Contacts of the helix formed by residues 98 - 122 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 4.8 7.9 - - + -
100B ARG* 3.6 17.7 - - + +
101B ALA* 3.5 32.8 - - + +
104B GLN* 3.7 22.9 - - + +
251B PHE* 4.9 4.9 - - + -
87F PHE* 4.6 3.5 - - - -
91F TYR* 3.6 26.5 - - + -
96F ALA* 2.7 26.9 + - + +
97F ASN* 1.3 72.9 - - - +
99F MSE 1.3 65.9 + - - +
100F ARG 3.4 2.2 - - - -
101F ALA* 3.3 20.9 + - + +
102F ALA* 3.0 17.8 + - - +
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Residues in contact with MSE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ARG* 5.4 1.4 - - - +
228B TRP* 3.4 58.7 - - + +
87F PHE* 3.9 25.4 - - + -
97F ASN 3.5 4.9 + - - -
98F ILE* 1.3 70.4 - - - +
100F ARG* 1.3 61.6 + - + +
102F ALA* 3.3 1.6 + - - +
103F ASN* 2.9 47.3 + - - +
252F THR* 3.6 34.1 - - + -
253F LEU* 5.2 1.3 - - - -
254F TYR* 4.0 20.2 - - + -
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Residues in contact with ARG 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASN* 2.9 33.1 + - - +
98B ILE* 3.6 22.0 - - + +
99B MSE 5.3 1.1 - - - +
98F ILE 3.4 0.6 - - - -
99F MSE 1.3 76.6 - - - +
101F ALA* 1.3 62.4 + - - +
103F ASN* 3.4 9.8 + - - +
104F GLN* 3.2 19.1 + - - +
227F SER 5.0 4.2 + - - -
228F TRP* 3.5 23.5 - - - +
248F GLN 4.1 6.7 + - - -
249F ALA* 3.6 14.1 + - - +
251F PHE* 3.4 35.0 - - + +
252F THR* 3.8 10.1 - - + +
255F ASP* 3.0 34.4 + - - -
273F ARG 4.9 1.2 - - - +
274F GLU 4.7 0.9 - - - +
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Residues in contact with ALA 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE* 3.5 17.7 - - + +
101B ALA* 3.5 31.6 - - + -
91F TYR* 4.7 3.4 - - + -
98F ILE* 3.3 22.0 + - + +
99F MSE 3.2 0.2 - - - -
100F ARG* 1.3 79.4 - - - +
102F ALA* 1.3 62.0 + - - +
104F GLN* 3.2 20.1 - - - +
105F ILE* 3.6 10.2 + - - +
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Residues in contact with ALA 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F PHE* 3.5 36.3 - - + -
91F TYR* 3.6 29.3 + - + -
98F ILE 3.0 9.4 + - - +
99F MSE 3.8 2.5 - - - +
101F ALA* 1.3 73.8 - - - +
103F ASN* 1.3 62.9 + - - +
105F ILE* 3.1 4.6 + - - +
106F PHE* 2.8 40.7 + - + -
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Residues in contact with ASN 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F MSE 2.9 34.6 + - - +
100F ARG* 3.5 4.5 - - - +
101F ALA 3.3 0.2 - - - -
102F ALA* 1.3 76.6 - - - +
104F GLN* 1.3 54.3 + - - +
106F PHE* 4.4 6.0 - - - +
107F SER* 2.8 35.3 + - - -
251F PHE 4.1 0.2 + - - -
252F THR* 3.9 21.4 - - - +
273F ARG 3.8 1.6 - - - -
274F GLU 2.9 29.9 + - - +
275F ILE* 3.3 22.8 + - - +
276F GLY* 3.4 13.8 - - - +
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Residues in contact with GLN 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 4.2 11.9 - - - +
98B ILE* 3.8 23.7 - - + +
51F CYS* 3.7 16.6 - - - +
52F THR* 3.2 46.1 + - - +
