Contacts of the helix formed by residues 90 - 115 (chain G) in PDB entry 4GTU
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 GLU 90 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G GLU 4.2 0.6 + - - -
89G THR* 1.3 72.0 - - - +
91G GLU* 1.3 64.2 + - - +
93G LYS* 3.3 12.3 + - + +
94G ILE* 3.1 26.7 + - - +
67H HIS* 4.5 7.3 - - + -
78H TYR* 3.2 24.9 - - - -
81H ARG* 2.7 47.4 + - + -
82H LYS* 3.7 22.9 - - + +
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Residues in contact with GLU 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89G THR* 3.6 17.9 + - - +
90G GLU* 1.3 78.3 - - - +
92G GLU* 1.3 68.4 + - - +
94G ILE* 3.1 20.1 + - - +
95G ARG* 3.4 19.8 + - + +
67H HIS* 5.5 7.2 - - - +
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Residues in contact with GLU 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G GLY* 4.3 1.6 - - - -
88G GLU* 3.1 36.6 - - - +
89G THR* 2.9 30.0 + - - +
91G GLU* 1.3 87.2 - - + +
93G LYS* 1.3 62.6 + - - +
95G ARG* 3.0 13.4 + - - +
96G VAL* 2.9 27.0 + - - +
148G VAL* 3.8 26.3 - - + +
149G GLY* 5.3 2.6 - - - -
150G ASP 5.3 0.9 + - - -
151G LYS* 3.6 28.0 - - - +
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Residues in contact with LYS 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G CYS* 6.3 0.9 - - - -
87G GLY* 4.0 29.4 - - - -
88G GLU 4.3 11.0 + - - -
89G THR 2.7 18.0 + - - +
90G GLU* 3.5 13.5 - - - +
91G GLU 3.2 0.2 - - - -
92G GLU* 1.3 72.4 - - - +
94G ILE* 1.3 57.6 + - - +
96G VAL* 3.1 5.5 + - - +
97G ASP* 3.0 33.8 + - - +
81H ARG* 3.2 44.4 - - - +
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Residues in contact with ILE 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G GLU* 3.2 30.5 - - - +
91G GLU* 3.1 11.0 + - - +
93G LYS* 1.3 76.5 - - - +
95G ARG* 1.3 62.1 + - + +
97G ASP* 3.7 5.1 - - - +
98G ILE* 3.2 28.6 + - + +
67H HIS* 4.1 22.7 - - + +
68H LYS 5.5 1.1 - - - +
69H ILE* 3.6 37.0 - - + -
78H TYR* 3.5 24.9 - - + -
81H ARG* 3.4 9.0 - - - +
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Residues in contact with ARG 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G GLU* 3.5 21.1 - - + +
92G GLU* 3.0 10.5 + - - +
94G ILE* 1.3 77.8 - - + +
96G VAL* 1.3 65.7 + - - +
99G LEU* 3.3 26.5 + - - +
140G PHE* 2.9 64.2 + - + +
144G ARG* 3.0 43.7 - - - +
147G PHE 2.8 22.2 + - - -
148G VAL* 3.5 32.0 + - + +
55H ASP* 4.5 5.1 + - - -
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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
----------------------------------------------------------
86G CYS* 4.4 9.9 - - - -
87G GLY* 3.6 25.4 - - - +
92G GLU 2.9 19.4 + - - +
93G LYS* 3.1 7.8 + - - +
95G ARG* 1.3 77.6 - - - +
97G ASP* 1.3 69.6 + - - +
100G GLU* 3.2 23.0 + - - +
148G VAL* 3.6 18.2 - - + -
153G THR* 4.6 4.5 - - + -
154G PHE* 3.5 36.3 - - + -
155G VAL* 3.3 12.8 - - + +
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Residues in contact with ASP 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G LYS* 3.0 16.1 + - - +
94G ILE* 3.7 9.4 - - + +
95G ARG 3.3 0.2 - - - -
96G VAL* 1.3 78.5 - - - +
98G ILE* 1.3 68.7 + - - +
100G GLU* 2.8 19.0 + - - +
101G ASN* 2.9 21.8 + - - +
69H ILE* 5.7 0.2 - - + -
74H ALA* 3.9 23.6 - - + +
77H CYS* 3.5 21.4 - - - +
81H ARG* 2.7 27.7 + - - -
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Residues in contact with ILE 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94G ILE* 3.2 19.8 + - + +
97G ASP* 1.3 78.9 - - - +
99G LEU* 1.3 59.1 + - - +
100G GLU 3.0 0.3 + - - -
101G ASN* 3.3 2.7 + - - +
102G GLN* 2.7 36.5 + - + +
140G PHE* 4.2 12.1 - - + -
55H ASP* 4.8 11.9 - - + +
56H PHE* 3.5 35.0 - - + -
68H LYS 4.4 6.1 - - - +
