Contacts of the helix formed by residues 109 - 136 (chain A) in PDB entry 5X6E
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 ASN 109 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A GLU* 5.4 0.4 + - - -
11A TYR* 3.7 27.3 - - + -
105A LEU 3.5 2.6 + - - -
106A LEU* 2.6 22.5 + - - +
108A LYS* 1.3 82.7 - - + +
110A LEU* 1.3 57.0 + - - +
111A THR* 2.6 43.9 + - - -
112A HIS* 2.9 35.0 + - + +
113A PHE* 3.3 13.9 + - - +
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Residues in contact with LEU 110 (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 LEU 3.3 21.1 - - - +
107A SER 4.0 12.8 - - - +
108A LYS 5.5 0.4 - - - -
109A ASN* 1.3 72.0 + - - +
111A THR* 1.3 64.0 + - - +
112A HIS 3.3 1.3 - - - -
113A PHE* 3.6 20.6 - - + -
114A PHE* 3.4 32.3 + - + +
107B SER* 3.2 41.3 - - - +
110B LEU* 4.2 17.0 - - + -
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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
----------------------------------------------------------
4A GLN* 3.9 22.9 + - + +
7A GLU* 4.3 16.4 - - - +
109A ASN* 2.6 22.0 + - - -
110A LEU* 1.3 74.2 - - - +
112A HIS* 1.3 60.7 + - + +
114A PHE* 4.2 2.8 + - - +
115A TYR 4.1 4.5 + - - -
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Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 4.6 6.5 - - + -
7A GLU* 2.2 64.7 + - - -
8A PHE* 3.6 30.5 - + + -
10A LYS* 3.8 3.8 - - + -
11A TYR* 3.1 28.9 - + + +
106A LEU* 5.6 1.3 - - + -
109A ASN* 2.9 31.0 + - + +
111A THR* 1.3 79.6 - - + +
113A PHE* 1.3 69.9 + - - +
114A PHE 3.2 0.4 - - - -
115A TYR* 2.9 25.2 + - + +
116A VAL* 3.4 8.6 + - - +
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Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 5.6 0.7 - - + -
106A LEU* 2.9 58.9 - - + +
107A SER* 4.2 4.0 - - - -
109A ASN 3.3 16.2 + - - +
110A LEU* 3.6 22.7 - - + +
112A HIS* 1.3 77.4 - - - +
114A PHE* 1.3 69.7 + + + +
116A VAL* 2.9 27.7 + - - +
117A PHE* 3.5 3.1 + - + -
110B LEU* 5.0 4.9 - - + -
113B PHE* 3.0 53.2 - + - -
114B PHE* 3.7 21.3 - + - -
117B PHE* 4.7 10.3 - + - -
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 6.2 0.4 - - - +
110A LEU* 3.4 36.2 + - + +
111A THR 4.7 3.4 - - - +
112A HIS 3.2 0.6 - - - -
113A PHE* 1.3 87.3 - + + +
115A TYR* 1.3 54.2 + - - +
117A PHE* 2.9 23.4 + + - +
118A GLN* 2.7 37.3 + - + +
74B ILE* 4.3 36.6 - - + -
102B LEU 5.0 0.9 - - - -
103B LYS* 4.5 17.7 - - - -
106B LEU* 4.7 6.7 - - + -
107B SER* 4.8 9.9 - - - -
110B LEU* 6.5 0.9 - - + -
113B PHE* 3.7 32.1 - + - -
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Residues in contact with TYR 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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2A ASN 5.5 2.7 - - - -
4A GLN* 3.7 41.1 - - + +
5A ALA* 3.1 35.3 - - + +
8A PHE* 3.9 39.3 - + + -
40A PHE* 3.9 9.6 - + - -
66A ALA* 3.9 18.0 + - - +
67A PHE* 4.4 2.4 + - - -
68A VAL* 4.7 5.8 - - + -
111A THR 4.1 2.2 + - - -
112A HIS* 2.9 18.7 + - - +
114A PHE* 1.3 78.0 - - - +
116A VAL* 1.3 60.5 + - + +
118A GLN* 2.6 25.3 - - - +
119A THR* 3.1 29.3 - - + +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 4.1 21.5 - - + -
