Contacts of the helix formed by residues 86 - 111 (chain B) in PDB entry 1GUL
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 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 4.1 15.7 - - + -
77A ASP* 4.2 29.4 - - + +
78A LYS* 3.8 35.4 - - + +
85B ASN* 1.3 73.0 - - - +
87B LYS* 1.3 62.6 + - + +
89B ARG* 4.0 15.0 - - + +
90B THR* 2.5 53.9 + - - +
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Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 5.2 3.4 + - - +
63A MET* 4.2 25.5 - - + +
74A TYR* 3.3 34.6 + - - -
78A LYS* 4.8 7.1 - - - +
85B ASN* 2.8 17.8 + - - +
86B LEU* 1.3 90.5 - - + +
88B GLU* 1.3 61.0 + - + +
90B THR* 3.3 5.2 + - - +
91B LEU* 3.2 28.9 + - + +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLY* 3.5 14.4 - - - -
84B LYS* 2.8 31.5 + - - +
85B ASN* 3.0 31.1 + - - +
87B LYS* 1.3 72.2 - - + +
89B ARG* 1.3 68.0 + - - +
90B THR 3.0 1.3 - - - -
91B LEU* 2.8 17.3 + - + +
92B ILE* 2.9 19.0 + - - +
149B VAL* 3.9 19.2 - - + +
150B GLY* 4.0 24.4 - - - -
152B GLN* 5.5 2.1 - - - +
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Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ASP* 4.8 1.8 - - - -
89A ARG* 3.6 35.8 - - - +
73B HIS* 5.3 2.4 - - - +
77B ASP* 2.7 43.0 + - - -
82B PHE* 3.6 55.2 + - + +
85B ASN 2.8 20.4 + - - +
86B LEU* 3.4 21.1 - - + +
88B GLU* 1.3 72.5 - - - +
90B THR* 1.3 64.5 + - - +
92B ILE* 3.6 1.9 - - - +
93B ASP* 2.9 27.7 + - + +
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Residues in contact with THR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 4.1 22.2 - - + +
65A LEU* 4.1 20.2 - - + -
70A SER* 5.6 3.4 - - - +
74A TYR* 3.8 20.4 - - + +
86B LEU* 2.5 46.1 + - - +
87B LYS* 3.4 5.8 - - - -
89B ARG* 1.3 76.3 - - - +
91B LEU* 1.3 62.9 + - + +
93B ASP* 3.4 6.3 - - + +
94B MET* 3.0 28.9 + - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 5.8 6.7 - - + -
87B LYS* 3.2 19.7 + - + +
88B GLU* 2.8 13.6 + - + +
90B THR* 1.3 70.9 - - + +
92B ILE* 1.3 66.2 + - - +
94B MET* 3.2 12.1 + - - +
95B TYR* 2.8 55.5 + - + +
149B VAL* 4.0 21.5 - - + -
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU 4.3 0.4 - - - +
82B PHE* 3.7 23.1 - - + -
83B GLY* 3.5 30.5 - - - +
88B GLU 3.1 15.9 - - - +
89B ARG 3.6 3.8 - - - +
91B LEU* 1.3 75.0 - - - +
93B ASP* 1.3 64.5 + - - +
95B TYR* 3.6 1.9 - - - +
96B VAL* 2.9 32.0 + - + +
149B VAL* 3.9 24.7 - - + +
154B SER* 3.5 24.2 - - - +
155B LEU* 4.2 10.8 - - + -
156B ALA* 3.9 26.7 - - - +
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER* 3.1 26.4 + - - +
73A HIS* 2.9 38.3 + - - +
73B HIS* 4.6 4.9 + - - -
82B PHE* 4.3 16.9 - - + -
89B ARG* 2.9 19.2 + - + +
90B THR* 3.4 7.3 - - - +
92B ILE* 1.3 77.8 - - - +
94B MET* 1.3 64.6 + - - +
96B VAL* 3.1 7.1 + - - +
97B GLU* 2.8 33.4 + - - +
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Residues in contact with MET 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 4.5 13.0 - - + -
52A PHE* 3.6 8.8 - - + -
64A LYS 4.2 3.4 - - - +
65A LEU* 3.3 29.4 - - + -
66A VAL* 2.6 61.0 - - + +
67A GLN* 4.2 2.4 - - + +
70A SER* 3.8 20.9 - - - -
90B THR* 3.0 19.9 + - + +
91B LEU* 3.2 15.2 + - - +
93B ASP* 1.3 76.5 - - - +
95B TYR* 1.3 70.1 - - + +
97B GLU* 3.2 2.2 + - - +
98B GLY 2.9 20.1 + - - -