69H ILE* 3.6 35.9 - - + -
70H THR* 3.7 31.2 - - - +
71H GLN* 5.4 0.8 - - + +
74H ALA* 4.4 1.8 - - + -
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Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95G ARG 3.3 18.9 + - - +
98G ILE* 1.3 80.0 - - - +
100G GLU* 1.3 60.4 + - - +
102G GLN* 4.0 1.8 - - + -
103G ALA* 3.1 24.7 + - + +
137G PHE* 3.8 21.5 - - + -
140G PHE* 3.7 21.1 - - + -
147G PHE* 4.1 13.0 - - + -
155G VAL* 4.3 20.8 - - + +
158G LEU* 4.4 1.9 - - - +
159G ALA* 4.1 22.7 - - + -
56H PHE* 3.5 36.3 - - + -
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Residues in contact with GLU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G ASN* 3.3 41.2 + - - +
77G CYS* 3.7 19.6 - - - -
96G VAL* 3.2 20.6 + - - +
97G ASP* 2.8 10.1 + - - +
99G LEU* 1.3 79.5 - - - +
101G ASN* 1.3 71.2 + - - +
102G GLN 3.1 1.6 + - - -
103G ALA* 4.0 0.9 - - - +
104G MET* 3.2 24.9 + - - +
154G PHE* 3.2 34.1 - - + -
155G VAL* 4.3 3.6 - - + +
158G LEU* 4.1 10.8 - - + +
100H GLU* 5.3 4.9 - - - +
101H ASN* 5.0 0.7 + - - +
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Residues in contact with ASN 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G ASN* 5.3 2.5 - - - +
97G ASP* 2.9 21.8 + - - +
98G ILE 4.1 0.4 - - - +
100G GLU* 1.3 86.0 - - - +
102G GLN* 1.3 56.7 + - - +
104G MET* 4.7 3.6 - - - +
105G ASP* 3.1 15.9 + - - +
71H GLN* 3.1 41.7 + - + +
73H ASN* 3.0 42.0 + - - +
74H ALA* 4.6 4.9 - - + +
100H GLU* 4.5 8.5 + - - -
104H MET* 5.2 8.2 - - - +
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Residues in contact with GLN 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G ILE* 2.7 30.6 + - + +
99G LEU* 4.4 4.3 - - + -
101G ASN* 1.3 73.9 - - - +
103G ALA* 1.3 63.7 + - - +
104G MET 3.3 0.2 - - - -
105G ASP* 3.0 28.9 + - - +
106G VAL* 3.1 18.8 + - - +
109G GLN* 5.6 0.6 - - - +
137G PHE* 4.5 6.3 - - + -
56H PHE* 3.8 53.1 - - + +
57H PRO 6.0 0.2 + - - -
58H ASN* 4.3 8.6 + - - +
70H THR* 5.3 1.9 + - - -
71H GLN* 2.7 30.9 + - + +
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Residues in contact with ALA 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G LEU* 3.1 32.1 + - + +
100G GLU 4.0 0.2 - - - +
102G GLN* 1.3 77.7 - - - +
104G MET* 1.3 60.9 - - - +
106G VAL* 2.8 30.4 - - - +
107G SER* 3.0 8.7 + - - -
137G PHE* 4.4 7.3 - - + -
158G LEU* 3.6 24.7 - - + -
159G ALA* 4.9 2.2 - - - +
162G VAL* 3.5 13.9 - - + +
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Residues in contact with MET 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G LEU* 4.9 20.4 - - + +
72G SER* 4.1 18.2 - - - +
73G ASN* 3.2 37.0 - - - +
76G LEU* 5.7 1.1 - - + -
100G GLU 3.2 14.2 + - - +
101G ASN* 4.7 4.0 - - - +
103G ALA* 1.3 78.6 - - - +
105G ASP* 1.3 61.9 + - - +
107G SER* 3.0 27.9 + - - -
108G ASN* 3.0 31.5 + - - +
158G LEU* 4.5 15.1 - - + +
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Residues in contact with ASP 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ASN 3.1 19.2 + - - +
102G GLN* 3.0 25.9 + - - +
104G MET* 1.3 78.6 - - - +
106G VAL* 1.3 56.5 + - - +
108G ASN* 3.8 7.0 + - - +
109G GLN* 2.8 57.4 + - - +
58H ASN* 4.7 6.5 + - - -
71H GLN* 3.5 17.4 + - - +
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Residues in contact with VAL 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G GLN* 3.1 17.6 + - - +
103G ALA* 2.8 26.9 - - - +
105G ASP* 1.3 81.7 - - - +
107G SER* 1.3 61.6 + - - +
109G GLN* 3.2 11.9 + - - +
110G LEU* 2.8 31.2 + - - +
126G TYR* 3.8 10.4 + - - +
133G MET* 4.6 19.3 - - + -
137G PHE* 4.3 17.7 - - + -
162G VAL* 3.5 30.3 - - + -
166G HIS* 4.7 7.8 - - + -