38A CYS* 5.6 5.2 - - - -
68A VAL* 4.0 22.0 - - + -
70A MET* 5.0 6.3 - - - -
102A LEU* 6.1 1.3 - - + -
106A LEU* 3.8 25.8 - - + -
112A HIS 4.0 7.0 - - - +
113A PHE 2.9 14.1 + - - +
115A TYR* 1.3 85.0 - - + +
117A PHE* 1.3 60.6 + - - +
119A THR* 2.2 29.1 + - - -
120A LEU* 3.4 5.0 + - - +
117B PHE* 4.0 24.0 - - + -
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.5 3.2 + - + +
114A PHE* 2.9 23.9 + + - +
116A VAL* 1.3 80.7 - - - +
118A GLN* 1.3 62.6 + - + +
120A LEU* 3.2 9.2 - - + +
121A GLN* 3.0 35.5 + - - +
70B MET* 4.5 9.6 - - + -
74B ILE* 3.4 32.5 - - + -
106B LEU* 6.0 1.3 - - + -
113B PHE* 4.3 17.3 - + + -
116B VAL* 4.4 23.3 - - + -
117B PHE* 3.9 36.6 - + + -
120B LEU* 3.5 33.9 - - + -
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLN* 4.4 12.1 + - - +
114A PHE* 2.7 27.1 + - + +
115A TYR* 2.6 38.9 - - - +
117A PHE* 1.3 77.8 - - + +
119A THR* 1.3 57.1 + - - +
120A LEU 3.0 1.1 - - - -
121A GLN* 3.1 22.3 - - + +
122A LYS* 2.3 47.2 + - + +
73B PHE* 5.0 4.3 - - + -
74B ILE* 5.3 3.8 - - + +
75B ASP* 3.8 43.8 + - + +
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA 5.9 0.2 - - - +
67A PHE* 3.3 44.8 - - + -
68A VAL* 3.2 25.9 - - + +
115A TYR* 3.1 38.8 - - + +
116A VAL* 2.2 27.4 + - - -
118A GLN* 1.3 78.7 + - - +
120A LEU* 1.3 61.7 + - - +
122A LYS* 3.3 9.9 + - - +
123A GLN* 3.2 18.0 + - - +
301A GSH 5.8 0.9 - - - +
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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
----------------------------------------------------------
70A MET* 5.6 5.4 - - + -
116A VAL 3.4 4.7 + - - +
117A PHE* 3.2 16.2 - - + +
118A GLN 3.0 0.2 - - - -
119A THR* 1.3 83.2 + - - +
121A GLN* 1.3 53.5 + - - +
123A GLN* 3.3 12.3 + - - +
124A VAL* 3.2 31.7 + - - +
117B PHE* 3.4 46.2 - - + +
120B LEU* 3.5 32.1 - - + -
121B GLN* 4.0 14.4 - - + +
124B VAL* 3.8 24.9 - - + -
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Residues in contact with GLN 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 3.0 25.8 + - - +
118A GLN* 2.8 19.1 + - - +
120A LEU* 1.3 72.4 - - - +
122A LYS* 1.3 62.1 + - - +
123A GLN 3.2 0.9 - - - -
124A VAL* 3.2 29.0 - - + +
125A SER* 3.3 8.7 + - - -
70B MET* 3.5 29.7 - - + +
72B GLY 2.4 35.8 + - - -
73B PHE* 3.4 24.7 - - + +
74B ILE* 3.8 11.6 + - - +
80B VAL* 3.8 4.0 - - + +
120B LEU* 4.4 12.1 - - + +
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Residues in contact with LYS 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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67A PHE* 4.2 13.9 - - + -
118A GLN* 2.3 42.0 + - + +
119A THR* 3.5 11.2 - - - +
121A GLN* 1.3 70.0 - - - +
123A GLN* 1.3 56.4 - - - +
125A SER* 2.9 17.1 + - - -
126A TYR* 3.2 7.1 - - - +
224A TRP* 3.0 22.0 + - + +
228A ALA* 4.0 20.2 - - + -
229A CYS* 3.6 16.8 - - - +
301A GSH 2.3 45.1 + - - -
73B PHE* 4.3 14.1 - - + -
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Residues in contact with GLN 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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61A GLN* 2.8 38.5 + - - +