53F VAL 4.0 1.2 - - - -
54F ALA* 3.0 29.2 + - - +
60F THR* 4.5 6.5 - - - +
100F ARG 3.2 8.6 + - - +
101F ALA* 3.2 12.8 - - - +
103F ASN* 1.3 81.4 - - - +
105F ILE* 1.3 66.0 + - + +
107F SER* 3.7 9.7 - - - -
273F ARG* 3.5 20.5 + - + +
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Residues in contact with ILE 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F CYS* 3.1 26.4 - - + -
52F THR 5.1 0.4 - - - +
60F THR* 4.3 30.5 - - + +
63F ILE* 4.2 10.8 - - + -
64F LEU* 3.6 35.4 - - + +
67F LEU* 3.8 22.4 - - + -
91F TYR* 4.0 11.9 - - - +
101F ALA 3.8 12.8 - - - +
102F ALA 3.1 5.1 + - - +
104F GLN* 1.3 89.2 - - + +
106F PHE* 1.3 65.3 + - - +
107F SER 3.0 2.2 + - - -
108F GLY 3.2 2.3 + - - -
109F ILE* 3.6 9.6 + - + +
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Residues in contact with PHE 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F LEU* 3.6 26.0 - - + -
83F ILE* 3.5 42.0 - - + -
86F ILE* 3.9 17.5 - - + -
87F PHE* 3.7 42.0 - + + -
91F TYR* 4.2 1.3 - + - -
102F ALA* 2.8 47.0 + - + +
103F ASN* 4.2 7.4 - - - +
105F ILE* 1.3 70.4 - - - +
107F SER* 1.3 66.4 + - - +
109F ILE* 3.7 18.4 - - + -
110F ASP* 2.8 27.7 + - - +
276F GLY* 3.9 9.9 - - - +
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Residues in contact with SER 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F GLU 4.5 2.6 + - - -
51F CYS* 5.8 0.4 - - - -
103F ASN 2.8 19.2 + - - -
104F GLN 3.7 9.2 - - - -
105F ILE 3.0 0.2 - - - -
106F PHE* 1.3 76.9 - - - +
108F GLY* 1.3 57.8 + - - +
110F ASP* 3.8 1.9 - - - +
111F MSE 3.0 37.9 + - - +
272F PRO* 3.0 37.4 + - - +
273F ARG* 3.4 10.7 + - - +
276F GLY 3.6 11.6 - - - -
277F GLY* 3.7 2.8 - - - +
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Residues in contact with GLY 108 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ILE* 3.5 14.6 - - - +
49F GLY* 3.8 0.7 - - - -
50F GLU 3.3 28.7 + - - -
51F CYS* 3.6 13.9 - - - -
105F ILE 3.2 4.6 + - - -
107F SER* 1.3 80.0 - - - +
109F ILE* 1.3 63.2 + - - +
111F MSE 3.2 4.9 - - - +
112F ALA 2.9 19.1 + - - -
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Residues in contact with ILE 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ILE* 4.1 10.5 - - + +
39F ILE* 3.9 2.4 - - + +
51F CYS* 4.7 0.2 - - - -
64F LEU* 3.8 22.7 - - + -
67F LEU* 4.1 24.5 - - + +
68F ALA* 4.1 16.8 - - + +
71F LEU* 3.9 25.1 - - + -
83F ILE* 4.4 17.5 - - + -
86F ILE* 5.6 1.6 - - + -
105F ILE* 3.6 6.8 + - + +
106F PHE* 3.2 28.2 + - + +
108F GLY* 1.3 75.3 - - - +
110F ASP* 1.3 64.1 + - - +
112F ALA* 3.1 6.5 + - - +
113F MSE 2.9 29.7 + - + +
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Residues in contact with ASP 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F VAL* 3.5 18.3 - - - +
83F ILE* 4.0 13.8 - - + +
106F PHE 2.8 19.6 + - - +
107F SER 3.8 2.5 - - - +
109F ILE* 1.3 73.1 - - - +
111F MSE 1.3 63.7 + - - +
113F MSE 3.2 1.4 + - - +