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Residues in contact with SER 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ALA 3.0 14.7 + - - -
104G MET* 3.0 27.8 + - - +
106G VAL* 1.3 78.4 - - - +
108G ASN* 1.3 54.2 + - - +
110G LEU* 3.3 6.0 + - - +
111G ALA* 2.7 35.8 + - - +
158G LEU* 5.1 2.3 - - - +
161G ASP* 5.5 2.6 + - - -
162G VAL* 3.8 13.9 - - - +
165G LEU* 5.5 10.9 - - - +
166G HIS* 5.9 1.1 - - - -
208G TYR* 4.8 1.7 + - - -
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Residues in contact with ASN 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G LEU* 5.9 4.2 - - - +
104G MET* 3.0 36.4 + - - +
105G ASP* 4.1 6.7 - - - +
107G SER* 1.3 74.5 - - - +
109G GLN* 1.3 59.7 + - + +
111G ALA* 3.7 9.1 - - - +
112G ARG* 2.6 63.4 + - - +
104H MET* 5.5 6.4 - - - +
108H ASN* 4.7 5.9 - - - +
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Residues in contact with GLN 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G GLN* 5.6 0.6 - - - +
105G ASP* 2.8 46.0 + - - +
106G VAL* 3.2 15.3 + - - +
108G ASN* 1.3 80.4 - - + +
110G LEU* 1.3 59.1 + - - +
112G ARG* 4.0 9.7 - - - +
113G VAL* 3.5 25.6 + - - +
126G TYR* 4.0 16.3 - - + +
133G MET* 4.3 16.2 - - - +
58H ASN* 6.0 0.4 - - - +
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Residues in contact with LEU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G VAL 2.8 16.4 + - - +
107G SER* 3.7 3.6 - - - +
109G GLN* 1.3 76.3 - - - +
111G ALA* 1.3 59.7 - - - +
112G ARG 3.2 0.4 - - - -
113G VAL* 3.2 8.4 - - + +
114G CYS* 3.0 34.0 + - - +
126G TYR* 4.0 26.7 - - + +
165G LEU* 3.6 28.0 - - + -
166G HIS* 3.9 19.5 - - + +
169G PHE* 3.6 40.8 - - + -
208G TYR* 3.1 21.3 - - + +
214G TRP* 5.5 0.7 - - + -
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Residues in contact with ALA 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G SER 2.7 22.3 + - - +
108G ASN* 3.7 11.4 - - - +
110G LEU* 1.3 74.7 - - - +
112G ARG* 1.3 57.5 + - - +
115G TYR* 3.0 41.1 + - + +
208G TYR* 3.8 21.5 + - + -
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Residues in contact with ARG 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G ASN* 2.6 42.2 + - - +
109G GLN* 4.0 10.6 - - - +
111G ALA* 1.3 76.1 - - - +
113G VAL* 1.3 60.1 + - + +
115G TYR* 4.1 3.0 - - - +
116G SER* 2.8 34.6 + - - +
122G LEU* 5.5 0.2 - - - -
108H ASN* 3.5 21.0 + - - +
112H ARG* 3.1 53.3 - - - +
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Residues in contact with VAL 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G GLN 3.5 15.7 + - - +
110G LEU* 3.2 23.3 - - + +
112G ARG* 1.3 76.4 - - + +
114G CYS* 1.3 69.8 + - - +
116G SER* 3.6 16.6 + - - +
119G PHE* 3.9 17.7 - - + -
122G LEU* 4.1 38.9 - - + +
123G LYS* 5.6 1.8 - - - +
126G TYR* 4.6 19.5 - - + -
169G PHE* 5.6 4.3 - - + -
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Residues in contact with CYS 114 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G LEU* 3.0 24.6 + - - +
111G ALA 3.9 0.7 - - - +
113G VAL* 1.3 80.5 - - - +
115G TYR* 1.3 60.9 + - - +
119G PHE* 4.3 7.6 - - - -
169G PHE* 3.7 18.2 - - - -
208G TYR* 3.9 22.2 - - + -
212G ALA* 5.2 0.2 - - - -
213G VAL* 3.3 28.9 + - - +
214G TRP* 3.4 49.3 + - + +
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Residues in contact with TYR 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ALA* 3.0 26.7 + - + +
112G ARG* 4.1 3.4 - - - +
114G CYS* 1.3 75.8 - - - +
116G SER* 1.3 66.4 + - - +
117G PRO* 3.4 3.5 - - - +
208G TYR* 3.5 28.0 - + + -
209G THR* 2.7 33.0 + - - +
211G VAL* 4.5 15.5 - - + +
212G ALA* 3.7 23.3 - - + +
213G VAL* 3.2 14.9 + - - +
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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