Contacts of the helix formed by residues 98 - 122 (chain G) in PDB entry 2PGW
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 ILE 98 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PRO* 4.7 7.9 - - + -
100A ARG* 3.6 17.5 - - + +
101A ALA* 3.4 33.7 - - + +
104A GLN* 3.7 22.7 - - + +
251A PHE* 4.9 4.7 - - + -
87G PHE* 4.7 2.4 - - - -
91G TYR* 3.6 28.3 - - + -
96G ALA* 2.8 29.5 + - + +
97G ASN* 1.3 72.3 - - - +
99G MSE 1.3 62.9 + - - +
100G ARG 3.4 2.2 - - - -
101G ALA* 3.2 20.5 + - + +
102G ALA* 3.0 17.9 + - - +
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Residues in contact with MSE 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ARG* 5.3 1.4 - - - +
228A TRP* 3.4 58.5 - - + +
2100A GOL 5.7 0.4 - - - -
87G PHE* 3.9 25.1 - - + -
97G ASN 3.3 5.5 + - - -
98G ILE* 1.3 73.3 - - - +
100G ARG* 1.3 59.3 + - + +
102G ALA* 3.1 2.3 + - - +
103G ASN* 2.8 47.3 + - - +
252G THR* 3.8 33.0 - - + -
253G LEU* 5.2 1.3 - - - -
254G TYR* 4.0 20.6 - - + -
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Residues in contact with ARG 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASN* 2.9 32.3 + - - +
98A ILE* 3.6 21.5 - - + +
99A MSE 5.3 0.9 - - - +
98G ILE 3.4 1.0 - - - -
99G MSE 1.3 76.2 - - + +
101G ALA* 1.3 62.6 + - - +
103G ASN* 3.2 11.2 + - - +
104G GLN* 3.2 18.9 + - - +
227G SER* 5.1 3.6 + - - -
228G TRP* 3.5 24.8 - - - +
248G GLN 3.9 6.5 + - - -
249G ALA* 3.8 13.1 + - - +
251G PHE* 3.4 38.0 - - + +
252G THR* 3.8 10.9 - - + +
255G ASP* 3.0 34.2 + - - -
273G ARG 4.8 1.4 - - - +
274G GLU 4.7 0.9 - - - +
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Residues in contact with ALA 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE* 3.4 19.2 - - + +
101A ALA* 3.5 31.9 - - + -
91G TYR* 4.4 2.8 + - + -
98G ILE* 3.2 19.8 + - + +
100G ARG* 1.3 79.4 - - - +
102G ALA* 1.3 62.9 + - - +
104G GLN* 3.3 19.7 - - - +
105G ILE* 3.7 10.6 - - - +
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Residues in contact with ALA 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G PHE* 3.5 38.6 - - + -
91G TYR* 3.8 22.1 + - + -
98G ILE 3.0 8.1 + - - +
99G MSE 3.1 6.0 + - - +
101G ALA* 1.3 74.9 - - - +
103G ASN* 1.3 63.2 + - - +
105G ILE* 3.0 4.9 + - - +
106G PHE* 2.9 41.2 + - + -
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Residues in contact with ASN 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99G MSE 2.8 36.0 + - - +
100G ARG* 3.2 8.2 + - - +
102G ALA* 1.3 78.7 - - - +
104G GLN* 1.3 61.2 + - - +
106G PHE* 4.5 5.1 - - - +
107G SER* 2.9 28.2 + - - -
251G PHE 4.1 0.2 + - - -
252G THR* 4.1 13.7 - - - +
273G ARG 3.7 2.2 - - - +
274G GLU 2.9 29.9 + - - +
275G ILE* 3.4 22.7 + - - +
276G GLY* 3.5 12.5 - - - +
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Residues in contact with GLN 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA* 4.1 11.7 - - - +
98A ILE* 3.8 23.7 - - + +
