Contacts of the helix formed by residues 105 - 136 (chain D) in PDB entry 2WLM
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ASP 4.7 5.8 - - - +
74D VAL* 2.8 37.9 + - + +
75D ILE 3.9 4.7 - - - +
76D GLU* 3.4 47.3 - - - +
103D ILE* 4.1 0.4 - - + +
104D PRO* 1.3 80.9 - - - +
106D GLY* 1.3 65.5 + - - +
109D ALA* 3.1 15.8 - - - +
110D ASN* 4.6 0.2 - - - +
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Residues in contact with GLY 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D ILE* 1.3 81.1 - - - +
107D PRO* 1.3 74.7 - - - +
108D LEU 3.4 1.6 - - - -
109D ALA 3.3 0.3 + - - -
110D ASN* 2.6 36.2 + - - +
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Residues in contact with PRO 107 (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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84A THR* 5.9 6.1 - - + -
88A PHE* 4.3 9.5 - - + -
106D GLY* 1.3 83.5 - - - +
108D LEU* 1.3 69.0 + - + +
110D ASN* 3.3 6.5 + - + +
111D THR* 2.8 34.9 + - - +
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Residues in contact with LEU 108 (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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71D CYS* 3.8 32.1 - - + -
74D VAL* 5.4 3.1 - - + -
106D GLY 3.4 1.0 - - - -
107D PRO* 1.3 82.7 - - + +
109D ALA* 1.3 67.8 + - - +
111D THR* 3.4 6.2 + - - +
112D LEU* 3.2 24.8 + - - +
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Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D TYR* 3.4 14.2 - - + -
71D CYS* 4.9 0.4 - - - -
74D VAL* 3.6 22.4 - - + +
75D ILE* 5.7 0.2 - - + -
104D PRO* 3.9 4.0 - - + -
105D ILE 3.1 42.7 + - - +
106D GLY 3.3 2.0 + - - +
108D LEU* 1.3 81.5 - - - +
110D ASN* 1.3 63.2 + - - +
112D LEU* 3.3 7.4 - - - +
113D VAL* 3.1 22.8 + - - +
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Residues in contact with ASN 110 (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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88A PHE* 3.1 39.8 - - + +
92A GLN* 4.3 8.7 + - - -
104D PRO* 2.8 35.6 - - - +
105D ILE 4.2 0.6 - - - +
106D GLY 2.6 39.0 + - - +
107D PRO* 4.3 1.0 - - - +
109D ALA* 1.3 73.7 - - - +
111D THR* 1.3 65.9 + - - +
113D VAL* 2.8 19.1 + - + +
114D THR* 2.8 17.0 + - - +
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Residues in contact with THR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 3.7 13.6 - - - -
107D PRO* 2.8 25.3 + - - +
108D LEU* 3.4 7.8 + - - +
110D ASN* 1.3 77.0 - - - +
112D LEU* 1.3 64.1 + - - +
114D THR* 3.1 9.6 + - - +
115D LEU* 3.0 31.6 + - + +
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D PHE* 3.5 16.0 - - + -
67D ALA* 3.5 48.9 - - + +
68D TYR* 3.5 26.9 + - + +
71D CYS* 4.3 9.4 - - - -
108D LEU 3.2 12.6 + - - +
109D ALA 3.3 9.2 - - - +
110D ASN 3.2 0.2 - - - -
111D THR* 1.3 78.5 - - - +
113D VAL* 1.3 57.1 + - - +
115D LEU* 3.4 15.6 + - + +
116D GLU* 2.9 30.3 + - - +
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 6.2 0.4 - - + -
91A VAL* 5.4 2.9 - - + -
92A GLN* 5.3 4.7 - - - +
97A ILE* 4.2 13.7 - - + -
99A TYR* 3.9 21.8 - - + +
68D TYR* 3.3 17.5 - - + +
89D PHE* 4.4 2.7 - - + -
93D THR* 3.7 17.3 + - - +
104D PRO* 3.8 20.2 - - + -
109D ALA 3.1 16.7 + - - +
110D ASN* 2.8 20.7 + - + +
112D LEU* 1.3 71.2 - - - +
114D THR* 1.3 60.0 + - + +
115D LEU 3.0 4.8 + - - -
116D GLU* 3.0 5.6 + - - +
117D ALA* 2.9 27.5 + - - +
