Contacts of the helix formed by residues 111 - 135 (chain A) in PDB entry 2WWB
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 LEU 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 3.8 32.1 - - + +
108A ASP 4.1 12.6 - - - +
109A ARG* 3.6 7.1 - - + +
110A ALA* 1.4 78.2 - - - +
112A PHE* 1.3 51.9 + - - +
113A ASN* 3.1 12.6 + - - +
114A GLY* 3.3 13.8 + - - -
115A ALA 3.8 5.7 + - - -
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 4.7 0.9 - - + -
4A LYS 4.1 9.0 - - - -
5A PHE* 4.6 3.6 - - - -
6A LEU* 5.5 1.3 - - + -
91A MET* 4.8 5.2 - - - +
94A LEU* 2.9 85.4 - - + +
95A ALA* 3.9 4.5 - - - +
99A ILE* 3.5 31.9 - - + -
108A ASP* 3.0 44.9 - - + +
109A ARG* 4.0 0.9 - - - -
110A ALA* 3.1 22.5 - - - +
111A LEU* 1.3 72.5 - - - +
113A ASN* 1.4 60.6 + - - +
114A GLY 3.4 0.7 - - - -
115A ALA* 3.6 8.1 - - + +
116A GLN* 3.4 20.6 + - - +
119A PHE* 6.5 0.2 - + - -
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Residues in contact with ASN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 3.5 37.5 - - - +
95A ALA* 4.8 11.1 - - - +
110A ALA 3.5 20.6 + - - -
111A LEU* 4.5 2.7 - - - +
112A PHE* 1.4 77.2 - - - +
114A GLY* 1.4 61.5 + - - +
116A GLN* 3.3 15.6 + - - +
117A LYS* 3.5 23.3 + - - +
382A VAL 4.7 11.9 + - - +
383A SER* 5.0 9.0 - - - -
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU* 4.0 9.6 - - - +
107A LYS* 3.9 12.0 + - - -
111A LEU 3.3 8.5 + - - -
113A ASN* 1.4 76.2 - - - +
115A ALA* 1.4 62.9 + - - +
117A LYS* 3.7 17.5 + - - +
118A LEU* 3.7 15.8 - - - +
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.2 15.0 - - + -
94A LEU* 5.9 0.9 - - + -
107A LYS* 3.6 21.9 - - - +
108A ASP* 4.1 11.0 - - + -
111A LEU 3.8 3.4 + - - -
112A PHE* 3.6 16.4 + - + +
114A GLY* 1.4 75.9 - - - +
116A GLN* 1.4 61.1 + - - +
117A LYS 3.5 0.3 + - - -
118A LEU* 3.6 5.2 + - - +
119A PHE* 3.2 47.2 + - + -
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Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A SER* 3.3 46.4 - - - +
88A GLY* 4.7 3.0 - - - -
90A ILE* 4.9 7.2 - - + -
91A MET* 3.5 38.8 - - + +
94A LEU* 6.1 2.2 - - + -
112A PHE 3.4 10.8 + - - +
113A ASN 3.3 9.4 + - - +
114A GLY 3.3 0.4 - - - -
115A ALA* 1.4 77.6 - - - +
117A LYS* 1.4 72.9 + - - +
119A PHE* 3.1 12.2 + - + +
120A GLY* 2.9 25.1 + - - -
123A ILE* 6.5 0.2 - - + -
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Residues in contact with LYS 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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17A PRO 4.3 5.2 - - - +
18A GLU* 3.6 33.3 - - + +
91A MET* 3.9 20.4 - - - -
113A ASN* 3.5 24.7 + - - +
114A GLY* 4.0 4.5 - - - +
115A ALA 3.4 0.8 - - - -
116A GLN* 1.4 86.8 - - - +
118A LEU* 1.4 61.1 + - - +
120A GLY* 3.5 9.0 + - - -
121A MET* 4.2 6.8 + - - +
163A LEU* 5.9 1.4 - - - +
166A ASP* 5.5 2.2 - - - +
167A GLU* 3.8 31.0 - - - +
170A GLN* 4.7 23.8 - - - -
171A LYS* 6.0 1.3 - - - -
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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
----------------------------------------------------------
8A VAL* 4.1 9.2 - - + -
13A CYS* 3.3 56.3 - - + +
16A LEU* 3.6 35.8 - - + +
17A PRO 3.9 5.8 - - - +
18A GLU* 3.4 34.1 - - + +
107A LYS* 4.0 11.7 - - - +
114A GLY 3.7 13.2 + - - +
115A ALA 3.6 5.8 + - - +
117A LYS* 1.4 75.4 - - - +
119A PHE* 1.4 68.2 + - + +
120A GLY 3.4 0.9 + - - -
121A MET* 3.6 14.9 + - - +
122A ILE* 4.0 0.5 - - - +
61C GLU 4.2 2.0 - - - +
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.9 40.8 - - + -
7A GLU 3.4 27.1 - - - -