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Residues in contact with TYR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 4.0 26.3 - - + +
52A PHE* 4.4 6.5 - + - -
91B LEU* 2.8 48.8 + - + +
92B ILE 3.6 4.0 - - - +
94B MET* 1.3 78.5 - - + +
96B VAL* 1.3 61.5 + - - +
98B GLY* 3.3 0.5 + - - -
99B THR* 2.6 34.5 + - - +
135B VAL* 5.3 0.4 - - + -
136B PHE* 4.0 19.9 - + + -
139B ILE* 3.2 33.3 - - + +
148B LEU* 4.3 14.8 - - + -
149B VAL* 3.4 31.4 - - + -
156B ALA* 3.8 18.4 - - + -
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 5.4 3.8 - - + -
73B HIS* 5.8 4.0 - - - +
92B ILE* 2.9 23.6 + - + +
93B ASP* 3.3 5.6 - - - +
95B TYR* 1.3 80.8 - - - +
97B GLU* 1.3 69.9 + - - +
99B THR* 3.2 6.3 + - - -
100B LEU* 2.8 41.1 + - + +
155B LEU* 3.9 24.5 - - + +
156B ALA* 3.7 28.9 - - - +
159B ILE* 4.5 13.0 - - + -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 3.4 27.7 - - + +
69A ARG* 3.5 18.5 + - + +
70A SER* 3.0 26.0 - - - +
73A HIS* 4.9 1.0 - - - -
97A GLU* 5.5 0.2 - - - +
69B ARG* 2.7 44.0 + - - +
73B HIS* 4.2 13.7 + - - -
93B ASP* 2.8 26.8 + - - +
94B MET 3.9 0.2 - - - +
96B VAL* 1.3 77.0 - - - +
98B GLY* 1.3 65.4 + - - +
100B LEU* 3.2 7.2 + - - +
101B ASP* 3.1 26.4 + - - +
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 3.7 20.6 - - - -
67A GLN* 3.4 20.1 - - - +
94B MET 2.9 10.5 + - - -
97B GLU* 1.3 75.7 - - - +
99B THR* 1.3 65.2 + - - +
101B ASP* 2.9 19.3 + - - +
102B LEU 3.4 1.2 + - - -
132B TYR* 3.3 18.6 - - - -
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PHE* 4.9 0.2 - - - -
95B TYR* 2.6 25.8 + - - +
96B VAL* 3.6 3.5 - - - -
98B GLY* 1.3 76.2 - - - +
100B LEU* 1.3 57.0 + - - +
102B LEU* 2.8 28.4 + - + +
103B LEU* 2.9 12.4 + - - +
132B TYR* 4.8 4.0 - - - -
136B PHE* 3.6 18.2 - - + -
156B ALA 5.3 1.2 + - - -
159B ILE* 3.8 20.4 - - + +
160B LEU* 4.1 17.9 + - + +
163B THR* 3.4 31.0 - - + +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 4.6 7.2 - - - +
68B THR* 5.6 5.2 - - + -
69B ARG* 3.8 48.9 + - + +
72B LEU* 4.8 14.6 - - + -
96B VAL* 2.8 36.5 + - + +
97B GLU* 3.2 8.7 + - - +
99B THR* 1.3 71.3 - - - +
101B ASP* 1.3 63.4 + - - +
103B LEU* 3.7 26.5 - - + +
104B GLU* 3.0 26.0 + - - +
159B ILE* 3.9 13.9 - - + -
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 4.2 4.0 + - - +
67A GLN* 3.1 24.9 + - - +
301A IBG 3.3 29.8 + - - +
69B ARG* 4.6 9.7 + - - -
97B GLU 3.1 13.8 + - - +
98B GLY 2.9 11.4 + - - +
100B LEU* 1.3 80.6 - - - +
102B LEU* 1.3 60.9 + - - +
104B GLU* 3.6 14.1 - - - +
105B LEU* 4.2 8.8 + - - +
132B TYR* 3.7 13.6 + - - +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLY 3.4 1.9 + - - +
99B THR* 2.8 15.2 + - + +
101B ASP* 1.3 77.3 - - - +
103B LEU* 1.3 66.8 + - - +
104B GLU 3.0 2.0 + - - -
105B LEU* 3.0 32.8 + - + +
106B LEU* 3.9 3.6 + - + +
124B MET* 4.4 6.3 - - + +
127B LYS* 4.2 18.4 - - + -
128B ALA* 4.2 12.3 - - + +
132B TYR* 3.7 47.5 + - + -
133B PHE* 4.5 6.1 - - + -
136B PHE* 6.3 0.4 - - + -
160B LEU* 6.0 1.6 - - + -
163B THR* 4.0 20.6 - - + -
167B LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER* 3.8 22.7 - - - +
99B THR 2.9 14.0 + - - +
100B LEU* 3.7 23.8 - - + +
102B LEU* 1.3 78.6 - - - +
104B GLU* 1.3 62.7 + - - +
106B LEU* 2.8 34.7 + - + +
107B ILE* 3.0 29.3 + - + +