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Residues in contact with THR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 3.4 35.6 + - - -
58A LEU* 4.8 9.4 - - - +
87A PHE* 4.7 5.6 - - + -
88A PHE* 3.2 31.0 - - + -
91A VAL* 3.9 28.9 - - + -
110D ASN 2.8 18.7 + - - +
111D THR* 3.4 9.6 + - - +
113D VAL* 1.3 75.1 - - + +
115D LEU* 1.3 62.3 + - - +
117D ALA* 4.2 4.9 - - - -
118D LEU* 3.7 5.2 + - - +
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Residues in contact with LEU 115 (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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54A THR* 5.9 5.6 - - + -
64D PHE* 4.3 17.9 - - + -
111D THR* 3.0 22.9 + - + +
112D LEU* 3.5 15.5 - - + +
114D THR* 1.3 78.2 + - - +
116D GLU* 1.3 66.2 + - - +
118D LEU* 3.4 14.8 + - + +
119D CYS* 3.0 28.0 + - - +
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Residues in contact with GLU 116 (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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61D ASN* 3.6 4.2 - - - +
64D PHE* 3.2 41.9 - - + +
68D TYR* 3.2 18.4 + - - -
90D SER* 2.6 27.4 + - - +
93D THR* 2.7 32.0 - - + +
94D MET* 3.5 21.6 - - + +
112D LEU 2.9 10.5 + - - +
113D VAL 3.4 7.6 - - - +
115D LEU* 1.3 73.3 - - - +
117D ALA* 1.3 68.3 + - - +
119D CYS* 2.7 5.7 + - + +
120D GLY* 2.6 22.0 + - - -
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Residues in contact with ALA 117 (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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57A TYR* 3.9 16.2 - - - +
91A VAL* 6.1 0.4 - - + -
95A ALA* 4.2 20.2 - - + -
97A ILE* 4.4 13.9 - - + -
93D THR 4.8 9.5 + - - +
94D MET* 4.7 4.2 - - - +
96D THR* 5.0 7.4 - - + +
113D VAL 2.9 14.8 + - - +
114D THR* 4.0 3.6 - - - +
116D GLU* 1.3 76.6 - - - +
118D LEU* 1.3 65.9 + - - +
120D GLY* 2.8 10.0 + - - -
121D MET* 3.0 13.2 + - - +
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Residues in contact with LEU 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 5.5 3.1 - - + -
53A ILE* 4.1 25.4 - - + -
54A THR* 4.0 27.6 - - + +
57A TYR* 3.9 32.6 + - + -
114D THR 3.7 11.5 + - - +
115D LEU* 3.4 18.6 + - + +
116D GLU 3.3 0.4 - - - -
117D ALA* 1.3 77.8 - - - +
119D CYS* 1.3 67.2 + - - +
121D MET* 3.3 5.5 + - + +
122D LEU* 3.0 47.1 + - + +
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Residues in contact with CYS 119 (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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64D PHE* 4.2 23.3 - - + -
94D MET* 4.9 4.5 - - + -
115D LEU* 3.0 21.1 + - - +
116D GLU* 2.7 21.0 + - + +
118D LEU* 1.3 76.7 - - - +
120D GLY* 1.3 61.3 + - - +
122D LEU* 3.3 10.0 + - - +
123D GLY* 2.9 21.3 + - - -
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Residues in contact with GLY 120 (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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94D MET* 3.4 37.4 - - - +
116D GLU 2.6 14.3 + - - -
117D ALA 2.8 6.0 + - - -
119D CYS* 1.3 73.8 - - - +
121D MET* 1.3 60.6 + - - -
123D GLY* 3.1 2.6 + - - -
124D LEU* 3.0 19.8 + - - +
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Residues in contact with MET 121 (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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124A LEU* 3.6 28.7 - - + +
