Contacts of the helix formed by residues 86 - 111 (chain E) in PDB entry 1GUM
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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85E ASN* 1.3 76.4 - - - +
87E LYS* 1.3 61.2 + - + +
89E ARG* 3.2 15.2 - - + +
90E THR* 2.5 53.8 + - - +
74F TYR* 3.6 30.1 - - + -
77F ASP* 4.2 30.5 - - + +
78F LYS* 3.9 22.4 - - + +
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Residues in contact with LYS 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E ASN* 2.7 15.8 + - - +
86E LEU* 1.3 81.1 - - + +
88E GLU* 1.3 66.2 + - + +
90E THR* 3.4 3.8 + - - +
91E LEU* 3.1 28.3 + - + +
61F ASP* 4.6 5.3 + - - +
63F MET* 3.5 35.0 - - + +
74F TYR* 3.1 34.2 + - - -
78F LYS* 5.6 3.0 - - - +
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Residues in contact with GLU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E GLY* 3.6 9.1 - - - -
84E LYS* 3.0 37.7 + - - +
85E ASN* 3.0 35.8 + - - +
87E LYS* 1.3 75.9 - - + +
89E ARG* 1.3 56.7 + - - +
91E LEU* 2.7 30.3 + - + +
92E ILE* 3.0 15.7 + - - +
149E VAL* 4.0 18.7 - - + +
150E GLY* 4.1 24.5 - - - +
152E GLN* 5.2 2.3 + - - -
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Residues in contact with ARG 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E HIS* 5.1 5.1 + - - +
77E ASP* 3.0 42.0 + - - -
82E PHE* 3.5 55.6 + - + +
85E ASN 2.7 22.9 + - - +
86E LEU* 3.2 20.9 - - + +
88E GLU* 1.3 72.7 - - - +
90E THR* 1.3 66.3 + - - +
92E ILE* 3.3 5.3 + - - +
93E ASP* 2.9 26.4 + - + +
77F ASP* 4.4 2.6 + - - -
89F ARG* 3.0 39.1 - - - +
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Residues in contact with THR 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E LEU* 2.5 44.6 + - - +
87E LYS* 3.5 8.0 - - - -
89E ARG* 1.3 75.7 - - - +
91E LEU* 1.3 62.9 + - + +
93E ASP* 3.3 9.0 - - - +
94E MET* 3.1 26.4 + - + +
63F MET* 3.9 21.1 - - + -
65F LEU* 4.0 20.2 - - + -
70F SER* 5.3 4.7 - - - +
74F TYR* 3.8 18.8 - - + +
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Residues in contact with LEU 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E LYS* 3.1 20.8 + - + +
88E GLU* 2.7 13.9 + - + +
90E THR* 1.3 69.9 - - + +
92E ILE* 1.3 70.4 + - - +
93E ASP 3.0 1.6 - - - -
94E MET* 3.0 11.7 + - - -
95E TYR* 2.7 52.4 + - + +
149E VAL* 3.8 26.2 - - + -
63F MET* 5.6 6.1 - - + -
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Residues in contact with ILE 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E PHE* 4.0 17.5 - - + -
83E GLY* 3.9 22.4 - - - +
88E GLU 3.2 18.8 - - - +
89E ARG* 3.5 6.7 - - - +
91E LEU* 1.3 76.3 - - - +
93E ASP* 1.3 55.2 + - - +
95E TYR* 3.2 3.0 + - - +
96E VAL* 2.7 44.3 + - + +
149E VAL* 4.0 21.5 - - + +
154E SER* 3.2 30.1 - - - +
155E LEU* 4.1 9.0 - - + -
156E ALA* 3.7 29.6 - - + +
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Residues in contact with ASP 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E HIS* 4.3 4.3 + - - -
82E PHE* 4.4 15.5 - - + -
89E ARG* 2.9 18.8 + - + +
90E THR* 3.3 9.1 - - - +
92E ILE* 1.3 78.2 - - - +
94E MET* 1.3 64.4 + - - +
96E VAL* 3.0 6.7 + - - +
97E GLU* 2.8 39.8 + - - +
70F SER* 3.0 32.0 + - - +
73F HIS* 3.3 30.9 + - - +
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Residues in contact with MET 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E THR* 3.1 15.8 + - + +
91E LEU* 3.0 15.7 + - - +
93E ASP* 1.3 78.6 - - - +
95E TYR* 1.3 66.1 + - + +
97E GLU* 3.8 1.3 - - - +
98E GLY 2.9 20.1 + - - -
51F LEU* 4.3 18.8 - - + -
52F PHE* 3.7 6.6 - - - -