159B ILE* 4.8 0.2 - - + -
162B GLN* 3.8 23.3 - - + +
163B THR* 3.8 32.0 - - + +
166B ALA* 5.0 3.4 - - + -
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 2.9 42.1 + - - -
100B LEU 3.0 19.6 + - - +
101B ASP* 3.6 12.1 - - - +
103B LEU* 1.3 77.5 - - - +
105B LEU* 1.3 66.0 + - + +
107B ILE* 3.0 11.4 + - - +
108B MET* 2.8 53.2 + - - +
301B IBG 5.0 0.5 - - - -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASP 4.3 8.5 - - - +
102B LEU* 3.3 22.4 - - + +
104B GLU* 1.3 79.9 - - + +
106B LEU* 1.3 64.3 + - + +
108B MET* 4.0 24.3 - - + +
109B HIS* 3.1 24.4 + - - +
120B GLU* 5.0 8.5 - - - +
123B ASN* 4.1 20.6 - - - +
124B MET* 3.8 46.1 - - + +
127B LYS* 4.2 12.1 - - + -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 4.1 11.0 - - + +
103B LEU* 2.8 28.1 + - + +
105B LEU* 1.3 82.9 - - + +
107B ILE* 1.4 62.4 + - + +
109B HIS* 3.3 17.6 - - - +
110B PRO* 3.3 7.1 - - - +
124B MET* 3.8 24.9 - - + -
163B THR* 4.8 1.6 - - + -
166B ALA* 4.1 30.3 - - + +
167B LEU* 3.9 30.5 - - + -
170B LYS* 4.2 20.8 + - + -
208B PRO* 5.9 0.3 - - - +
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY* 3.9 27.9 - - - +
15B ARG* 4.0 32.8 - - + +
18B SER* 6.0 0.2 - - - +
103B LEU* 3.0 32.5 + - + +
104B GLU* 3.5 23.6 - - - +
106B LEU* 1.4 77.1 - - + +
108B MET* 1.3 61.0 + - - +
110B PRO* 3.5 11.1 - - - +
111B PHE* 3.6 14.0 - - - -
301B IBG 3.6 25.6 - - + -
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Residues in contact with MET 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLU* 2.8 45.9 + - - +
105B LEU* 4.0 28.9 - - + +
107B ILE* 1.3 73.8 - - - +
109B HIS* 1.3 66.9 + - - +
110B PRO* 3.3 0.2 - - - -
111B PHE* 2.9 24.1 + - - +
112B LEU* 3.7 20.6 + - + +
120B GLU* 5.4 6.7 - - - +
301B IBG 4.6 12.6 - - + -
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Residues in contact with HIS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU 3.1 12.2 + - - +
106B LEU 3.3 11.9 - - - +
108B MET* 1.3 75.1 - - - +
110B PRO* 1.3 69.8 - - + +
111B PHE 3.0 1.6 + - - -
112B LEU* 3.1 21.1 + - + +
117B GLN* 2.8 66.6 + - + -
118B GLN* 5.7 0.7 - - - -
120B GLU* 3.9 12.8 - - + -
121B VAL* 3.7 13.4 - - + +
124B MET* 3.6 19.7 - - + -
170B LYS* 2.7 32.3 + - + +
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Residues in contact with PRO 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU 3.3 11.2 - - - +
107B ILE 3.5 9.2 - - - +
108B MET 3.3 4.5 - - - -
109B HIS* 1.3 99.3 - - + +
111B PHE* 1.3 70.3 + - + +
112B LEU 3.3 3.9 + - - +
117B GLN* 3.6 14.5 + - - +
170B LYS* 5.5 2.0 - - - +
208B PRO* 3.8 29.4 - - + +
212B TYR* 5.4 0.9 - - + -
213B VAL* 3.8 32.8 - - + +
217B TYR* 5.1 0.2 + - - -
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Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ILE 3.6 23.8 - - - -
108B MET* 2.9 10.9 + - + +
110B PRO* 1.3 88.3 - - + +
112B LEU* 1.3 65.5 - - - +
113B LYS* 4.6 6.4 + - - +
212B TYR* 3.9 20.0 - + - -
213B VAL* 3.8 19.3 - - + -
216B VAL* 3.0 36.3 - - + -
217B TYR* 3.7 37.5 + + + +
301B IBG 4.1 32.8 - + + -
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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
------------------------------------------------------------
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