Contacts of the helix formed by residues 98 - 122 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 4.7 1.7 - - - -
91B TYR* 3.7 27.6 - - + -
96B ALA* 2.8 25.6 + - + +
97B ASN* 1.3 72.7 - - - +
99B MSE 1.3 64.8 + - - +
100B ARG* 3.3 2.9 - - - -
101B ALA* 3.2 20.9 + - + -
102B ALA* 3.0 17.6 + - - +
55F PRO* 4.8 7.0 - - + -
100F ARG* 3.6 20.9 - - + +
101F ALA* 3.5 31.0 - - + +
104F GLN* 3.8 22.9 - - + +
228F TRP* 4.6 0.2 - - - -
251F PHE* 4.8 5.6 - - + -
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Residues in contact with MSE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.9 24.4 - - + -
97B ASN 3.5 5.3 + - - -
98B ILE* 1.3 72.6 - - - +
100B ARG* 1.3 57.9 + - - +
102B ALA* 3.1 2.4 + - - +
103B ASN* 2.8 45.2 + - - +
252B THR* 3.6 34.3 - - + -
253B LEU* 5.2 1.6 - - - -
254B TYR* 3.9 20.6 - - + -
100F ARG* 5.3 1.4 - - - +
228F TRP* 3.3 62.0 - - + +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ILE 3.3 1.0 - - - -
99B MSE 1.3 75.6 - - + +
101B ALA* 1.3 62.4 + - - +
103B ASN* 3.2 12.2 + - - +
104B GLN* 3.2 21.0 + - - +
227B SER 5.2 2.8 + - - -
228B TRP* 3.5 23.8 - - - +
248B GLN 3.9 5.7 + - - -
249B ALA* 3.7 13.7 + - - +
251B PHE* 3.3 45.8 - - + +
252B THR* 3.8 10.7 - - + +
255B ASP* 3.1 29.4 + - - -
273B ARG 4.8 1.4 - - - +
274B GLU 4.8 0.5 - - - +
97F ASN* 2.9 29.4 + - - +
98F ILE* 3.6 18.4 - - + +
99F MSE 5.4 0.9 - - - +
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 4.5 2.9 + - + -
98B ILE* 3.2 22.0 + - + +
100B ARG* 1.3 77.7 - - - +
102B ALA* 1.3 62.6 + - - +
104B GLN* 3.2 19.1 - - - +
105B ILE* 3.7 10.4 + - - +
98F ILE* 3.5 19.3 - - + +
101F ALA* 3.5 32.5 - - + -
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PHE* 3.4 39.3 - - + -
91B TYR* 3.8 21.4 + - + -
98B ILE 3.0 8.9 + - - +
99B MSE 3.5 5.4 - - - +
101B ALA* 1.3 75.2 - - - +
103B ASN* 1.3 67.5 + - - +
105B ILE* 2.9 6.4 + - - +
106B PHE* 2.9 35.3 + - + -
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B MSE 2.8 32.8 + - - +
100B ARG* 3.5 6.5 - - - +
102B ALA* 1.3 73.0 - - - +
104B GLN* 1.3 56.7 + - - +
106B PHE* 4.4 8.0 - - - +
107B SER* 2.8 34.1 + - - -
252B THR* 3.9 22.4 - - - +
273B ARG 3.8 1.8 - - - -
274B GLU 2.9 29.5 + - - +
275B ILE* 3.3 22.3 + - - +
276B GLY* 3.5 12.3 - - - +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS* 3.7 15.6 - - - +
52B THR* 3.2 47.8 + - - +
53B VAL 3.9 0.6 - - - -
54B ALA* 2.9 30.6 + - - +
60B THR* 4.5 5.3 - - - +
100B ARG 3.2 10.9 + - - +
101B ALA 3.2 12.5 - - - +
102B ALA 3.1 0.6 + - - -
103B ASN* 1.3 77.2 - - - +
105B ILE* 1.3 65.4 + - + +
107B SER* 3.7 9.0 - - - -
273B ARG* 3.6 19.2 + - + +
96F ALA* 4.2 10.4 - - - +
98F ILE* 3.7 24.5 - - + +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS* 3.1 16.7 - - + -
52B THR 5.2 0.2 - - - +
60B THR* 4.2 26.2 - - + +
63B ILE* 3.9 22.7 - - + -
64B LEU* 3.5 41.0 - - + +
67B LEU* 3.7 21.1 - - + -
91B TYR* 4.0 6.1 - - - +
101B ALA 3.8 13.5 - - - +
102B ALA 2.9 3.9 + - - +
104B GLN* 1.3 88.5 - - + +
106B PHE* 1.3 66.4 - - - +
107B SER 3.0 2.8 + - - -
108B GLY 3.1 11.3 + - - -
109B ILE* 3.5 6.9 + - + +
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 4.0 14.1 - - + -
83B ILE* 3.4 52.8 - - + +
86B ILE* 3.9 24.0 - - + -
87B PHE* 3.7 41.7 - + + -
91B TYR* 4.4 3.6 - + - -
102B ALA* 2.9 32.5 + - + +
103B ASN* 4.1 9.0 - - - +
105B ILE* 1.3 75.7 - - - +
107B SER* 1.3 53.5 + - - +
