Contacts of the helix formed by residues 98 - 122 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 4.6 1.7 - - - -
91C TYR* 3.6 27.4 - - + -
96C ALA* 2.8 28.5 + - + +
97C ASN* 1.3 72.5 - - - +
99C MSE 1.3 58.5 + - - +
100C ARG 3.4 2.7 - - - -
101C ALA* 3.2 20.7 + - + +
102C ALA* 2.9 24.6 + - - +
55H PRO* 4.7 6.7 - - + -
100H ARG* 3.6 18.4 - - + +
101H ALA* 3.5 32.5 - - + +
104H GLN* 3.8 22.9 - - + +
251H PHE* 4.8 4.9 - - + -
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Residues in contact with MSE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 4.0 24.2 - - + -
97C ASN 3.5 4.6 + - - -
98C ILE* 1.3 74.5 - - - +
100C ARG* 1.3 52.9 + - + +
102C ALA* 3.2 2.0 + - - +
103C ASN* 2.7 52.7 + - - +
252C THR* 3.6 35.2 - - + -
253C LEU* 5.2 1.3 - - - -
254C TYR* 4.0 20.4 - - + +
100H ARG* 5.3 1.4 - - - +
228H TRP* 3.4 59.6 - - + +
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Residues in contact with ARG 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE 3.4 0.4 - - - -
99C MSE 1.3 75.2 - - + +
101C ALA* 1.3 62.3 + - - +
103C ASN* 3.3 10.6 + - - +
104C GLN* 3.1 19.8 + - - +
227C SER* 5.1 2.4 + - - -
228C TRP* 3.6 20.9 - - - -
248C GLN 4.0 5.3 + - - -
249C ALA* 3.7 13.9 + - - +
251C PHE* 3.4 45.1 - - + +
252C THR* 3.8 10.4 - - + +
255C ASP* 3.0 29.8 + - - -
273C ARG 4.8 1.0 - - - +
274C GLU 4.7 0.9 - - - +
2300C GOL 4.1 16.4 + - - -
97H ASN* 3.0 29.4 + - - +
98H ILE* 3.5 21.0 - - + +
99H MSE 5.3 1.3 - - - +
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TYR* 4.8 2.2 - - + -
98C ILE* 3.2 20.4 + - + +
100C ARG* 1.3 75.3 - - - +
102C ALA* 1.3 66.1 + - - +
104C GLN* 3.2 20.8 + - - +
105C ILE* 3.6 10.0 + - - +
98H ILE* 3.5 18.5 - - + +
101H ALA* 3.4 33.0 - - + -
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE* 3.4 39.0 - - + -
91C TYR* 3.7 24.8 - - + -
98C ILE 2.9 12.7 + - - +
99C MSE 3.5 3.4 - - - +
101C ALA* 1.3 75.8 - - - +
103C ASN* 1.3 65.0 + - - +
105C ILE* 3.1 5.9 + - - +
106C PHE* 3.0 32.0 + - + -
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Residues in contact with ASN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C MSE 2.7 46.6 + - - +
100C ARG* 3.4 5.1 - - - +
101C ALA 3.2 0.2 - - - -
102C ALA* 1.3 74.5 - - - +
104C GLN* 1.3 62.3 + - - +
106C PHE* 4.5 7.1 - - - +
107C SER* 2.9 23.2 + - - -
252C THR* 3.9 13.7 - - - +
273C ARG 3.8 2.0 - - - +
274C GLU 3.0 28.8 + - - +
275C ILE* 3.5 23.0 + - - +
276C GLY* 3.4 15.4 - - - +
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Residues in contact with GLN 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C CYS* 3.7 15.8 - - - +
52C THR* 3.1 48.5 + - - +
53C VAL* 3.9 2.0 - - - +
54C ALA* 3.0 28.9 + - - +
60C THR* 4.4 7.0 - - - +
100C ARG 3.1 11.7 + - - +
101C ALA* 3.2 12.3 + - - +
103C ASN* 1.3 76.4 - - - +
105C ILE* 1.3 67.9 + - + +
107C SER* 3.8 8.3 - - - -
273C ARG* 3.6 20.7 + - + +
96H ALA* 4.1 12.0 - - - +
98H ILE* 3.9 22.4 - - + +
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Residues in contact with ILE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C CYS* 3.1 26.3 - - + -
52C THR 5.2 0.2 - - - +
60C THR* 4.3 31.0 - - + +
63C ILE* 4.2 10.3 - - + -
64C LEU* 3.6 37.5 - - + +
67C LEU* 3.6 21.8 - - + -
91C TYR* 4.0 13.0 - - - +
101C ALA 3.7 13.9 - - - +
102C ALA 3.1 5.1 + - - +
104C GLN* 1.3 87.7 - - + +
106C PHE* 1.3 65.3 + - - +
107C SER 3.1 3.0 + - - -
108C GLY 3.2 1.9 + - - -
109C ILE* 3.6 8.7 + - + +
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Residues in contact with PHE 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.9 14.8 - - + -