114F TRP* 3.0 48.6 + - - -
276F GLY 3.8 12.1 - - - +
277F GLY* 3.9 2.2 - - - -
278F ILE* 2.6 35.5 + - - +
279F GLN* 3.1 17.2 + - - +
280F PRO* 4.3 3.2 - - - +
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Residues in contact with MSE 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F ILE 4.3 1.6 - - - -
49F GLY* 4.0 4.9 - - - -
50F GLU 3.8 28.7 - - - +
107F SER* 3.0 35.7 + - - +
108F GLY 3.2 10.1 - - - +
110F ASP* 1.3 77.7 + - - +
112F ALA* 1.3 60.0 + - - +
114F TRP* 3.6 2.8 + - - +
115F ASP* 3.2 22.2 + - - +
272F PRO* 4.2 18.6 - - + -
273F ARG 5.7 0.2 - - - +
278F ILE* 4.0 13.6 - - + +
305F ILE* 4.2 11.2 - - - -
306F THR* 4.0 20.0 - - + +
309F ALA* 3.6 34.5 - - + -
356F LEU* 3.6 15.2 - - + +
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Residues in contact with ALA 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ILE* 3.8 8.3 - - + +
39F ILE* 3.5 24.9 - - + +
47F GLY* 3.4 14.6 - - - +
48F ILE 3.7 13.9 + - - +
49F GLY 3.6 18.4 - - - +
108F GLY 2.9 10.1 + - - +
109F ILE 3.1 3.1 + - - +
111F MSE 1.3 74.1 - - - +
113F MSE 1.3 60.5 + - - +
115F ASP* 3.3 0.6 + - - -
116F LEU* 2.9 30.0 + - - +
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Residues in contact with MSE 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 3.6 24.7 - - + -
39F ILE* 3.8 19.1 - - + -
71F LEU* 4.2 9.9 - - + -
75F SER 3.7 9.0 - - - +
76F PRO* 3.5 37.9 - - + +
79F VAL* 3.6 36.6 - - + -
82F LEU* 3.7 19.7 - - + -
109F ILE* 2.9 25.2 + - + +
110F ASP 3.2 7.2 + - - +
112F ALA* 1.3 76.4 - - - +
114F TRP* 1.3 58.3 + - - +
116F LEU* 3.3 6.6 + - - +
117F GLN* 2.9 32.1 + - - +
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Residues in contact with TRP 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LEU 4.5 9.9 - - - -
129C LEU 4.7 0.2 - - - -
130C GLY* 4.2 12.6 - - - -
79F VAL* 3.9 17.3 - - + +
110F ASP* 3.0 56.1 + - - +
113F MSE 1.3 74.0 - - + +
115F ASP* 1.3 60.6 + - - +
117F GLN* 3.2 29.4 + - - +
118F GLY* 2.8 27.7 + - - -
125F VAL* 3.8 17.4 - - + +
128F LEU* 4.1 28.4 - - + +
129F LEU* 4.3 23.3 - - + -
278F ILE* 4.1 24.0 - - + -
279F GLN* 3.7 38.8 - - + +
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Residues in contact with ASP 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F GLY* 3.4 0.9 - - - -
48F ILE* 2.8 27.8 + - - +
111F MSE 3.2 13.9 + - - +
112F ALA 3.5 8.3 - - - +
113F MSE 3.3 0.2 - - - -
114F TRP* 1.3 77.5 - - - +
116F LEU* 1.3 58.6 + - - +
118F GLY 3.3 0.2 + - - -
119F LYS* 2.8 65.9 + - - +
125F VAL* 4.3 0.6 - - - +
355F GLY* 3.4 7.7 - - - -
356F LEU* 2.7 47.3 + - + +
357F GLY 4.3 1.2 + - - -
358F PHE* 4.3 4.6 - - - -
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Residues in contact with LEU 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F ILE* 4.5 5.8 - - + -
39F ILE* 4.0 30.5 - - + +
41F ALA* 4.1 9.2 - - + -
45F THR* 3.6 42.4 - - + +
