Contacts of the helix formed by residues 86 - 111 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ASN* 1.3 73.2 - - - +
87G LYS* 1.3 64.9 - - + +
89G ARG* 4.0 15.7 - - + +
90G THR* 2.5 53.6 + - - +
74H TYR* 4.1 16.6 - - + -
77H ASP* 4.2 28.3 - - + +
78H LYS* 4.0 32.3 - - + +
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Residues in contact with LYS 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ASN* 2.8 17.5 + - - +
86G LEU* 1.3 88.9 - - + +
88G GLU* 1.3 60.2 - - + +
90G THR* 3.4 5.4 - - - +
91G LEU* 3.2 27.8 + - + +
61H ASP* 5.3 2.8 + - - +
63H MET* 4.1 25.4 - - + +
74H TYR* 3.5 34.1 + - - -
78H LYS* 5.0 5.6 - - - +
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Residues in contact with GLU 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G GLY* 3.5 14.3 - - - -
84G LYS* 2.8 31.8 + - - +
85G ASN* 3.0 32.9 + - - +
87G LYS* 1.3 71.6 - - + +
89G ARG* 1.3 69.0 + - - +
90G THR 3.0 1.3 - - - -
91G LEU* 2.8 16.9 + - + +
92G ILE* 2.9 19.1 + - - +
149G VAL* 3.9 18.6 - - + +
150G GLY* 4.0 24.6 - - - -
152G GLN* 5.5 2.6 - - - +
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Residues in contact with ARG 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G HIS* 5.3 2.4 - - - +
77G ASP* 2.7 43.0 + - - -
82G PHE* 3.6 56.8 + - + +
85G ASN 2.8 20.8 + - - +
86G LEU* 3.4 22.0 - - + +
88G GLU* 1.3 73.1 - - - +
90G THR* 1.3 65.0 + - - +
92G ILE* 3.6 1.7 - - - +
93G ASP* 2.9 27.0 + - + +
77H ASP* 5.0 1.8 - - - -
89H ARG* 3.8 33.8 - - - +
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Residues in contact with THR 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G LEU* 2.5 44.8 + - - +
87G LYS* 3.4 6.8 - - - +
89G ARG* 1.3 76.6 - - - +
91G LEU* 1.3 62.9 + - + +
93G ASP* 3.3 6.6 + - + +
94G MET* 3.0 30.1 + - + +
63H MET* 4.1 22.6 - - + +
65H LEU* 4.1 19.1 - - + -
70H SER* 5.3 3.8 - - - +
74H TYR* 4.0 19.2 - - + +
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Residues in contact with LEU 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G LYS* 3.2 19.9 + - + +
88G GLU* 2.8 14.6 + - + +
90G THR* 1.3 69.7 - - + +
92G ILE* 1.3 67.8 + - - +
94G MET* 3.2 12.2 + - - +
95G TYR* 2.8 57.0 + - + +
149G VAL* 4.0 21.8 - - + -
51H LEU* 6.4 0.2 - - + -
63H MET* 6.0 4.7 - - + -
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Residues in contact with ILE 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G LEU 4.3 0.4 - - - +
82G PHE* 3.7 23.1 - - + -
83G GLY* 3.5 31.2 - - - +
88G GLU 2.9 15.2 + - - +
89G ARG 3.6 3.6 - - - +
91G LEU* 1.3 74.7 - - - +
93G ASP* 1.3 64.1 + - - +
95G TYR* 3.6 1.6 - - - +
96G VAL* 2.9 31.0 + - + +
149G VAL* 3.9 25.1 - - + +
154G SER* 3.5 23.8 - - - +
155G LEU* 4.2 10.3 - - + -
156G ALA* 3.9 26.5 - - - +
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Residues in contact with ASP 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G HIS* 4.6 4.0 + - - -
82G PHE* 4.2 18.5 - - + -
89G ARG* 2.9 19.2 + - + +
90G THR* 3.4 8.6 - - - +
92G ILE* 1.3 78.3 - - - +
94G MET* 1.3 64.8 + - - +
96G VAL* 3.1 7.0 + - - +
97G GLU* 2.8 34.8 + - - +
70H SER* 3.1 27.6 + - - +
73H HIS* 2.9 35.0 + - - +
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Residues in contact with MET 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G THR* 3.0 20.3 + - + +
91G LEU* 3.6 15.3 - - - +
93G ASP* 1.3 76.2 - - - +
95G TYR* 1.3 69.9 + - + +
97G GLU* 3.2 1.8 + - - +
98G GLY 2.9 19.8 + - - -
51H LEU* 4.4 13.2 - - + -
52H PHE* 3.6 9.2 - - + -
64H LYS 4.2 3.4 - - - +
65H LEU* 3.4 27.6 - - + -
66H VAL* 2.6 61.5 - - + +
67H GLN* 4.2 3.3 - - + +
70H SER* 3.9 20.4 - - - -
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Residues in contact with TYR 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 2.8 47.4 + - + +