8A VAL* 4.5 9.0 - - + -
12A PHE* 4.8 7.9 - + - -
16A LEU* 5.0 1.3 - - + -
90A ILE* 5.9 4.3 - - + -
94A LEU* 5.4 11.9 - - + -
108A ASP* 5.6 1.3 - - + -
112A PHE* 6.4 0.4 - + - -
115A ALA* 3.2 36.1 + - + -
116A GLN* 3.1 13.5 + - + +
118A LEU* 1.4 82.3 - - + +
120A GLY* 1.4 63.2 + - - +
121A MET 3.3 0.2 - - - -
122A ILE* 3.3 28.4 + - + +
123A ILE* 3.3 31.1 - - + +
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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
----------------------------------------------------------
83A PRO* 5.7 0.7 - - - +
84A ILE* 6.1 0.2 - - - -
87A SER* 4.0 18.1 + - - -
116A GLN* 2.9 20.2 + - - -
117A LYS 3.5 4.9 + - - -
118A LEU 3.3 1.4 - - - -
119A PHE* 1.4 77.2 - - - +
121A MET* 1.4 57.5 + - - +
123A ILE* 3.4 3.5 + - - +
124A THR* 3.1 24.9 + - - -
163A LEU* 3.3 18.0 - - - +
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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
----------------------------------------------------------
16A LEU* 5.2 4.5 - - + -
17A PRO* 3.8 54.1 - - + +
19A ILE* 5.2 1.8 - - + -
117A LYS 4.4 4.7 - - - +
118A LEU 3.9 9.2 - - - +
119A PHE 3.3 0.2 - - - -
120A GLY* 1.4 74.5 - - - +
122A ILE* 1.4 62.5 + - - +
123A ILE 3.6 0.2 + - - -
124A THR* 3.6 11.0 + - - -
125A ILE* 3.6 18.5 - - - +
160A LEU* 3.9 23.4 - - + +
163A LEU* 3.7 24.9 - - + +
164A LEU* 3.9 22.4 - - + -
167A GLU* 4.0 27.8 - - + +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 4.7 11.4 - - + -
16A LEU* 3.6 40.8 - - + -
118A LEU 4.0 1.6 - - - +
119A PHE* 3.3 30.5 + - + +
121A MET* 1.4 75.5 - - - +
123A ILE* 1.4 60.4 + - + +
125A ILE* 3.3 18.7 + - + +
126A GLY* 2.9 23.1 + - - -
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Residues in contact with ILE 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PRO* 3.6 16.2 - - + +
86A THR* 5.0 6.7 - - + -
87A SER* 3.5 39.0 - - - +
90A ILE* 5.1 9.4 - - + -
116A GLN* 6.5 0.2 - - + -
119A PHE* 3.3 29.3 + - + +
120A GLY 3.4 1.5 + - - +
121A MET 3.3 0.6 - - - -
122A ILE* 1.4 76.3 - - + +
124A THR* 1.4 59.9 + - - +
126A GLY* 3.5 5.2 - - - +
127A GLN* 2.9 36.2 + - + +
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Residues in contact with THR 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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83A PRO* 3.8 26.8 - - + +
84A ILE* 5.5 1.2 - - + +
120A GLY 3.1 15.5 + - - -
121A MET* 3.6 9.0 + - - -
122A ILE 3.2 0.6 - - - -
123A ILE* 1.4 78.9 - - - +
125A ILE* 1.4 61.3 + - - +
127A GLN* 4.0 2.3 + - - +
128A SER* 3.7 6.9 + - - -
156A PHE* 3.1 48.0 - - + +
159A GLY* 4.1 5.2 - - - -
160A LEU* 3.8 24.4 - - + +
163A LEU* 3.4 16.8 - - - +
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 6.5 1.1 - - + -
121A MET 3.6 20.2 - - - +
122A ILE* 3.4 13.9 - - + +
124A THR* 1.4 74.7 - - - +
126A GLY* 1.4 61.4 + - - +
128A SER* 3.4 19.2 - - - -
129A ILE* 3.7 14.6 - - + +
152A THR* 4.5 7.8 - - + +
156A PHE* 3.9 39.5 - - + -
160A LEU* 6.4 0.7 - - + -
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Residues in contact with GLY 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ILE* 2.9 17.3 + - - -
123A ILE* 3.3 6.4 + - - -
125A ILE* 1.4 75.3 - - - +
127A GLN* 1.4 62.5 + - - +
128A SER 3.3 0.2 - - - -
129A ILE* 3.3 30.7 + - - +
130A VAL* 3.5 12.9 - - - +
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Residues in contact with GLN 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 6.1 4.0 - - - +
79A LEU* 4.3 20.5 - - + +
82A SER* 5.1 5.6 - - - -
83A PRO* 3.9 31.2 - - + +
86A THR* 3.9 23.1 + - - +