109B ILE* 3.1 18.2 + - + +
110B ASP* 2.8 36.4 + - - +
276B GLY* 3.7 9.6 - - - +
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Residues in contact with SER 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU 4.9 1.9 + - - -
51B CYS* 5.9 0.4 - - - -
103B ASN 2.8 14.0 + - - -
104B GLN 3.7 9.6 - - - -
105B ILE 3.0 0.4 + - - -
106B PHE* 1.3 76.6 - - - +
108B GLY* 1.3 56.9 + - - +
110B ASP* 3.6 1.2 + - - +
111B MSE 2.9 38.9 + - - +
272B PRO* 2.9 42.3 + - - +
273B ARG* 3.4 8.2 + - - -
276B GLY 3.5 12.9 + - - -
277B GLY* 4.0 2.3 - - - -
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Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.4 16.9 - - - +
49B GLY* 3.7 0.5 - - - -
50B GLU 3.3 28.6 + - - -
51B CYS* 3.7 13.7 - - - -
105B ILE 3.1 5.7 + - - -
107B SER* 1.3 76.4 + - - +
109B ILE* 1.3 59.4 + - - +
111B MSE 3.2 3.8 - - - +
112B ALA 3.0 23.9 + - - -
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.6 10.1 - - + -
39B ILE* 3.9 4.4 - - + +
64B LEU* 3.8 24.9 - - + -
67B LEU* 4.0 27.8 - - + +
68B ALA* 4.1 13.7 - - + +
71B LEU* 3.7 24.9 - - + -
83B ILE* 4.3 17.9 - - + -
86B ILE* 5.5 1.8 - - + -
105B ILE* 3.5 5.9 + - + +
106B PHE* 3.1 25.6 + - + +
108B GLY* 1.3 73.5 - - - +
110B ASP* 1.3 60.9 + - - +
112B ALA* 3.2 4.0 + - - +
113B MSE 2.8 38.7 + - + +
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 3.2 22.8 - - - +
80B ALA* 6.0 0.2 - - - -
83B ILE* 4.0 9.5 - - + +
106B PHE 2.8 18.9 + - - +
109B ILE* 1.3 72.9 - - - +
111B MSE 1.3 63.8 + - - +
113B MSE 3.1 0.9 + - - +
114B TRP* 3.0 53.9 + - - -
276B GLY 3.8 9.9 - - - +
277B GLY* 3.9 3.1 - - - -
278B ILE* 2.7 28.9 + - - +
279B GLN* 3.1 16.9 + - - +
280B PRO* 4.1 7.8 - - - +
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Residues in contact with MSE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE 4.4 0.2 - - - -
49B GLY* 4.0 5.6 - - - -
50B GLU 3.8 29.4 - - - +
107B SER* 2.9 41.3 + - - +
108B GLY 3.2 6.3 - - - +
110B ASP* 1.3 79.1 + - - +
112B ALA* 1.3 60.3 + - - +
114B TRP* 3.6 2.4 + - - +
115B ASP* 3.2 22.0 + - - +
272B PRO* 4.1 18.4 - - + -
277B GLY* 5.7 0.2 - - - -
278B ILE* 4.1 13.6 - - + +
305B ILE* 4.2 11.0 - - - -
306B THR* 4.1 16.6 - - + +
309B ALA* 3.6 34.1 - - + -
356B LEU* 3.6 17.0 - - + +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.8 7.4 - - + +
39B ILE* 3.6 22.7 - - + -
47B GLY* 3.5 13.4 - - - +
48B ILE 3.8 12.8 - - - +
49B GLY* 3.5 18.6 - - - +
108B GLY 3.0 14.3 + - - +
111B MSE 1.3 73.6 - - - +
113B MSE 1.3 62.1 + - - +
115B ASP* 3.2 2.6 + - - +
116B LEU* 2.8 30.1 + - - +
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Residues in contact with MSE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.6 27.1 - - + -
39B ILE* 3.7 18.2 - - + -
71B LEU* 4.4 7.0 - - + -
75B SER 3.6 9.2 - - - +
76B PRO* 3.4 40.4 - - + +
79B VAL* 3.6 42.8 - - + +
82B LEU* 4.0 9.6 - - + -
109B ILE* 2.8 27.7 + - + +
110B ASP 3.6 4.7 - - - +
112B ALA* 1.3 76.8 - - - +
114B TRP* 1.3 58.0 + - - +
116B LEU* 3.4 5.7 + - - +
117B GLN* 2.9 33.6 + - - +
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Residues in contact with TRP 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 4.3 12.1 - - - -
129A LEU 4.6 0.2 - - - -
130A GLY* 4.1 17.5 - - - -
79B VAL* 3.8 13.9 - - + +
110B ASP* 3.0 59.6 + - - +
113B MSE 1.3 75.1 - - - +
115B ASP* 1.3 60.2 + - - +
