Contacts of the helix formed by residues 98 - 122 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C PRO* 4.8 7.6 - - + -
100C ARG* 3.5 20.4 - - + +
101C ALA* 3.5 33.4 - - + +
104C GLN* 3.9 22.2 - - + +
228C TRP* 4.5 0.2 - - - -
251C PHE* 4.9 4.7 - - + -
87H PHE* 4.7 2.6 - - - -
91H TYR* 3.6 26.9 - - + -
96H ALA* 2.8 28.2 + - + +
97H ASN* 1.3 72.1 - - - +
99H MSE 1.3 64.0 + - - +
100H ARG 3.3 2.9 - - - -
101H ALA* 3.2 20.2 + - + +
102H ALA* 3.0 18.8 + - - +
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Residues in contact with MSE 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ARG* 5.3 1.4 - - - +
228C TRP* 3.3 64.5 - - + +
2300C GOL 5.9 0.4 - - - -
87H PHE* 4.0 24.7 - - + -
97H ASN 3.5 5.5 + - - -
98H ILE* 1.3 73.2 - - - +
100H ARG* 1.3 57.7 + - - +
102H ALA* 3.2 2.1 + - - +
103H ASN* 2.8 45.9 + - - +
252H THR* 3.6 35.9 - - + -
253H LEU* 5.2 1.6 - - - -
254H TYR* 4.0 19.3 - - + -
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Residues in contact with ARG 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ASN* 3.0 28.8 + - - +
98C ILE* 3.6 21.5 - - + +
99C MSE 5.3 0.9 - - - +
98H ILE 3.3 0.8 - - - -
99H MSE 1.3 76.0 - - + +
101H ALA* 1.3 63.3 + - - +
103H ASN* 3.3 11.7 + - - +
104H GLN* 3.1 18.9 + - - +
227H SER* 5.2 3.6 + - - -
228H TRP* 3.5 24.3 - - - +
248H GLN 3.9 5.5 + - - -
249H ALA* 3.8 13.3 + - - +
251H PHE* 3.4 45.4 - - + +
252H THR* 3.9 9.8 - - + +
255H ASP* 3.1 31.0 + - - -
273H ARG 4.8 1.2 - - - +
274H GLU 4.7 1.0 - - - +
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Residues in contact with ALA 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE* 3.5 18.5 - - + +
101C ALA* 3.4 32.8 - - + -
91H TYR* 4.5 2.6 + - + -
98H ILE* 3.2 19.5 + - + +
100H ARG* 1.3 76.4 - - - +
102H ALA* 1.3 66.8 + - - +
104H GLN* 3.3 18.5 + - - +
105H ILE* 3.7 10.6 + - - +
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Residues in contact with ALA 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H PHE* 3.4 38.6 - - + -
91H TYR* 3.7 24.2 + - + -
98H ILE 3.0 9.4 + - - +
99H MSE 3.5 5.4 - - - +
101H ALA* 1.3 75.6 - - - +
103H ASN* 1.3 65.2 + - - +
105H ILE* 3.0 6.6 + - - +
106H PHE* 2.9 33.7 + - + -
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Residues in contact with ASN 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H MSE 2.8 36.1 + - - +
100H ARG* 3.4 7.8 - - - +
102H ALA* 1.3 78.9 - - - +
104H GLN* 1.3 60.8 + - - +
106H PHE* 4.5 7.0 - - - +
107H SER* 3.0 27.0 + - - -
251H PHE 4.3 0.2 + - - -
252H THR* 3.9 13.9 - - - +
273H ARG 3.7 2.0 - - - +
274H GLU 2.9 29.5 + - - +
275H ILE* 3.4 21.8 + - - +
276H GLY* 3.5 12.8 - - - +
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Residues in contact with GLN 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ALA* 4.3 10.4 - - - +
98C ILE* 3.8 23.4 - - + +
51H CYS* 3.6 17.2 - - - +
52H THR* 3.2 47.5 + - - +
53H VAL 3.9 1.2 - - - -
54H ALA* 2.9 31.3 + - - +
60H THR* 4.6 4.8 - - - +
100H ARG 3.1 11.8 + - - +
101H ALA 3.3 12.3 - - - +
103H ASN* 1.3 77.5 - - - +
105H ILE* 1.3 66.4 + - + +
107H SER* 3.8 8.3 - - - -
273H ARG* 3.6 20.3 + - + +
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Residues in contact with ILE 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H CYS* 3.1 26.3 - - + -
52H THR 5.2 0.4 - - - +
60H THR* 4.1 31.9 - - + +
63H ILE* 4.1 10.5 - - + -
64H LEU* 3.6 36.1 - - + +
67H LEU* 3.6 22.2 - - + -
91H TYR* 4.0 11.7 - - - +
101H ALA 3.8 13.9 - - - +
102H ALA 3.0 4.8 + - - +
104H GLN* 1.3 88.0 - - + +
106H PHE* 1.3 63.1 + - - +
107H SER 3.0 5.4 + - - -
108H GLY 3.2 2.1 + - - -
109H ILE* 3.6 9.0 + - + +
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Residues in contact with PHE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67H LEU* 3.7 23.6 - - + -