63A TYR* 3.0 15.7 + - - -
67A PHE* 4.1 15.4 - - - -
68A VAL 5.0 2.4 + - - -
69A ILE* 6.1 1.2 - - - +
119A THR 3.2 10.8 + - - +
120A LEU* 3.7 14.4 - - - +
121A GLN 3.2 0.2 - - - -
122A LYS* 1.3 75.6 - - - +
124A VAL* 1.3 56.1 + - - +
125A SER 3.1 1.8 - - - -
126A TYR* 4.0 4.9 - - + -
127A SER* 2.7 51.4 + - - +
301A GSH 4.1 6.3 - - - -
124B VAL* 3.9 27.3 - - + +
128B LEU* 4.6 6.8 - - - +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LEU 3.2 14.1 + - - +
121A GLN* 3.2 28.0 - - + +
123A GLN* 1.3 74.8 - - - +
125A SER* 1.3 62.0 + - - +
127A SER* 4.3 4.3 - - - -
128A LEU* 3.2 33.9 + - + +
70B MET* 5.7 4.9 - - + -
80B VAL* 6.0 3.8 - - + -
120B LEU* 4.2 29.2 - - + +
123B GLN* 4.7 15.9 - - + +
124B VAL* 3.5 26.5 - - + +
127B SER* 5.0 2.8 + - - -
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Residues in contact with SER 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 GLN 3.3 10.9 + - - -
122A LYS* 2.9 9.5 + - - -
124A VAL* 1.3 80.6 - - - +
126A TYR* 1.3 52.9 + - - -
128A LEU* 3.2 6.7 + - - +
129A ALA* 2.7 37.1 + - - +
224A TRP* 2.5 34.2 + - - -
73B PHE* 4.1 4.4 - - - -
80B VAL* 3.5 32.3 - - - -
83B TYR* 4.2 4.9 + - - -
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Residues in contact with TYR 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 GLN* 3.5 33.4 - - + -
122A LYS 3.2 17.0 + - - +
123A GLN* 3.3 5.4 + - + +
125A SER* 1.3 81.4 + - - +
127A SER* 1.3 61.3 + - - +
129A ALA* 3.8 1.0 - - - +
130A LYS* 2.8 68.5 + - + +
149A ILE* 3.5 21.6 - - + +
221A LEU* 5.1 6.2 - - + +
224A TRP* 3.3 42.2 - + + +
225A PHE* 5.4 1.1 - + - -
301A GSH 2.2 50.3 + - + -
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Residues in contact with SER 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN* 4.2 6.8 + - - -
123A GLN* 2.7 40.1 + - - +
124A VAL* 4.3 3.8 - - - -
126A TYR* 1.3 76.6 - - - +
128A LEU* 1.3 57.5 + - - +
130A LYS* 3.7 6.3 - - - +
131A PHE* 2.8 31.7 + - - +
124B VAL* 5.2 2.3 - - - +
127B SER* 3.7 30.4 - - - -
128B LEU* 4.9 10.0 - - - +
131B PHE* 6.0 1.7 - - - +
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A VAL* 3.2 23.5 + - + +
125A SER* 3.2 6.1 + - - +
127A SER* 1.3 75.8 - - - +
129A ALA* 1.3 60.5 + - - +
131A PHE* 3.2 11.0 + - + +
132A ASN* 2.9 30.5 + - - +
48B LEU* 3.9 25.1 - - + -
60B LEU* 4.1 30.9 - - + +
61B GLN* 4.0 20.4 - - + +
63B TYR* 4.6 0.7 - - - +
83B TYR* 4.2 14.1 - - + +
123B GLN* 3.6 17.9 - - - +
127B SER* 4.1 11.2 - - - +
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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
----------------------------------------------------------
125A SER 2.7 21.0 + - - +
126A TYR 3.8 3.1 - - - +
128A LEU* 1.3 73.3 - - - +
130A LYS* 1.3 62.4 + - - +
132A ASN* 3.4 14.5 + - - +
133A ASP 3.5 1.9 + - - -
220A LYS* 3.6 31.2 - - + +
221A LEU* 3.2 16.7 - - + +
224A TRP* 4.1 16.8 - - + -
83B TYR* 3.6 16.0 + - - +
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Residues in contact with LYS 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU 4.0 12.8 + - - -
61A GLN* 5.0 0.4 - - - +
126A TYR* 2.8 62.3 + - + +