94D MET 5.0 0.4 + - - -
117D ALA 3.0 9.9 + - - +
118D LEU* 3.9 7.6 - - + +
120D GLY* 1.3 70.5 - - - +
122D LEU* 1.3 63.1 + - + +
124D LEU* 2.9 12.4 + - + +
125D ALA* 2.8 28.2 + - - +
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Residues in contact with LEU 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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50A ILE* 4.5 24.9 - - + -
53A ILE* 4.7 16.8 - - + -
124A LEU* 6.5 0.4 - - + -
127A ALA* 5.2 7.9 - - + -
131A ILE* 4.7 20.8 - - + +
118D LEU* 3.0 45.5 + - + +
119D CYS* 3.6 9.9 - - - +
121D MET* 1.3 77.3 - - + +
123D GLY* 1.3 64.1 + - - +
125D ALA* 3.0 10.1 + - + +
126D VAL* 2.9 29.4 + - + +
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Residues in contact with GLY 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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119D CYS 2.9 14.1 + - - -
120D GLY 3.1 5.4 + - - -
122D LEU* 1.3 77.3 - - - +
124D LEU* 1.3 50.2 + - - +
126D VAL* 3.1 8.4 + - - +
127D ALA* 2.7 37.4 + - - +
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Residues in contact with LEU 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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124A LEU* 4.3 25.4 - - + -
121C MET* 3.6 40.4 - - + +
122C LEU* 6.4 1.1 - - + -
124C LEU* 4.4 19.3 - - + -
125C ALA* 5.4 5.6 - - + +
120D GLY 3.0 11.2 + - - +
121D MET* 2.9 12.9 + - - +
123D GLY* 1.3 76.1 - - - +
125D ALA* 1.3 54.6 + - - +
127D ALA* 3.7 7.7 - - + +
128D ALA* 2.8 40.8 + - + +
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Residues in contact with ALA 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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124A LEU* 5.4 5.6 - - + +
127A ALA* 5.1 1.1 - - + -
128A ALA* 4.0 24.6 - - + +
131A ILE* 4.0 26.5 - - + +
121D MET 2.8 15.5 + - - +
122D LEU* 3.3 13.0 - - + +
124D LEU* 1.3 74.5 - - - +
126D VAL* 1.3 54.6 + - - +
128D ALA* 3.8 6.0 - - - +
129D SER* 2.6 34.5 + - - -
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Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 6.3 0.9 - - + -
131A ILE* 3.9 22.9 - - + -
135A PHE* 4.2 23.2 - - + -
122D LEU* 2.9 19.9 + - + +
123D GLY* 3.6 8.7 - - - +
125D ALA* 1.3 75.2 - - - +
127D ALA* 1.3 66.2 + - - +
129D SER* 3.5 6.0 + - - -
130D LEU* 3.2 39.1 + - + +
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Residues in contact with ALA 127 (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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122C LEU* 5.2 9.0 - - + -
125C ALA* 5.8 1.3 - - + -
49D PHE* 4.7 0.2 - - - -
53D ILE* 4.5 22.2 - - + -
123D GLY 2.7 20.4 + - - +
124D LEU* 3.7 10.8 - - + +
126D VAL* 1.3 71.7 - - - +
128D ALA* 1.3 56.1 + - - +
130D LEU* 3.2 10.1 + - - +
131D ILE* 2.8 42.5 + - + +
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA* 6.2 2.7 - - + -
125C ALA* 4.0 29.2 - - + +
128C ALA* 6.2 2.0 - - + -
129C SER* 4.8 1.0 + - - -
124D LEU* 2.8 26.0 + - + +
125D ALA* 3.8 6.5 - - - +
127D ALA* 1.3 73.0 - - - +
129D SER* 1.3 53.2 + - - +
131D ILE* 3.1 3.9 + - - +
132D TYR* 2.7 38.1 + - - +
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Residues in contact with SER 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ALA 4.8 0.3 + - - -
131A ILE* 4.6 1.2 - - - +
132A TYR* 3.4 49.7 + - - +
135A PHE* 4.6 13.0 - - - -
136A THR* 4.7 2.5 - - - -