83H ILE* 3.6 50.4 - - + +
86H ILE* 3.9 19.1 - - + -
87H PHE* 3.8 33.0 - + + -
91H TYR* 4.3 4.0 - + - -
102H ALA* 2.9 42.3 + - + +
103H ASN* 4.3 8.3 - - - +
105H ILE* 1.3 75.9 - - - +
107H SER* 1.3 54.2 + - - +
108H GLY 3.3 0.2 - - - -
109H ILE* 3.6 22.4 - - + +
110H ASP* 2.7 37.2 + - - +
276H GLY* 3.9 9.2 - - - +
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Residues in contact with SER 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H GLU 5.1 1.6 - - - -
51H CYS* 5.9 0.4 - - - -
103H ASN 3.0 19.8 + - - -
104H GLN 3.8 9.0 - - - -
105H ILE 3.0 0.6 + - - -
106H PHE* 1.3 76.4 - - - +
108H GLY* 1.3 58.1 + - - +
110H ASP* 3.8 1.6 - - - +
111H MSE 3.0 39.5 + - - +
272H PRO* 3.0 39.4 + - - +
273H ARG* 3.4 8.3 + - - +
276H GLY 3.7 12.3 + - - -
277H GLY* 4.2 1.9 - - - -
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Residues in contact with GLY 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 3.4 9.4 - - - +
50H GLU 3.3 27.2 + - - -
51H CYS* 3.7 13.0 - - - -
105H ILE 3.2 5.1 + - - -
107H SER* 1.3 76.1 - - - +
109H ILE* 1.3 64.8 + - - +
111H MSE 3.4 8.2 - - - +
112H ALA* 3.0 25.1 + - - +
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Residues in contact with ILE 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 4.1 7.1 - - + +
39H ILE* 3.9 0.6 - - + +
64H LEU* 4.0 22.0 - - + -
67H LEU* 4.0 23.3 - - + +
68H ALA* 4.1 20.0 - - + +
71H LEU* 3.8 25.6 - - + -
83H ILE* 4.1 20.2 - - + -
86H ILE* 5.6 1.8 - - + -
105H ILE* 3.6 5.2 + - + +
106H PHE* 3.2 32.4 + - + +
108H GLY* 1.3 77.2 - - - +
110H ASP* 1.3 63.2 + - - +
112H ALA* 3.2 5.8 + - - +
113H MSE 3.0 31.6 + - + +
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Residues in contact with ASP 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H VAL* 3.5 18.3 - - - +
80H ALA* 6.0 0.3 - - - -
83H ILE* 4.0 12.0 - - + +
106H PHE 2.7 20.8 + - - +
107H SER 3.8 2.7 - - - +
109H ILE* 1.3 74.6 - - - +
111H MSE 1.3 62.2 + - - +
113H MSE 3.2 2.6 + - - +
114H TRP* 3.0 48.5 + - - -
276H GLY 3.8 12.8 - - - +
277H GLY* 3.8 3.4 - - - -
278H ILE* 2.6 29.9 + - - +
279H GLN* 3.2 15.7 + - - +
280H PRO* 4.3 4.3 - - - +
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Residues in contact with MSE 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ILE 4.3 1.8 - - - +
49H GLY* 3.4 13.2 - - - -
50H GLU 3.8 26.0 - - - +
107H SER* 3.0 35.5 + - - +
108H GLY* 3.4 14.4 - - - +
110H ASP* 1.3 77.3 + - - +
112H ALA* 1.3 56.4 + - - +
114H TRP* 3.6 1.2 + - - +
115H ASP* 3.0 28.4 + - - +
272H PRO* 4.3 16.4 - - + -
277H GLY* 5.9 0.2 - - - -
278H ILE* 3.7 24.4 - - + +
305H ILE* 4.0 13.0 - - - -
306H THR* 4.2 16.4 - - + +
309H ALA* 3.9 23.1 - - + -
356H LEU* 3.7 10.9 - - + +
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Residues in contact with ALA 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 4.0 7.9 - - + +
39H ILE* 3.5 19.5 - - + +
47H GLY* 3.3 18.3 - - - +
48H ILE 3.8 13.2 - - - +
49H GLY 3.7 15.0 - - - +
108H GLY 3.0 18.0 + - - +
109H ILE 3.5 4.7 - - - +
111H MSE 1.3 79.9 - - - +
113H MSE 1.3 57.6 + - - +
115H ASP 3.3 0.5 + - - -
116H LEU* 2.9 25.1 + - - +
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Residues in contact with MSE 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 3.6 24.5 - - + -
39H ILE* 3.7 19.1 - - + -
71H LEU* 4.1 9.4 - - + -
75H SER 3.7 0.2 - - - +
76H PRO* 3.6 30.7 - - + +
79H VAL* 3.5 55.2 - - + -
82H LEU* 3.7 20.0 - - + -
109H ILE* 3.0 24.2 + - + +
110H ASP 3.2 3.8 + - - +
112H ALA* 1.3 77.7 - - - +
114H TRP* 1.3 57.1 + - - +
116H LEU* 3.4 6.3 + - - +
117H GLN* 2.8 32.7 + - - +
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Residues in contact with TRP 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU 4.4 11.7 - - - -