64F LYS 3.6 5.8 - - - +
65F LEU* 2.8 38.6 - - + -
66F VAL* 2.5 59.0 - - + +
67F GLN* 4.1 4.7 - - + +
70F SER* 3.5 15.0 - - - -
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Residues in contact with TYR 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LEU* 2.7 48.6 + - + +
92E ILE 3.5 5.6 - - - +
94E MET* 1.3 73.1 - - + +
96E VAL* 1.3 64.1 + - - +
98E GLY* 3.4 0.9 + - - -
99E THR* 2.7 30.7 + - - +
135E VAL* 5.3 0.2 - - + -
136E PHE* 4.0 20.1 - + + -
139E ILE* 3.4 32.9 - - + +
148E LEU* 4.2 15.5 - - + -
149E VAL* 3.5 28.7 - - + +
156E ALA* 3.7 22.2 - - + -
51F LEU* 4.0 22.0 - - + +
52F PHE* 4.3 11.0 - + - -
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Residues in contact with VAL 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LEU* 5.4 3.4 - - + -
73E HIS* 5.8 3.8 - - + +
92E ILE* 2.7 26.9 + - + +
93E ASP* 3.4 5.8 - - - +
95E TYR* 1.3 78.0 - - - +
97E GLU* 1.3 69.6 + - - +
99E THR* 3.1 5.0 + - - -
100E LEU* 2.9 39.6 + - + +
155E LEU* 4.1 20.9 - - + +
156E ALA* 3.5 31.0 - - - +
159E ILE* 4.2 16.8 - - + -
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Residues in contact with GLU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG* 3.0 39.3 + - - +
73E HIS* 3.8 17.5 + - - -
93E ASP* 2.8 26.9 + - - +
94E MET 3.8 0.2 - - - +
96E VAL* 1.3 78.4 - - - +
98E GLY* 1.3 65.4 + - - +
100E LEU* 3.2 6.6 + - - +
101E ASP* 3.0 26.7 + - - +
67F GLN* 3.2 29.4 - - + +
69F ARG* 4.0 14.8 - - + +
70F SER* 3.0 28.0 - - - +
73F HIS* 4.8 0.2 - - - -
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Residues in contact with GLY 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E MET 2.9 13.8 + - - -
95E TYR 3.8 2.5 - - - -
97E GLU* 1.3 76.4 - - - +
99E THR* 1.3 65.6 + - - +
101E ASP* 2.9 19.0 + - - +
102E LEU 3.3 1.0 + - - -
132E TYR* 3.3 20.8 - - - -
52F PHE* 3.9 12.8 - - - -
67F GLN* 3.6 19.8 - - - -
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Residues in contact with THR 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95E TYR* 2.7 19.5 + - - +
96E VAL* 3.1 3.8 + - - -
98E GLY* 1.3 75.8 - - - +
100E LEU* 1.3 60.2 + - - +
102E LEU* 2.8 13.3 + - + +
103E LEU* 2.7 26.0 + - - +
132E TYR* 4.9 4.0 - - - -
136E PHE* 3.7 18.7 - - + -
156E ALA 5.3 1.2 + - - -
159E ILE* 4.0 19.5 - - + +
160E LEU* 4.1 17.1 + - + +
163E THR* 3.4 31.4 - - + +
52F PHE* 5.3 0.2 - - - -
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E SER* 4.6 6.7 - - - +
68E THR* 6.1 2.2 - - + -
69E ARG* 3.9 47.3 - - + +
72E LEU* 4.6 12.3 - - + -
96E VAL* 2.9 33.5 + - + +
97E GLU* 3.4 9.2 - - - +
99E THR* 1.3 77.1 - - - +
101E ASP* 1.3 63.8 + - - +
103E LEU* 3.6 28.1 - - + +
104E GLU* 3.1 28.5 + - - +
159E ILE* 4.0 13.0 - - + -
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Residues in contact with ASP 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E ARG* 4.8 10.2 + - - -
97E GLU* 3.0 15.8 + - - +
98E GLY 2.9 9.3 + - - +
99E THR 2.9 1.0 - - - -
100E LEU* 1.3 82.0 - - - +
102E LEU* 1.3 59.8 + - - +
104E GLU* 3.3 16.8 - - - +
105E LEU* 4.2 7.6 - - - +
132E TYR* 3.7 14.4 + - - +
54F GLN* 4.5 6.4 + - - +
67F GLN* 3.6 25.6 + - - +
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E GLY 3.3 2.8 + - - +
99E THR* 2.8 15.3 + - + +
101E ASP* 1.3 71.6 - - - +
103E LEU* 1.3 66.7 + - - +
104E GLU 2.9 6.1 + - - -
105E LEU* 3.0 32.7 + - + +
106E LEU* 3.9 3.5 + - + +
124E MET* 4.2 7.4 - - + +
127E LYS* 4.1 9.2 - - + -
128E ALA* 4.1 23.1 - - + +
132E TYR* 4.0 45.9 + - + -
133E PHE* 4.5 6.5 - - + -
160E LEU* 6.1 2.0 - - + -
163E THR* 4.0 13.2 - - + -