125D ALA 2.6 24.3 + - - -
126D VAL* 3.7 6.9 + - - -
127D ALA 3.3 0.2 - - - -
128D ALA* 1.3 75.3 - - - +
130D LEU* 1.3 53.2 + - - +
132D TYR* 3.6 3.3 - - - +
133D ALA* 2.6 40.3 + - - +
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Residues in contact with LEU 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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135A PHE* 3.6 23.6 - - + -
38D TYR* 4.2 15.5 - - + -
41D LEU* 4.1 39.0 - - + -
42D LEU* 4.2 6.3 - - + -
49D PHE* 3.9 22.9 - - + -
53D ILE* 5.7 3.1 - - + -
126D VAL* 3.2 29.0 + - + +
127D ALA* 3.5 8.7 - - - +
129D SER* 1.3 77.5 - - - +
131D ILE* 1.3 65.2 + - - +
133D ALA* 2.9 5.5 + - - +
134D ARG* 2.8 30.0 + - + +
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LEU* 4.7 15.0 - - + +
125C ALA* 4.0 15.9 - - + +
126C VAL* 3.8 38.8 - - + +
129C SER* 4.6 0.4 - - - +
46D TRP* 4.2 14.0 - - + -
49D PHE* 3.3 30.3 - - + -
53D ILE* 4.5 6.1 - - + -
127D ALA* 2.8 35.3 + - + +
128D ALA 3.3 5.2 - - - +
130D LEU* 1.3 71.9 - - - +
132D TYR* 1.3 53.8 + - - +
134D ARG* 3.2 6.5 + - - +
135D PHE* 2.6 44.1 + - + +
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Residues in contact with TYR 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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132A TYR* 3.7 31.2 - + + -
129C SER* 3.4 43.9 + - - +
132C TYR* 3.6 39.5 - + + -
133C ALA* 4.8 2.1 - - - -
128D ALA 2.7 19.8 + - - +
129D SER* 3.7 4.9 - - - +
131D ILE* 1.3 73.6 - - - +
133D ALA* 1.3 59.7 + - - +
135D PHE* 4.2 1.3 - - - -
136D THR* 2.6 71.4 + - + +
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Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A TYR* 4.9 1.8 - - + +
136A THR* 4.4 9.2 - - + -
250A PHE 5.6 1.2 - - - +
38D TYR* 4.0 16.2 - - + +
42D LEU* 3.7 20.7 - - + +
129D SER 2.6 23.4 + - - +
130D LEU* 3.4 4.7 - - - +
132D TYR* 1.3 83.0 - - + +
134D ARG* 1.3 61.0 + - - +
136D THR* 3.9 7.6 + - - +
137D ARG* 3.7 14.8 + - - +
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Residues in contact with ARG 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU 2.5 37.9 + - - -
42D LEU* 3.9 26.0 + - + +
44D VAL 2.9 29.7 + - - -
46D TRP* 3.4 61.0 + - + +
49D PHE* 3.5 36.0 - - - +
130D LEU 2.8 34.2 + - - +
131D ILE 3.5 6.3 - - - +
133D ALA* 1.3 73.1 - - - +
135D PHE* 1.3 63.7 + - - +
137D ARG* 3.5 25.2 - - - +
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Residues in contact with PHE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C HIS* 4.5 21.3 - + - -
38C TYR* 3.9 25.4 - + - +
41C LEU* 4.8 8.5 - - + -
126C VAL* 4.1 23.6 - - + -
129C SER* 4.6 12.8 - - - -
130C LEU* 3.4 42.0 - - + -
46D TRP* 4.2 20.4 - + + -
131D ILE* 2.6 33.6 + - + +
132D TYR* 4.0 4.5 - - - +
134D ARG* 1.3 76.3 - - - +
136D THR* 1.3 58.4 + - + +
137D ARG 2.9 10.5 + - - +
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Residues in contact with THR 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ALA* 5.6 0.9 - - - +
38C TYR* 3.3 28.3 - - + +
129C SER* 4.7 7.0 - - - +
133C ALA* 4.3 10.8 - - + -
132D TYR* 2.6 68.3 + - + +
133D ALA* 3.9 5.0 + - - +
134D ARG 3.4 0.4 - - - -
135D PHE* 1.3 74.4 - - + +
137D ARG* 1.3 64.5 + - - +
138D PRO* 3.8 0.8 - - - +
252D GLN* 3.6 23.5 + - - +
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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