92G ILE 3.6 3.6 - - - +
94G MET* 1.3 80.0 - - + +
96G VAL* 1.3 61.4 + - - +
98G GLY* 3.3 0.5 + - - -
99G THR* 2.6 35.2 + - - +
135G VAL* 5.3 0.4 - - + -
136G PHE* 4.0 20.6 - + + -
139G ILE* 3.2 33.7 - - + +
148G LEU* 4.3 14.1 - - + -
149G VAL* 3.4 31.8 - - + +
156G ALA* 3.8 19.1 - - + +
51H LEU* 4.1 25.5 - - + +
52H PHE* 4.3 6.1 - + - -
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Residues in contact with VAL 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G LEU* 5.4 4.0 - - + -
73G HIS* 5.8 3.8 - - + +
92G ILE* 2.9 23.0 + - + +
93G ASP* 3.3 6.5 - - - +
95G TYR* 1.3 79.7 - - - +
97G GLU* 1.3 70.0 + - - +
99G THR* 3.2 5.8 + - - -
100G LEU* 2.8 41.2 + - + +
155G LEU* 3.9 24.5 - - + +
156G ALA* 3.7 28.9 - - - +
159G ILE* 4.5 13.2 - - + -
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Residues in contact with GLU 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ARG* 2.7 45.0 + - - +
73G HIS* 4.2 13.9 + - - -
93G ASP* 2.8 26.9 + - - +
96G VAL* 1.3 77.9 - - - +
98G GLY* 1.3 65.3 + - - +
100G LEU* 3.2 7.5 + - - +
101G ASP* 3.1 26.0 + - - +
67H GLN* 3.4 27.8 - - + +
69H ARG* 3.5 19.5 + - + +
70H SER* 3.2 24.0 - - - +
73H HIS* 5.0 0.7 - - - -
97H GLU* 5.5 0.2 - - - +
----------------------------------------------------------
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Residues in contact with GLY 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G MET 2.9 11.3 + - - -
97G GLU* 1.3 76.3 - - - +
99G THR* 1.3 64.3 + - - +
101G ASP* 2.9 19.4 + - - +
102G LEU 3.4 1.2 + - - -
132G TYR* 3.3 21.1 - - - -
52H PHE* 3.8 18.6 - - - -
67H GLN* 3.4 19.6 - - - +
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Residues in contact with THR 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G TYR* 2.6 25.1 + - - +
96G VAL* 3.6 4.9 - - - -
98G GLY* 1.3 76.9 - - - +
100G LEU* 1.3 56.2 + - - +
102G LEU* 2.8 27.7 + - + +
103G LEU* 2.9 12.0 + - - +
132G TYR* 4.5 3.9 - - - -
136G PHE* 3.6 19.2 - - + -
156G ALA 5.3 1.2 + - - -
159G ILE* 3.8 20.0 - - + +
160G LEU* 4.1 18.2 - - + +
163G THR* 3.4 30.7 - - + +
52H PHE* 5.0 0.2 - - - -
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Residues in contact with LEU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G SER* 4.6 7.2 - - - +
68G THR* 5.6 5.2 - - + -
69G ARG* 3.8 47.8 - - + +
72G LEU* 4.8 14.1 - - + -
96G VAL* 2.8 37.8 + - + +
97G GLU* 3.2 8.7 + - - +
99G THR* 1.3 71.4 - - - +
101G ASP* 1.3 63.7 + - - +
103G LEU* 3.7 26.9 - - + +
104G GLU* 3.0 26.3 + - - +
159G ILE* 3.9 14.1 - - + -
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Residues in contact with ASP 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G ARG* 4.6 10.0 + - - -
97G GLU* 3.1 13.7 + - - +
98G GLY 2.9 12.3 + - - +
100G LEU* 1.3 79.7 - - - +
102G LEU* 1.3 60.1 + - - +
104G GLU* 3.6 14.9 - - - +
105G LEU* 4.2 9.0 + - - +
132G TYR* 3.7 14.0 + - - +
54H GLN* 4.2 4.9 + - - +
67H GLN* 3.2 24.0 + - - +
301H IBG 3.3 28.1 + - - +
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Residues in contact with LEU 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G GLY 3.4 1.7 + - - +
99G THR* 2.8 15.2 + - + +
101G ASP* 1.3 78.1 - - - +
103G LEU* 1.3 65.4 + - - +
104G GLU 3.0 2.8 + - - -
105G LEU* 3.0 32.8 + - + +
106G LEU* 3.9 3.3 + - + +
124G MET* 4.4 6.5 - - + +
127G LYS* 4.2 18.2 - - + -
128G ALA* 4.2 12.8 - - + +
132G TYR* 3.7 48.4 + - + -
133G PHE* 4.5 6.5 - - + -
136G PHE* 6.3 0.2 - - + -
160G LEU* 6.0 1.6 - - + -
163G THR* 4.0 20.2 - - + -
167G LEU* 4.1 18.2 - - + -
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Residues in contact with LEU 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18G SER* 3.8 22.0 - - - +
99G THR 2.9 14.3 + - - +