117B GLN* 3.5 32.9 - - - +
118B GLY 2.9 23.2 + - - -
125B VAL* 3.4 20.3 - - + +
128B LEU* 4.0 30.7 - - + +
129B LEU* 4.3 19.5 - - + -
278B ILE* 4.1 24.2 - - + -
279B GLN* 3.7 37.5 - - + +
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Residues in contact with ASP 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY* 3.2 2.4 - - - -
48B ILE* 2.7 31.6 + - - +
111B MSE 3.2 15.3 + - - +
112B ALA 3.2 8.6 + - - +
114B TRP* 1.3 76.2 - - - +
116B LEU* 1.3 56.4 + - - +
118B GLY 3.2 1.4 + - - -
119B LYS* 2.9 67.4 + - - +
125B VAL* 4.3 0.6 - - - +
355B GLY* 3.4 7.2 - - - -
356B LEU* 2.9 42.0 + - + +
357B GLY 4.3 0.9 + - - -
358B PHE* 4.5 4.9 + - - -
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 4.5 2.0 - - + -
39B ILE* 3.8 31.6 - - + +
41B ALA* 4.1 10.1 - - + +
45B THR* 3.5 46.0 - - + +
47B GLY* 3.7 13.8 - - - +
76B PRO* 3.7 26.7 - - + -
112B ALA 2.8 16.2 + - - +
113B MSE 3.6 6.3 - - - +
115B ASP* 1.3 75.5 - - - +
117B GLN* 1.3 65.0 + - - +
119B LYS* 3.4 3.6 + - - +
120B LEU* 3.0 42.2 + - + +
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Residues in contact with GLN 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN 4.1 8.1 - - - +
128A LEU* 5.4 1.2 - - - -
130A GLY* 5.5 0.7 + - - -
76B PRO* 3.0 30.9 + - + +
77B HIS* 3.3 37.1 + - + +
79B VAL* 3.5 24.2 - - - +
113B MSE 2.9 22.4 + - - +
114B TRP* 3.5 38.2 - - - +
115B ASP 3.3 0.2 - - - -
116B LEU* 1.3 76.0 - - - +
118B GLY* 1.3 62.6 + - - +
120B LEU* 3.5 5.4 + - - +
121B ALA* 3.2 22.7 + - - +
128B LEU* 4.0 13.2 - - + +
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Residues in contact with GLY 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TRP 2.9 13.2 + - - -
117B GLN* 1.3 75.1 - - - +
119B LYS* 1.3 52.7 + - - +
121B ALA 3.2 2.1 + - - -
122B GLY 2.7 31.0 + - - -
123B LEU 2.9 24.8 + - - -
128B LEU* 3.7 13.2 - - - +
355B GLY* 3.4 16.8 - - - -
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B THR* 3.6 21.2 - - + +
46B VAL 2.9 31.8 + - - +
48B ILE* 4.4 13.7 - - - +
115B ASP* 2.9 45.2 + - - +
116B LEU* 3.9 0.9 - - - +
118B GLY* 1.3 76.3 - - - +
120B LEU* 1.3 61.2 + - - +
122B GLY* 3.3 9.5 + - - -
354B PRO* 4.0 27.4 - - + +
355B GLY 3.6 0.6 - - - +
357B GLY 5.6 0.7 - - - +
358B PHE* 4.8 16.1 + - - +
359B GLN* 6.0 1.9 - - - +
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B VAL* 4.3 23.6 - - + -
43B ASP* 3.5 16.8 - - - +
45B THR* 3.3 31.0 - - - +
76B PRO* 4.1 19.1 - - + -
77B HIS* 4.4 12.6 - - + +
116B LEU* 3.0 43.4 + - + +
117B GLN* 3.8 6.1 - - - +
119B LYS* 1.3 78.8 - - - +
121B ALA* 1.3 58.5 + - - +
122B GLY 3.7 0.2 + - - -
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA* 5.1 15.0 - - + -
123A LEU* 6.1 3.4 - - + -
77B HIS* 6.2 2.0 - - + -
117B GLN 3.2 12.6 + - - +
118B GLY 3.2 3.6 + - - +
120B LEU* 1.3 78.6 - - - +
122B GLY* 1.3 64.2 + - - +
123B LEU* 3.7 25.9 - - + +
128B LEU* 4.7 7.0 - - + -
----------------------------------------------------------
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Residues in contact with GLY 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLY 2.7 8.4 + - - -
119B LYS 3.3 10.2 + - - -
120B LEU 3.4 0.4 - - - -
121B ALA* 1.3 79.9 - - - +
123B LEU* 1.3 63.4 + - - +
124B PRO* 4.7 0.7 - - - +
354B PRO* 4.0 22.1 - - - +
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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