83C ILE* 3.5 38.8 - - + -
86C ILE* 3.7 25.8 - - + -
87C PHE* 3.7 43.7 - + + -
91C TYR* 4.3 4.7 - + - -
102C ALA* 3.0 40.4 + - + +
103C ASN* 4.2 8.5 - - - +
105C ILE* 1.3 76.8 - - - +
107C SER* 1.3 56.5 + - - +
109C ILE* 3.6 20.0 - - + +
110C ASP* 2.8 33.4 + - - +
276C GLY* 3.7 11.0 - - - +
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU 4.9 2.3 + - - -
51C CYS* 5.9 0.2 - - - -
103C ASN 2.9 14.9 + - - -
104C GLN 3.8 9.4 - - - -
105C ILE 3.1 0.6 - - - -
106C PHE* 1.3 77.2 - - - +
108C GLY* 1.3 56.7 - - - +
110C ASP* 3.9 1.6 - - - +
111C MSE 2.9 36.5 + - - +
272C PRO* 3.1 43.8 + - - +
273C ARG* 3.4 7.8 + - - +
276C GLY 3.6 12.1 + - - -
277C GLY* 4.2 2.6 - - - -
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Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.4 17.4 - - - +
49C GLY* 3.8 0.5 - - - -
50C GLU 3.4 26.6 + - - -
51C CYS* 3.7 13.0 - - - -
105C ILE 3.2 5.5 + - - -
107C SER* 1.3 76.2 - - - +
109C ILE* 1.3 61.1 + - - +
111C MSE 3.3 5.4 - - - +
112C ALA* 2.8 24.9 + - - +
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Residues in contact with ILE 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 4.1 9.8 - - + +
39C ILE* 3.8 4.0 - - + +
64C LEU* 3.8 25.6 - - + -
67C LEU* 4.0 24.2 - - + +
68C ALA* 4.2 13.0 - - + +
71C LEU* 3.8 28.0 - - + -
83C ILE* 4.4 17.3 - - + -
86C ILE* 5.7 1.3 - - + -
105C ILE* 3.6 7.1 + - + +
106C PHE* 3.2 30.6 + - + +
108C GLY* 1.3 77.2 - - - +
110C ASP* 1.3 58.4 + - - +
112C ALA* 3.1 4.7 + - - +
113C MSE 2.8 36.5 + - + +
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL* 3.2 18.8 - - - +
83C ILE* 4.0 10.5 - - + +
106C PHE 2.8 20.0 + - - +
107C SER 4.0 2.0 - - - +
109C ILE* 1.3 74.0 - - - +
111C MSE 1.3 63.6 + - - +
113C MSE 3.2 5.9 + - - +
114C TRP* 2.9 55.4 + - - -
276C GLY 3.9 10.1 - - - +
277C GLY* 4.0 2.9 - - - -
278C ILE 2.7 29.4 + - - -
279C GLN* 3.2 16.7 + - - +
280C PRO* 4.2 4.8 - - - +
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Residues in contact with MSE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE 4.3 0.7 - - - -
49C GLY* 4.0 5.8 - - - -
50C GLU 3.8 27.8 - - - +
107C SER* 2.9 39.7 + - - +
108C GLY 3.3 6.3 - - - +
110C ASP* 1.3 80.0 + - - +
112C ALA* 1.3 62.3 + - - +
114C TRP* 3.5 2.8 + - - +
115C ASP* 3.2 20.8 + - - +
272C PRO* 4.1 17.5 - - + -
278C ILE* 4.1 12.5 - - + +
305C ILE* 4.1 12.3 - - - -
306C THR* 4.0 18.2 - - - +
309C ALA* 3.7 26.5 - - + -
356C LEU* 3.7 21.7 - - + +
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Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.7 11.4 - - + +
39C ILE* 3.6 19.5 - - + -
47C GLY* 3.5 10.3 - - - +
48C ILE 3.7 12.6 - - - +
49C GLY* 3.6 16.8 - - - +
108C GLY 2.8 16.5 + - - +
109C ILE 3.6 3.4 - - - +
111C MSE 1.3 77.1 - - - +
113C MSE 1.3 57.1 + - - +
115C ASP* 3.3 2.3 + - - +
116C LEU* 2.9 29.8 + - - +
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Residues in contact with MSE 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.7 24.5 - - + -
39C ILE* 3.8 19.3 - - + -
71C LEU* 4.1 9.4 - - + -
75C SER 3.7 7.9 - - - +
76C PRO* 3.6 37.2 - - + +
79C VAL* 3.7 44.4 - - + -
82C LEU* 3.8 13.5 - - + -
109C ILE* 2.8 30.8 + - + +
110C ASP 3.2 5.1 + - - +
112C ALA* 1.3 72.4 - - - +
114C TRP* 1.3 57.8 + - - +
116C LEU* 3.3 7.3 + - - +
117C GLN* 2.9 32.4 + - - +
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Residues in contact with TRP 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL* 3.8 17.2 - - + +
110C ASP* 2.9 57.6 + - - +