123A ILE* 2.9 23.1 + - + +
124A THR 4.3 0.7 - - - +
125A ILE 3.4 0.2 - - - -
126A GLY* 1.4 72.8 - - - +
128A SER* 1.4 63.4 + - - +
130A VAL* 3.3 30.3 + - - +
131A TYR* 3.3 11.8 + - - +
300A ASN* 4.8 7.8 + - - +
303A VAL* 6.2 1.8 - - - +
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Residues in contact with SER 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 4.9 2.2 - - - -
124A THR 3.7 10.6 + - - -
125A ILE 3.4 13.8 + - - -
127A GLN* 1.4 75.6 - - - +
129A ILE* 1.4 63.0 + - - +
131A TYR* 3.3 17.6 + - - +
132A VAL* 3.5 13.5 + - - +
152A THR* 3.7 29.2 + - - -
155A LEU* 3.6 37.2 - - - +
156A PHE* 3.9 3.1 + - - +
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Residues in contact with ILE 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ILE* 3.7 16.4 - - + +
126A GLY* 3.3 21.5 + - - +
128A SER* 1.4 73.6 - - - +
130A VAL* 1.4 65.2 + - + +
132A VAL* 3.5 12.1 + - + +
133A MET* 3.2 37.0 + - + +
152A THR* 5.5 7.6 - - + +
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Residues in contact with VAL 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY 3.5 16.4 - - - +
127A GLN* 3.4 25.8 - - - +
128A SER 3.3 0.6 - - - -
129A ILE* 1.4 74.9 - - + +
131A TYR* 1.4 61.7 + - - +
133A MET* 3.5 26.2 + - + +
134A THR* 3.1 30.7 + - - +
303A VAL* 3.8 24.4 - - + +
304A ILE* 6.2 2.2 - - + -
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Residues in contact with TYR 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ALA* 3.2 27.9 + - + +
60A ASP 4.0 0.2 - - - -
61A PRO* 3.7 22.6 - - + +
65A MET* 6.0 1.8 - - + -
78A GLU* 3.3 33.2 - - - +
79A LEU* 3.5 35.7 - - + -
127A GLN* 3.3 5.7 + - - +
128A SER* 3.3 12.1 + - - +
129A ILE 3.3 0.6 - - - -
130A VAL* 1.4 80.5 - - - +
132A VAL* 1.4 61.8 + - + +
133A MET 3.7 0.2 + - - -
134A THR 3.9 0.3 + - - -
135A GLY 3.8 0.7 + - - -
136A MET* 3.2 79.5 + - + +
137A TYR* 3.8 18.3 + + + -
155A LEU* 4.8 5.8 - - + -
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Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A SER 3.5 12.3 + - - +
129A ILE* 3.5 17.0 - - + +
131A TYR* 1.4 78.8 - - + +
133A MET* 1.4 65.9 + - + +
135A GLY* 3.3 5.0 + - - -
137A TYR* 4.2 24.2 - - + -
139A ASP* 2.9 40.4 - - - +
141A SER* 5.9 0.2 - - - -
148A CYS* 4.4 21.3 - - + +
151A ILE* 4.4 15.0 - - + -
152A THR* 5.0 4.0 - - - +
155A LEU* 5.9 2.2 - - + -
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Residues in contact with MET 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ILE* 3.2 35.4 + - + +
130A VAL* 3.6 31.6 - - + +
131A TYR 3.4 0.2 - - - -
132A VAL* 1.4 77.6 - - + +
134A THR* 1.4 64.8 + - - +
141A SER* 5.2 4.3 + - - -
307A MET* 3.3 42.5 - - + +
311A ARG* 4.7 5.9 - - - -
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Residues in contact with THR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.1 20.3 + - - +
131A TYR 4.4 0.2 - - - -
132A VAL 3.3 0.2 - - - -
133A MET* 1.4 77.7 - - - +
135A GLY* 1.4 59.1 + - - +
136A MET* 4.0 22.4 - - + -
303A VAL* 3.4 34.2 - - + +
306A GLN* 4.2 23.1 - - + +
307A MET* 3.9 22.3 - - - +
311A ARG* 4.0 21.1 + - - +
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Residues in contact with GLY 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A VAL 3.3 14.8 + - - -
133A MET 3.3 1.0 + - - -
134A THR* 1.4 80.7 - - - +
136A MET* 1.4 59.2 + - - +
137A TYR 3.2 5.4 - - - -
138A GLY* 3.6 10.1 + - - -
139A ASP* 4.0 23.7 - - - +
141A SER* 6.1 0.7 - - - -
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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