51G CYS* 3.6 17.2 - - - +
52G THR* 3.3 43.3 + - - +
53G VAL 4.0 0.8 - - - -
54G ALA* 2.9 30.0 + - - +
60G THR* 4.3 7.1 - - - +
100G ARG 3.2 8.3 + - - +
101G ALA 3.3 12.1 - - - +
102G ALA 3.1 0.2 - - - -
103G ASN* 1.3 80.8 - - - +
105G ILE* 1.3 66.1 + - + +
107G SER* 3.8 8.8 - - - -
273G ARG* 3.6 19.9 + - + +
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Residues in contact with ILE 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51G CYS* 3.2 16.5 - - + -
52G THR 5.3 0.2 - - - +
60G THR* 4.4 29.2 - - + +
63G ILE* 4.1 10.5 - - + -
64G LEU* 3.6 38.4 - - + +
67G LEU* 3.7 21.1 - - + -
91G TYR* 4.0 12.6 - - - +
101G ALA 3.7 15.7 - - - +
102G ALA 3.0 5.1 + - - +
104G GLN* 1.3 88.9 - - + +
106G PHE* 1.3 65.7 + - - +
107G SER 3.0 2.7 + - - -
108G GLY 3.2 10.4 + - - -
109G ILE* 3.5 9.6 + - + +
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Residues in contact with PHE 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G LEU* 3.8 15.7 - - + -
83G ILE* 3.5 39.4 - - + +
86G ILE* 3.7 27.1 - - + -
87G PHE* 3.7 44.4 - + + -
91G TYR* 4.2 5.4 - + - -
102G ALA* 2.9 41.6 + - + +
103G ASN* 4.4 6.5 - - - +
105G ILE* 1.3 73.5 - - - +
107G SER* 1.3 56.4 + - - +
108G GLY 3.3 0.2 - - - -
109G ILE* 3.7 20.2 - - + -
110G ASP* 2.7 37.1 + - - +
276G GLY* 3.8 9.9 - - - +
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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
----------------------------------------------------------
50G GLU 4.9 3.0 + - - -
51G CYS* 6.1 0.2 - - - -
103G ASN 2.9 19.5 + - - -
104G GLN 3.8 9.0 - - - -
106G PHE* 1.3 77.1 - - - +
108G GLY* 1.3 62.9 + - - +
110G ASP* 3.5 2.1 + - - +
111G MSE 3.0 28.3 + - - +
272G PRO* 3.0 39.0 + - - +
273G ARG* 3.5 8.6 + - - +
276G GLY 3.6 12.5 + - - -
277G GLY* 3.7 1.8 - - - +
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Residues in contact with GLY 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ILE* 3.5 15.5 - - - +
49G GLY* 3.7 0.5 - - - -
50G GLU 3.4 28.4 + - - -
51G CYS* 3.7 13.8 - - - -
105G ILE 3.2 5.3 + - - -
107G SER* 1.3 78.2 - - - +
109G ILE* 1.3 62.6 + - - +
111G MSE 3.1 5.8 - - - +
112G ALA 3.0 18.7 + - - -
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Residues in contact with ILE 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ILE* 4.1 12.3 - - + +
39G ILE* 4.4 0.9 - - + -
64G LEU* 3.7 27.8 - - + -
67G LEU* 4.1 21.3 - - + +
68G ALA* 4.1 14.1 - - + +
71G LEU* 3.7 26.9 - - + -
83G ILE* 4.5 16.2 - - + -
86G ILE* 5.7 1.6 - - + -
105G ILE* 3.5 6.0 + - + +
106G PHE* 3.2 28.6 + - + +
108G GLY* 1.3 74.0 - - - +
110G ASP* 1.3 66.5 + - - +
112G ALA* 3.2 5.6 + - - +
113G MSE 2.9 32.7 + - + +
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Residues in contact with ASP 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G VAL* 3.4 13.5 - - - +
83G ILE* 4.0 12.9 - - + +
106G PHE 2.7 20.8 + - - +
