYS 2.6 22.7 + - - -
120A GLY* 3.6 3.1 - - - -
121A MET 3.2 0.4 - - - -
122A LEU* 1.3 73.7 - - - +
124A LEU* 1.3 56.5 + - - +
126A VAL* 3.4 5.6 + - - +
127A ALA* 2.9 31.6 + - - +
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Residues in contact with LEU 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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120A GLY 2.9 16.0 + - - +
121A MET* 3.6 4.9 - - - +
123A GLY* 1.3 75.2 - - - +
125A ALA* 1.3 59.6 + - - +
127A ALA* 3.4 5.8 + - + +
128A ALA* 2.8 40.9 + - + +
124B LEU* 3.8 29.4 - - + -
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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 MET* 3.3 10.6 + - - +
122A LEU* 3.2 10.9 + - - +
124A LEU* 1.3 81.9 - - - +
126A VAL* 1.3 60.8 + - - +
128A ALA* 3.3 5.3 + - - +
129A SER* 2.9 28.1 + - - -
124B LEU* 4.5 6.9 - - + +
127B ALA 4.8 0.7 - - - -
128B ALA* 3.8 37.6 - - + +
131B ILE* 4.0 13.9 - - + -
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Residues in contact with VAL 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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122A LEU* 2.9 24.6 + - + +
123A GLY* 3.8 5.4 - - - +
125A ALA* 1.3 75.7 - - - +
127A ALA* 1.3 59.7 + - - +
129A SER* 2.8 23.6 + - - -
130A LEU* 2.9 31.1 + - + +
46B TRP* 6.5 0.4 - - + -
131B ILE* 4.3 23.3 - - + -
135B PHE* 4.5 15.3 - - + -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 4.8 0.2 - - - -
53A ILE* 4.7 21.8 - - + -
123A GLY 2.9 18.6 + - - +
124A LEU* 3.8 7.2 - - + +
126A VAL* 1.3 77.9 - - - +
128A ALA* 1.3 59.2 + - - +
130A LEU* 3.7 9.3 + - - +
131A ILE* 3.0 37.7 + - + +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 2.8 28.5 + - + +
125A ALA* 3.6 6.3 - - - +
127A ALA* 1.3 74.5 - - - +
129A SER* 1.3 65.7 + - - +
131A ILE* 3.6 8.4 + - - +
132A TYR* 3.0 23.4 + - - +
128B ALA* 6.1 2.2 - - + -
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Residues in contact with SER 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA 2.9 17.4 + - - -
126A VAL 2.8 9.0 + - - -
128A ALA* 1.3 73.5 - - - +
130A LEU* 1.3 67.3 + - - -
132A TYR* 3.0 5.7 + - - +
133A ALA* 2.8 24.3 + - - +
128B ALA 4.5 2.3 + - - -
131B ILE* 4.0 3.5 - - - +
132B TYR* 3.7 38.8 + - - +
135B PHE* 3.7 27.4 - - - -
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Residues in contact with LEU 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 4.2 30.7 - - + -
41A LEU* 3.7 32.3 - - + -
42A LEU* 4.3 10.3 - - + -
49A PHE* 3.7 27.1 - - + -
53A ILE* 5.3 4.7 - - + -
126A VAL* 2.9 32.3 + - + +
127A ALA* 3.9 6.7 - - - +
129A SER* 1.3 77.6 - - - +
131A ILE* 1.3 58.2 + - - +
133A ALA* 3.1 5.0 + - + +
134A ARG* 2.8 37.4 + - - +
135B PHE* 4.9 9.0 - - + -
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Residues in contact with ILE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 4.3 14.8 - - + -
49A PHE* 3.7 22.7 - - + -
53A ILE* 5.3 2.9 - - + -
127A ALA* 3.0 26.0 + - + +
128A ALA* 3.9 7.6 - - - +
130A LEU* 1.3 77.1 - - - +
132A TYR* 1.3 62.6 + - - +
134A ARG* 3.5 3.5 + - - +
135A PHE* 3.2 46.6 + - + -
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Residues in contact with TYR 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA 3.0 12.4 + - - +
129A SER* 3.0 9.4 + - - +
131A ILE* 1.3 75.3 - - - +
133A ALA* 1.3 58.0 + - - +
135A PHE* 2.8 43.1 + + + +
136A THR* 3.1 32.3 + - + +
252A GLN* 5.8 0.2 + - - -
132B TYR* 3.5 37.0 - + + -
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 5.5 4.5 - - + +
42A LEU* 3.4 25.8 - - + -
129A SER 2.8 16.8 + - - +
130A LEU* 3.4 5.8 - - + +
132A TYR* 1.3 74.7 - - - +
134A ARG* 1.3 57.8 + - - +
136A THR* 2.7 33.3 + - - +
137A ARG* 3.2 15.7 - - - +
132B TYR* 4.3 15.5 - - + +
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Residues in contact with ARG 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU 3.0 29.8 + - - +
42A LEU* 3.6 23.5 + - + +
44A VAL 2.9 24.5 + - - -
45A SER* 3.6 0.4 - - - +
46A TRP* 2.9 77.3 - - + +
49A PHE* 3.5 30.1 - - - +
130A LEU 2.8 22.1 + - - +
131A ILE 3.8 4.9 - - - +
133A ALA* 1.3 72.8 - - - +
135A PHE* 1.3 61.8 + - - +
136A THR 3.5 0.3 + - - -
137A ARG* 3.7 20.7 + - - +
138A PRO* 5.7 0.2 - - - +
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Residues in contact with PHE 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 3.5 31.4 - + - -
131A ILE* 3.2 28.6 + - + -
132A TYR* 2.8 27.8 + + + +
134A ARG* 1.3 79.6 - - - +
136A THR* 1.3 58.0 + - + +
137A ARG 3.4 3.1 + - - -
138A PRO* 3.8 9.2 - - - +
250A PHE* 5.5 1.7 - - - +
252A GLN* 3.7 7.8 + - - +
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR* 3.3 46.0 - - + +
133A ALA* 2.7 26.0 + - - +
135A PHE* 1.3 80.0 - - + +
137A ARG* 1.3 60.7 + - - +
138A PRO* 3.5 0.7 - - - +
252A GLN* 3.0 31.0 + - - +
132B TYR* 4.2 5.4 + - - +
251B ALA* 4.2 12.3 - - - +
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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