127A SER* 3.7 5.2 - - - +
129A ALA* 1.3 72.4 - - - +
131A PHE* 1.3 64.7 + - - +
132A ASN 3.2 0.2 + - - -
133A ASP* 3.3 1.6 + - - -
134A PHE* 3.0 50.9 + - + -
146A GLN* 3.2 24.5 + - - -
149A ILE* 3.3 9.6 - - - +
221A LEU* 3.5 16.7 - - + +
301A GSH 4.1 1.8 + - - -
131B PHE* 3.4 33.3 - - + -
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Residues in contact with PHE 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER 2.8 22.2 + - - +
128A LEU* 3.2 9.6 + - + +
130A LYS* 1.3 75.4 - - - +
132A ASN* 1.3 56.6 + - - +
134A PHE* 4.5 5.2 - - + -
135A SER* 2.3 46.6 + - - -
58B MET* 3.5 21.5 - - + -
59B ASN 4.7 0.2 - - - -
60B LEU* 3.7 36.1 - - + -
127B SER* 5.7 3.8 - - - +
130B LYS* 4.0 20.6 - - + -
131B PHE* 4.5 27.1 - + + -
134B PHE* 3.4 48.2 - + + -
177B SER 4.4 0.4 - - - -
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Residues in contact with ASN 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU 2.9 13.2 + - - +
129A ALA* 3.5 10.1 - - - +
130A LYS 3.1 0.4 - - - -
131A PHE* 1.3 79.5 - - - +
133A ASP* 1.3 82.6 + - - +
134A PHE 3.6 0.2 + - - -
135A SER* 3.9 2.9 - - - -
136A ILE* 3.4 30.2 + - - +
220A LYS* 3.4 21.4 - - + +
50B SER* 3.5 20.6 + - - -
58B MET* 3.3 31.6 - - - +
60B LEU* 3.7 14.2 - - + +
83B TYR* 5.4 0.4 - - + -
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 3.5 0.4 + - - -
130A LYS 3.3 2.2 + - - -
132A ASN* 1.3 99.1 + - - +
134A PHE* 1.3 62.9 + - + +
135A SER 3.4 0.4 - - - -
136A ILE* 2.9 27.2 - - + +
137A ASN* 4.9 0.2 - - - +
141A GLY* 4.5 10.3 - - - +
145A GLY* 6.1 0.2 - - - -
217A TYR 3.8 17.9 - - - +
218A ALA* 3.1 14.1 - - + -
219A PRO* 3.6 15.3 - - - +
220A LYS* 2.8 34.2 + - - +
221A LEU* 3.1 23.2 - - + +
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Residues in contact with PHE 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LYS* 3.0 47.9 + - + +
131A PHE* 4.3 4.7 - - + +
133A ASP* 1.3 83.4 - - + +
135A SER* 1.3 63.4 + - - +
138A GLY 3.4 18.5 - - - +
141A GLY 5.1 0.2 - - - -
142A SER* 3.4 52.9 + - - +
145A GLY* 3.9 17.3 - - - -
146A GLN* 4.2 17.3 - - + -
177A SER 4.1 10.5 - - - -
178A SER* 4.2 5.6 - - - -
179A GLY 5.5 0.2 - - - -
221A LEU* 4.8 5.2 - - + -
131B PHE* 3.4 37.7 - + + -
135B SER* 4.9 4.0 - - - +
139B LYS* 5.0 0.9 + - - -
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 2.3 41.4 + - - -
132A ASN 3.9 0.9 - - - -
133A ASP 3.4 0.4 - - - -
134A PHE* 1.3 79.7 - - - +
136A ILE* 1.3 60.9 + - - +
137A ASN 4.2 0.2 + - - -
138A GLY* 4.5 3.3 + - - -
58B MET* 3.4 34.3 - - - +
134B PHE* 5.1 2.9 - - - -
139B LYS* 2.5 32.0 + - - +
178B SER 4.4 0.7 - - - -
179B GLY* 3.7 11.0 - - - +
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASN* 3.4 31.9 - - - +
133A ASP* 2.9 31.1 - - - +
134A PHE 3.6 2.6 - - - +
135A SER* 1.3 78.4 - - - +
137A ASN* 1.3 80.2 + - + +
138A GLY 3.3 1.6 + - - +
217A TYR 5.8 0.9 - - - +
219A PRO* 6.0 3.4 - - + -
52B SER* 5.6 5.6 - - - -
56B THR* 4.6 28.3 - - + +
57B ILE 5.5 4.0 - - - +
58B MET* 4.5 18.6 - - + -
179B GLY 4.1 16.2 - - - +
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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