107G SER 3.9 2.9 - - - +
109G ILE* 1.3 73.2 - - - +
111G MSE 1.3 63.7 + - - +
113G MSE 3.3 4.9 + - - +
114G TRP* 3.0 54.0 + - - -
276G GLY 3.8 10.5 - - - +
277G GLY* 3.9 2.7 - - - -
278G ILE* 2.7 29.0 + - - +
279G GLN* 3.1 17.8 + - - +
280G PRO* 4.2 5.8 - - - +
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Residues in contact with MSE 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G ILE 4.2 2.7 - - - -
49G GLY* 3.9 3.1 - - - -
50G GLU 3.8 25.6 - - - +
107G SER* 3.0 20.2 + - - +
108G GLY 3.1 10.1 - - - +
110G ASP* 1.3 78.0 + - - +
112G ALA* 1.3 63.8 + - - +
114G TRP* 3.3 2.4 + - - +
115G ASP* 3.0 22.2 + - - +
272G PRO* 5.5 6.3 - - + -
278G ILE* 4.0 15.0 - - + +
305G ILE* 3.0 49.6 - - + +
306G THR* 4.3 11.4 - - - -
309G ALA* 3.3 28.0 - - + -
356G LEU* 3.4 20.5 - - + +
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Residues in contact with ALA 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G ILE* 3.8 8.1 - - + +
39G ILE* 3.7 17.7 - - + -
47G GLY* 3.5 23.3 - - - +
48G ILE 3.7 11.8 + - - +
49G GLY 3.7 13.2 - - - +
108G GLY 3.0 6.9 + - - +
109G ILE 3.2 6.3 + - - +
111G MSE 1.3 79.0 - - - +
113G MSE 1.3 57.8 - - - +
115G ASP* 3.3 0.4 + - - -
116G LEU* 2.8 31.4 + - - +
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Residues in contact with MSE 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 3.6 22.4 - - + -
39G ILE* 3.5 24.9 - - + -
71G LEU* 4.1 7.6 - - + -
75G SER 3.8 6.1 - - - +
76G PRO* 3.4 41.8 - - + +
79G VAL* 3.7 42.0 - - + -
82G LEU* 4.1 8.1 - - + -
109G ILE* 2.9 28.7 + - + +
110G ASP 3.6 4.5 - - - +
111G MSE 3.3 0.2 - - - -
112G ALA* 1.3 77.2 - - - +
114G TRP* 1.3 56.4 + - - +
116G LEU* 3.4 5.6 + - - +
117G GLN* 2.9 34.3 + - - +
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Residues in contact with TRP 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128E LEU 4.4 9.6 - - - -
129E LEU 4.7 0.4 - - - -
130E GLY* 4.2 17.3 - - - -
79G VAL* 3.9 16.0 - - + +
110G ASP* 3.0 58.3 + - - +
111G MSE 4.0 2.9 - - - +
113G MSE 1.3 73.7 - - - +
115G ASP* 1.3 61.1 + - - +
116G LEU 3.1 0.2 - - - -
117G GLN* 3.5 31.7 - - - +
118G GLY 2.9 24.8 + - - -
125G VAL* 3.6 19.5 - - + +
128G LEU* 4.1 34.0 - - + +
129G LEU* 4.4 20.4 - - + -
278G ILE* 4.1 20.4 - - + -
279G GLN* 3.8 35.0 - - + +
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Residues in contact with ASP 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLY* 3.2 3.1 - - - -
48G ILE* 2.8 30.1 + - - +
111G MSE 3.0 16.6 + - - +
112G ALA 3.5 4.9 - - - +
114G TRP* 1.3 77.2 - - - +
116G LEU* 1.3 57.9 + - - +
118G GLY 3.3 0.2 + - - -
119G LYS* 2.9 62.8 + - - +
125G VAL* 4.3 0.8 - - - +
355G GLY* 3.5 6.8 - - - -
356G LEU* 2.7 45.6 + - + +
357G GLY 4.2 0.9 + - - -
358G PHE* 4.5 3.6 - - - -
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Residues in contact with LEU 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ILE* 4.5 4.9 - - + -