111C MSE 4.1 2.5 - - - +
113C MSE 1.3 73.3 - - - +
115C ASP* 1.3 60.6 + - - +
117C GLN* 3.7 30.0 - - - +
118C GLY 2.9 24.6 + - - -
125C VAL* 3.5 24.1 - - + +
128C LEU* 4.1 24.5 - - + +
129C LEU* 4.1 25.6 - - + -
278C ILE* 4.2 17.0 - - + -
279C GLN* 3.5 42.5 - - + +
128F LEU 4.4 12.6 - - - -
130F GLY* 4.2 13.7 - - - -
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Residues in contact with ASP 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY* 3.4 1.4 - - - -
48C ILE* 2.8 26.5 + - - +
111C MSE 3.2 14.8 + - - +
112C ALA 3.5 8.1 - - - +
114C TRP* 1.3 75.3 - - - +
116C LEU* 1.3 58.1 + - - +
118C GLY 3.3 1.6 + - - -
119C LYS* 2.8 70.9 + - - +
125C VAL* 4.3 0.6 - - - +
355C GLY* 3.5 1.4 - - - -
356C LEU* 2.8 49.7 + - + +
357C GLY 4.2 1.0 + - - -
358C PHE* 4.3 3.4 + - - -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.6 1.3 - - + -
39C ILE* 3.8 31.2 - - + +
41C ALA* 4.2 9.6 - - + -
45C THR* 3.4 45.8 - - + +
47C GLY* 3.8 12.5 - - - +
76C PRO* 3.5 34.3 - - + -
112C ALA 2.9 13.7 + - - +
113C MSE 3.4 10.3 - - - +
115C ASP* 1.3 77.4 - - - +
117C GLN* 1.3 61.9 + - - +
119C LYS* 3.2 4.2 + - - +
120C LEU* 2.9 35.7 + - + +
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Residues in contact with GLN 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PRO* 3.0 31.1 + - + +
77C HIS* 3.4 34.0 + - + +
79C VAL* 3.7 22.4 - - - +
113C MSE 2.9 18.2 + - - +
114C TRP* 3.3 36.3 + - - +
116C LEU* 1.3 75.3 - - - +
118C GLY* 1.3 63.0 + - - +
120C LEU* 3.3 10.5 + - - +
121C ALA* 3.0 24.6 + - - +
128C LEU* 4.0 12.4 - - + +
127F GLN 3.9 9.4 - - - +
128F LEU* 5.2 1.6 - - - -
130F GLY* 5.5 0.6 + - - -
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Residues in contact with GLY 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C TRP 2.9 11.5 + - - -
115C ASP 3.7 1.6 - - - -
117C GLN* 1.3 76.8 - - - +
119C LYS* 1.3 51.5 + - - +
121C ALA* 3.4 1.3 + - - -
122C GLY* 2.7 29.8 + - - -
123C LEU 2.9 30.4 + - - -
128C LEU* 3.6 14.5 - - - +
355C GLY* 3.4 11.6 + - - -
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C THR* 3.7 19.9 + - + -
46C VAL 3.0 26.0 + - - +
48C ILE* 4.3 9.5 - - - +
115C ASP* 2.8 51.3 + - - +
116C LEU 3.7 0.7 - - - +
118C GLY* 1.3 76.5 - - - +
120C LEU* 1.3 63.9 + - - +
122C GLY* 3.3 10.2 + - - -
354C PRO* 4.0 29.1 - - + +
357C GLY 5.8 0.2 - - - +
358C PHE* 5.0 16.8 + - - +
359C GLN* 6.1 2.0 - - - +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C VAL* 4.3 25.1 - - + -
43C ASP* 3.6 17.5 - - - +
45C THR* 3.5 27.8 - - - +
76C PRO* 4.3 17.0 - - + -
77C HIS* 4.3 15.3 - - + +
116C LEU* 2.9 40.8 + - + +
117C GLN* 3.7 5.4 - - - +
118C GLY 3.3 0.2 - - - -
119C LYS* 1.3 77.0 - - - +
121C ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C HIS* 6.2 1.6 - - + -
117C GLN 3.0 16.5 + - - +
118C GLY 4.1 1.8 - - - +
120C LEU* 1.3 77.6 - - + +
122C GLY* 1.3 61.0 - - - +
123C LEU* 3.6 26.7 + - + +
128C LEU* 4.5 8.5 - - + -
121F ALA* 5.2 13.5 - - + +
123F LEU* 5.9 4.5 - - + -
----------------------------------------------------------
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Residues in contact with GLY 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C GLY 2.7 14.2 + - - -
119C LYS 3.3 10.0 + - - -
120C LEU 3.8 0.2 + - - -
121C ALA* 1.3 76.0 - - - +
123C LEU* 1.3 61.5 + - - +
124C PRO* 4.7 1.4 - - - +
352C ARG 5.8 0.2 - - - +
354C PRO* 4.0 22.5 - - - +
----------------------------------------------------------
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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