47F GLY* 3.8 12.2 - - - +
76F PRO* 3.4 30.1 - - + -
112F ALA 2.9 12.8 + - - +
113F MSE 3.4 10.1 - - - +
114F TRP 3.2 0.2 - - - -
115F ASP* 1.3 78.4 - - - +
117F GLN* 1.3 57.3 + - - +
119F LYS* 3.2 3.9 + - - +
120F LEU* 2.9 45.0 + - + +
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Residues in contact with GLN 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C GLN 4.0 9.2 - - - +
128C LEU* 5.2 1.4 - - - -
130C GLY* 5.4 0.6 - - - -
76F PRO* 3.0 29.2 + - + +
77F HIS* 3.5 39.3 + - + +
79F VAL* 3.7 21.6 - - - +
113F MSE 2.9 16.3 + - - +
114F TRP* 3.2 39.5 + - - +
116F LEU* 1.3 75.6 - - - +
118F GLY* 1.3 58.5 + - - +
120F LEU* 3.7 4.9 - - - +
121F ALA* 3.0 30.1 + - - +
128F LEU* 4.0 12.3 - - + +
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Residues in contact with GLY 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F TRP 2.8 10.9 + - - -
117F GLN* 1.3 78.4 - - - +
119F LYS* 1.3 50.7 + - - +
121F ALA* 3.2 1.3 + - - -
122F GLY* 2.6 32.4 + - - -
123F LEU 2.9 25.3 + - - -
128F LEU* 3.6 14.3 - - - +
355F GLY* 3.4 16.3 + - - -
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Residues in contact with LYS 119 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F THR* 3.6 23.1 - - + -
46F VAL 2.8 30.4 + - - +
48F ILE* 4.5 11.7 - - - +
115F ASP* 2.8 47.7 + - - +
116F LEU 3.7 1.3 - - - +
118F GLY* 1.3 75.0 - - - +
120F LEU* 1.3 63.3 + - - +
122F GLY* 3.3 10.2 + - - -
354F PRO* 4.0 18.9 - - + +
355F GLY* 3.6 5.8 - - - +
357F GLY 5.9 0.4 - - - +
358F PHE* 4.9 16.6 + - - +
359F GLN* 5.7 4.0 - - - +
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Residues in contact with LEU 120 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F VAL* 4.3 18.2 - - + -
43F ASP* 3.5 28.9 - - - +
45F THR* 3.5 17.0 - - - +
76F PRO* 3.8 29.8 - - + -
77F HIS* 4.2 15.9 - - + +
116F LEU* 2.9 31.6 + - + +
117F GLN* 3.7 5.4 - - - +
119F LYS* 1.3 76.3 - - - +
121F ALA* 1.3 58.7 + - + +
122F GLY 3.7 0.2 + - - -
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Residues in contact with ALA 121 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C ALA* 5.2 13.2 - - + -
123C LEU* 6.1 3.8 - - + -
77F HIS* 6.1 1.8 - - + -
117F GLN 3.0 16.9 + - - +
118F GLY 3.9 2.5 - - - +
120F LEU* 1.3 75.7 - - - +
122F GLY* 1.3 63.2 + - - +
123F LEU* 3.5 27.9 + - + +
128F LEU* 4.5 8.5 - - + -
----------------------------------------------------------
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Residues in contact with GLY 122 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F GLY 2.6 14.4 + - - -
119F LYS 3.3 10.8 + - - -
120F LEU 3.7 0.2 + - - -
121F ALA* 1.3 75.1 - - - +
123F LEU* 1.3 63.7 + - - +
124F PRO* 4.7 1.2 - - - +
354F PRO* 4.0 20.5 - - - +
----------------------------------------------------------
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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