39G ILE* 3.7 34.3 - - + +
41G ALA* 4.3 8.7 - - + -
45G THR* 3.5 39.9 - - + +
47G GLY* 3.9 11.4 - - - +
76G PRO* 3.5 30.3 - - + -
112G ALA 2.8 18.8 + - - +
113G MSE 3.5 6.3 - - - +
115G ASP* 1.3 78.5 - - - +
117G GLN* 1.3 62.6 + - - +
119G LYS* 3.4 2.7 + - - +
120G LEU* 3.0 38.3 + - + +
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Residues in contact with GLN 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127E GLN 4.1 6.8 - - - +
128E LEU* 5.5 0.7 - - - -
130E GLY* 5.7 0.9 + - - -
76G PRO* 3.1 29.3 + - + +
77G HIS* 3.4 33.9 + - + +
79G VAL* 3.6 18.0 - - - +
113G MSE 2.9 22.4 + - - +
114G TRP* 3.2 41.1 + - - +
116G LEU* 1.3 74.9 - - - +
118G GLY* 1.3 58.9 + - - +
120G LEU* 3.4 9.2 + - - +
121G ALA* 3.0 30.0 + - - +
128G LEU* 4.0 11.1 - - + +
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Residues in contact with GLY 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G TRP 2.9 10.9 + - - -
117G GLN* 1.3 75.2 - - - +
119G LYS* 1.3 54.7 + - - +
121G ALA* 3.6 1.5 - - - -
122G GLY* 2.7 30.8 + - - -
123G LEU 2.9 25.7 + - - -
125G VAL* 5.2 0.2 - - - -
128G LEU* 3.7 14.2 - - - +
354G PRO* 4.0 0.2 - - - +
355G GLY* 3.4 16.1 + - - -
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Residues in contact with LYS 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G THR* 3.7 20.1 + - + +
46G VAL 3.0 26.7 + - - +
47G GLY* 4.5 0.2 - - - -
48G ILE* 4.5 14.1 - - - +
115G ASP* 2.9 49.4 + - - +
116G LEU 3.9 0.9 - - - +
118G GLY* 1.3 74.4 - - - +
120G LEU* 1.3 62.6 - - - +
122G GLY* 3.5 9.0 + - - -
354G PRO* 4.0 25.0 - - + +
355G GLY 3.6 0.2 - - - +
357G GLY 5.6 1.1 - - - +
358G PHE* 4.8 16.3 + - - +
359G GLN* 6.2 0.7 - - - +
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Residues in contact with LEU 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G VAL* 4.4 18.2 - - + -
43G ASP* 3.4 29.2 - - - +
45G THR* 3.4 16.6 - - + +
76G PRO* 3.7 30.1 - - + -
77G HIS* 4.3 14.6 - - + +
116G LEU* 3.0 35.6 + - + +
117G GLN* 3.7 5.6 - - - +
119G LYS* 1.3 79.5 - - - +
121G ALA* 1.3 58.8 + - - +
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Residues in contact with ALA 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121E ALA* 5.2 13.7 - - + -
123E LEU* 5.9 4.3 - - + -
77G HIS* 6.0 2.5 - - + -
117G GLN 3.0 16.8 + - - +
118G GLY 4.1 2.0 - - - +
120G LEU* 1.3 77.7 - - - +
122G GLY* 1.3 62.4 + - - +
123G LEU* 3.9 25.1 - - + +
128G LEU* 4.6 8.5 - - + -
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Residues in contact with GLY 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G GLY 2.7 13.6 + - - -
119G LYS 3.5 7.4 + - - -
120G LEU 3.4 3.2 - - - -
121G ALA* 1.3 76.2 - - - +
123G LEU* 1.3 64.2 + - - +
124G PRO* 4.9 0.2 - - - +
354G PRO* 4.2 19.6 - - - +
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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