167E LEU* 3.9 26.7 - - + -
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Residues in contact with LEU 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E SER* 3.9 6.3 - - - +
99E THR 2.7 17.9 + - - +
100E LEU* 3.6 26.7 - - + +
102E LEU* 1.3 73.6 - - - +
104E GLU* 1.3 63.7 + - - +
106E LEU* 2.8 39.2 + - + +
107E ILE* 3.0 26.6 + - + +
159E ILE* 4.8 0.7 - - + -
162E GLN* 3.7 35.2 - - + +
163E THR* 3.7 30.2 - - + +
166E ALA* 4.8 3.1 - - + -
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Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ARG* 2.7 43.6 + - - -
69E ARG* 5.7 3.3 + - - -
100E LEU* 3.1 15.1 + - - +
101E ASP* 3.3 18.6 - - - +
103E LEU* 1.3 79.4 - - - +
105E LEU* 1.3 61.8 + - + +
107E ILE* 3.0 9.0 + - - +
108E MET* 2.8 56.2 + - + +
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E ASP 4.2 9.9 - - - +
102E LEU* 3.3 26.0 - - + +
104E GLU* 1.3 80.1 - - + +
106E LEU* 1.3 61.8 + - + +
108E MET* 3.9 25.4 - - + +
109E HIS* 3.2 24.3 + - - +
120E GLU* 4.9 9.6 - - - +
123E ASN* 4.5 8.7 - - - +
124E MET* 3.5 44.5 - - + +
127E LYS* 4.4 14.1 - - + -
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU 4.8 2.9 - - - +
103E LEU* 2.8 26.9 + - + +
105E LEU* 1.3 82.5 - - + +
107E ILE* 1.3 64.4 - - + +
109E HIS* 3.2 4.0 - - - +
110E PRO* 3.1 20.8 - - - +
124E MET* 3.7 26.9 - - + -
163E THR* 4.2 4.7 - - + +
166E ALA* 3.5 37.5 - - + +
167E LEU* 3.8 24.0 - - + -
170E LYS* 4.2 20.9 + - + -
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Residues in contact with ILE 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E GLY* 3.6 29.4 - - - +
15E ARG* 4.0 53.4 - - + +
18E SER* 6.0 0.7 - - - +
103E LEU* 3.3 31.2 - - + +
104E GLU* 3.3 14.8 - - - +
106E LEU* 1.3 80.3 - - + +
108E MET* 1.3 60.5 + - + +
110E PRO* 3.5 11.0 - - - +
111E PHE* 4.1 10.6 - - - -
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Residues in contact with MET 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E GLU* 2.8 48.4 + - + +
105E LEU* 3.9 27.8 - - + +
107E ILE* 1.3 74.5 - - + +
109E HIS* 1.3 68.4 + - - +
110E PRO* 3.2 2.5 - - - -
111E PHE* 2.9 23.3 + - - +
112E LEU* 3.8 20.7 - - + +
120E GLU* 5.3 8.5 - - - +
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Residues in contact with HIS 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E LEU 3.2 12.3 + - - +
106E LEU* 3.2 11.0 - - - +
108E MET* 1.3 77.6 - - - +
110E PRO* 1.3 70.5 - - + +
111E PHE 2.9 1.7 + - - -
112E LEU* 3.0 19.2 + - + +
117E GLN* 2.9 70.0 + - + +
120E GLU* 4.2 11.7 - - + -
121E VAL* 3.6 10.4 - - + +
124E MET* 3.7 20.6 - - + -
170E LYS* 2.7 35.0 + - + +
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Residues in contact with PRO 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E LEU 3.1 11.0 - - - +
107E ILE 3.5 9.0 - - - +
108E MET 3.2 4.7 - - - -
109E HIS* 1.3 101.3 - - + +
111E PHE* 1.3 73.1 + - + +
112E LEU 3.2 5.3 + - - +
117E GLN* 3.7 13.2 + - - +
170E LYS* 5.2 2.5 - - - +
208E PRO* 4.0 30.3 - - + +
212E TYR* 5.8 0.2 - - + -
213E VAL* 4.2 25.2 - - + +
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Residues in contact with PHE 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ILE 4.1 10.8 - - - -
108E MET* 2.9 16.0 + - - +
110E PRO* 1.3 97.0 - - + +
112E LEU* 1.3 66.4 + - - +
113E LYS* 4.0 5.9 + - - +
212E TYR* 4.2 21.1 - + - -
213E VAL* 3.9 22.7 - - + -
216E VAL* 3.7 32.8 - - + -
217E TYR* 3.5 40.4 + + + +
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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