100G LEU* 3.7 24.2 - - + +
102G LEU* 1.3 78.3 - - - +
104G GLU* 1.3 63.5 + - - +
106G LEU* 2.8 34.4 + - + +
107G ILE* 3.0 27.5 + - + +
159G ILE* 4.8 0.4 - - + -
162G GLN* 3.8 22.4 - - + +
163G THR* 3.8 33.1 - - + +
166G ALA* 5.0 3.8 - - + -
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Residues in contact with GLU 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ARG* 2.9 42.7 + - - -
100G LEU 3.0 19.8 + - - +
101G ASP* 3.6 12.8 - - - +
102G LEU 3.0 0.2 + - - -
103G LEU* 1.3 76.9 - - - +
105G LEU* 1.3 66.1 + - + +
107G ILE* 3.0 12.3 + - - +
108G MET* 2.8 52.7 + - - +
301G IBG 5.0 0.3 - - - -
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Residues in contact with LEU 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ASP 4.3 9.0 - - - +
102G LEU* 3.3 22.9 - - + +
104G GLU* 1.3 80.3 - - + +
106G LEU* 1.3 64.9 + - + +
108G MET* 4.0 24.7 - - + +
109G HIS* 3.1 24.3 + - - +
120G GLU* 5.0 8.1 - - - +
123G ASN* 4.1 20.2 - - - +
124G MET* 3.8 45.2 - - + +
127G LYS* 4.2 11.9 - - + -
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Residues in contact with LEU 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LEU* 4.1 10.3 - - + +
103G LEU* 2.8 27.9 + - + +
105G LEU* 1.3 83.8 - - + +
107G ILE* 1.4 62.8 + - + +
109G HIS* 3.3 17.4 + - - +
110G PRO* 3.3 6.9 - - - +
124G MET* 3.8 24.5 - - + -
163G THR* 4.8 1.6 - - + -
166G ALA* 4.1 30.1 - - + +
167G LEU* 3.9 30.1 - - + -
170G LYS* 4.2 20.7 + - + -
208G PRO* 5.9 0.5 - - - +
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Residues in contact with ILE 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G GLY* 3.9 28.3 - - - +
15G ARG* 4.0 32.1 - - + +
18G SER* 6.0 0.4 - - - +
103G LEU* 3.0 32.7 + - + +
104G GLU* 3.0 23.3 + - - +
106G LEU* 1.4 77.7 - - + +
108G MET* 1.3 61.3 + - - +
110G PRO* 3.5 10.6 - - - +
111G PHE* 3.6 14.0 - - - -
301G IBG 3.6 26.5 - - + -
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Residues in contact with MET 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G GLU* 2.8 45.4 + - - +
105G LEU* 4.0 28.0 - - + +
107G ILE* 1.3 74.3 - - - +
109G HIS* 1.3 65.8 + - - +
110G PRO* 3.3 0.7 - - - -
111G PHE* 2.9 23.6 + - - +
112G LEU* 3.7 20.6 + - + +
120G GLU* 5.4 6.7 - - - +
301G IBG 4.6 12.6 - - + -
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Residues in contact with HIS 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G LEU 3.1 12.7 + - - +
106G LEU* 3.3 11.9 - - - +
108G MET* 1.3 74.7 - - - +
110G PRO* 1.3 69.8 - - + +
111G PHE 3.0 1.6 + - - -
112G LEU* 3.1 21.6 + - + +
117G GLN* 2.8 65.1 + - + -
118G GLN* 5.7 0.9 - - - -
120G GLU* 3.9 12.6 - - + -
121G VAL* 3.7 13.4 - - + +
124G MET* 3.6 20.6 - - + -
170G LYS* 2.7 33.2 + - + +
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Residues in contact with PRO 110 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G LEU 3.3 10.5 - - - +
107G ILE 3.5 8.7 - - - +
108G MET 3.3 4.9 - - - -
109G HIS* 1.3 98.9 - - + +
111G PHE* 1.3 71.1 + - + +
112G LEU 3.3 3.9 + - - +
117G GLN* 3.6 13.8 + - - +
170G LYS* 5.5 1.6 - - - +
208G PRO* 3.7 29.8 - - + +
212G TYR* 5.4 1.3 - - + -
213G VAL* 3.8 32.5 - - + +
217G TYR* 5.1 0.2 + - - -
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Residues in contact with PHE 111 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G GLY* 6.4 0.2 - - - -
107G ILE 3.6 24.5 - - - -
108G MET* 2.9 11.5 + - - +
110G PRO* 1.3 87.6 - - + +
112G LEU* 1.3 65.1 + - - +
113G LYS* 4.6 6.8 + - - +
212G TYR* 3.9 19.5 - + - -
213G VAL* 3.8 18.6 - - + -
216G VAL* 3.0 37.2 - - + -
217G TYR* 3.7 39.2 + + + +
301G IBG 4.1 30.7 - + + -
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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