130D GLY* 4.3 17.5 - - - -
79H VAL* 3.8 17.7 - - + +
110H ASP* 3.0 54.6 + - - -
113H MSE 1.3 75.9 - - + +
115H ASP* 1.3 60.5 - - - +
117H GLN* 3.6 30.7 - - - +
118H GLY 2.8 24.4 + - - -
125H VAL* 3.4 19.2 - - + +
128H LEU* 4.0 26.1 - - + +
129H LEU* 4.3 23.3 - - + -
278H ILE* 3.8 27.6 - - + -
279H GLN* 3.7 36.9 - - + +
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Residues in contact with ASP 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H GLY* 3.2 2.4 - - - -
48H ILE* 2.8 30.4 + - - +
111H MSE 3.0 18.3 + - - +
112H ALA 3.4 5.2 - - - +
114H TRP* 1.3 76.4 - - - +
116H LEU* 1.3 57.4 + - - +
118H GLY 3.3 0.2 + - - -
119H LYS* 2.9 66.7 + - - +
125H VAL* 4.2 0.6 - - - +
355H GLY* 3.4 7.1 - - - -
356H LEU* 2.8 41.4 + - + +
357H GLY 4.3 1.6 + - - -
358H PHE* 4.4 5.5 + - - -
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Residues in contact with LEU 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 4.6 3.6 - - + -
39H ILE* 3.9 31.2 - - + +
41H ALA* 4.2 13.5 - - + -
45H THR* 3.5 44.2 - - + +
47H GLY* 3.8 14.1 - - - +
76H PRO* 3.6 27.6 - - + -
112H ALA 2.9 16.2 + - - +
113H MSE 3.4 7.4 - - - +
114H TRP 3.2 0.2 - - - -
115H ASP* 1.3 77.6 - - - +
117H GLN* 1.3 61.6 + - - +
119H LYS* 3.3 3.5 + - - +
120H LEU* 3.0 36.7 + - + +
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Residues in contact with GLN 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D GLN 3.9 7.8 - - - +
128D LEU* 5.3 1.7 - - - -
130D GLY* 5.6 0.7 + - - -
76H PRO* 2.9 31.3 + - + +
77H HIS* 3.3 37.3 + - + +
79H VAL* 3.9 14.1 - - - +
113H MSE 2.8 21.6 + - - +
114H TRP* 3.3 43.7 + - - +
116H LEU* 1.3 72.7 - - - +
118H GLY* 1.3 62.8 + - - +
120H LEU* 3.4 8.9 + - - +
121H ALA* 3.0 25.3 + - - +
128H LEU* 4.0 11.9 - - + +
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Residues in contact with GLY 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TRP 2.8 16.5 + - - -
117H GLN* 1.3 77.2 - - - +
119H LYS* 1.3 52.0 + - - +
121H ALA* 3.2 1.6 + - - -
122H GLY* 2.6 32.2 + - - -
123H LEU 2.9 29.4 + - - -
128H LEU* 3.6 12.1 - - - +
355H GLY* 3.4 8.7 + - - -
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Residues in contact with LYS 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H THR* 3.7 21.9 + - + -
46H VAL* 2.8 31.8 + - - +
48H ILE* 4.5 13.3 - - - +
115H ASP* 2.9 44.0 + - - +
116H LEU 3.7 1.3 - - - +
118H GLY* 1.3 76.0 - - - +
120H LEU* 1.3 62.2 + - - +
122H GLY* 3.3 10.4 + - - -
354H PRO* 3.9 25.9 - - + +
355H GLY 3.6 0.2 - - - +
357H GLY 5.9 0.2 - - - +
358H PHE* 4.9 15.9 + - - +
359H GLN* 5.8 4.0 - - - +
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Residues in contact with LEU 120 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H VAL* 4.3 20.2 - - + -
41H ALA* 4.7 1.8 - - + -
43H ASP* 3.8 17.0 - - - +
45H THR* 3.4 32.3 - - - +
76H PRO* 3.7 29.6 - - + -
77H HIS* 4.5 11.9 - - + +
116H LEU* 3.0 32.0 + - + +
117H GLN* 3.8 5.2 - - - +
119H LYS* 1.3 75.5 - - - +
121H ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 121 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ALA* 5.4 11.7 - - + -
123D LEU* 6.2 3.1 - - + -
77H HIS* 6.1 1.8 - - - +
117H GLN 3.0 17.6 + - - +
118H GLY 3.9 2.5 - - - +
120H LEU* 1.3 76.8 - - - +
122H GLY* 1.3 64.2 + - - +
123H LEU* 3.9 28.3 - - + +
128H LEU* 4.4 7.6 - - + -
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Residues in contact with GLY 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118H GLY 2.6 13.6 + - - -
119H LYS 3.3 9.8 + - - -
121H ALA* 1.3 76.7 - - - +
123H LEU* 1.3 64.6 + - - +
124H PRO* 4.8 0.7 - - - +
354H PRO* 4.0 21.3 - - - +
----------------------------------------------------------
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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