Contacts of the helix formed by residues 98 - 122 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 4.6 3.0 - - - -
91D TYR* 3.6 28.0 - - + -
96D ALA* 2.7 27.8 + - + +
97D ASN* 1.3 72.1 - - - +
99D MSE 1.3 64.5 + - - +
100D ARG* 3.3 2.7 - - - -
101D ALA* 3.3 14.2 + - + -
102D ALA* 3.0 18.9 + - - +
55E PRO* 4.8 8.1 - - + -
100E ARG* 3.6 18.4 - - + +
101E ALA* 3.5 39.7 - - + +
104E GLN* 3.7 22.0 - - + +
251E PHE* 4.9 4.0 - - + -
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Residues in contact with MSE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 3.9 24.2 - - + -
97D ASN 3.5 5.7 + - - -
98D ILE* 1.3 73.8 - - - +
100D ARG* 1.3 58.3 + - + +
102D ALA* 3.2 1.2 + - - +
103D ASN* 2.9 47.7 + - - +
252D THR* 3.7 33.4 - - + -
253D LEU* 5.2 1.6 - - - -
254D TYR* 4.0 19.7 - - + -
100E ARG* 5.4 1.2 - - - +
228E TRP* 3.2 63.2 - - + +
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Residues in contact with ARG 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ILE 3.3 0.6 - - - -
99D MSE 1.3 76.6 - - - +
101D ALA* 1.3 63.8 + - - +
103D ASN* 3.2 11.4 + - - +
104D GLN* 3.2 18.7 + - - +
227D SER 5.2 2.8 + - - -
228D TRP* 3.5 25.4 - - - +
248D GLN 4.1 6.3 + - - -
249D ALA* 3.7 13.5 + - - +
251D PHE* 3.5 39.6 - - + +
252D THR* 3.9 10.0 - - + +
255D ASP* 3.0 32.6 + - - -
273D ARG 4.9 1.0 - - - +
274D GLU 4.7 1.2 - - - +
97E ASN* 2.8 28.6 + - - +
98E ILE* 3.6 20.5 - - + +
99E MSE 5.2 1.8 - - - +
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D TYR* 4.9 1.8 - - + -
98D ILE* 3.3 18.7 + - + +
99D MSE 3.3 0.2 - - - -
100D ARG* 1.3 78.6 - - - +
102D ALA* 1.3 62.3 + - - +
104D GLN* 3.3 19.9 - - - +
105D ILE* 3.7 10.9 + - - +
98E ILE* 3.4 19.1 - - + +
101E ALA* 3.4 33.4 - - + -
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Residues in contact with ALA 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PHE* 3.5 38.6 - - + -
91D TYR* 3.8 24.6 + - + -
98D ILE 3.0 11.0 + - - +
99D MSE 3.6 2.5 - - - +
101D ALA* 1.3 75.8 - - - +
103D ASN* 1.3 61.8 + - - +
105D ILE* 3.0 5.2 + - - +
106D PHE* 2.8 40.1 + - + -
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Residues in contact with ASN 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D MSE 2.9 40.4 + - - +
100D ARG* 3.2 4.4 + - - +
102D ALA* 1.3 77.3 - - - +
104D GLN* 1.3 55.2 + - - +
106D PHE* 4.4 7.4 - - - +
107D SER* 2.8 36.0 + - - -
251D PHE 4.4 0.2 + - - -
252D THR* 4.0 13.1 - - - +
273D ARG 3.7 2.0 - - - +
274D GLU 3.0 28.6 + - - +
275D ILE* 3.4 21.1 + - - +
276D GLY* 3.4 13.0 - - - +
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Residues in contact with GLN 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D CYS* 3.6 17.7 - - - +
52D THR* 3.1 48.8 + - - +
53D VAL 4.0 1.0 - - - -
54D ALA* 3.0 29.6 + - - +
60D THR* 4.5 6.4 - - - +
100D ARG 3.2 8.9 + - - +
101D ALA 3.3 12.0 - - - +
102D ALA 3.1 0.4 - - - -
103D ASN* 1.3 78.6 - - - +
105D ILE* 1.3 66.4 + - + +
107D SER* 3.8 8.1 - - - -
273D ARG* 3.5 20.1 + - + +
96E ALA* 4.1 11.5 - - - +
98E ILE* 3.8 22.2 - - + +
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Residues in contact with ILE 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D CYS* 3.1 26.4 - - + -
52D THR 5.2 0.4 - - - +
60D THR* 4.2 32.1 - - + +
63D ILE* 4.1 17.0 - - + -
64D LEU* 3.7 31.9 - - + +
67D LEU* 3.5 27.1 - - + -
91D TYR* 4.1 5.6 - - - +
101D ALA 3.7 13.0 - - - +
102D ALA 3.0 5.0 + - - +
104D GLN* 1.3 86.9 - - - +
106D PHE* 1.3 64.6 + - - +
107D SER 3.1 3.2 + - - -
108D GLY 3.1 2.1 + - - -
109D ILE* 3.6 7.9 + - + +
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Residues in contact with PHE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D LEU* 3.9 19.1 - - + -
83D ILE* 3.5 41.2 - - + +
86D ILE* 3.7 25.4 - - + -
87D PHE* 3.7 44.4 - + + -
91D TYR* 4.2 4.0 - + - -
102D ALA* 2.8 45.3 + - + +
103D ASN* 4.1 9.4 - - - +
105D ILE* 1.3 70.7 - - - +
107D SER* 1.3 59.3 + - - +
109D ILE* 3.7 13.7 - - + -
110D ASP* 2.8 34.7 + - - +
276D GLY* 3.8 10.1 - - - +
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Residues in contact with SER 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D GLU 4.5 4.6 + - - -
51D CYS* 6.0 0.2 - - - -
103D ASN 2.8 15.6 + - - -
104D GLN 3.8 8.7 - - - -
105D ILE 3.1 0.2 - - - -
106D PHE* 1.3 75.8 - - - +
108D GLY* 1.3 58.1 + - - +
110D ASP* 3.9 1.4 - - - +
111D MSE 3.0 33.7 + - - +
272D PRO* 2.8 43.6 + - - +
273D ARG* 3.4 8.2 + - - -
276D GLY 3.6 12.1 + - - -
277D GLY* 3.6 1.6 - - - +
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Residues in contact with GLY 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 3.5 18.1 - - - +
49D GLY* 3.9 0.3 - - - -
50D GLU 3.3 24.4 + - - -
51D CYS* 3.6 14.6 - - - -
105D ILE 3.1 5.1 + - - -
107D SER* 1.3 78.5 - - - +
109D ILE* 1.3 64.7 + - - +
111D MSE 3.2 5.7 - - - +
112D ALA 3.0 18.7 + - - -
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Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 3.8 17.2 - - + +
39D ILE* 3.9 3.5 - - + +
51D CYS* 4.7 0.2 - - - -
64D LEU* 3.8 16.2 - - + -
67D LEU* 5.3 3.1 - - + -
68D ALA* 3.4 39.9 - - + +
71D LEU* 3.7 25.8 - - + -
83D ILE* 4.2 19.3 - - + -
86D ILE* 6.2 0.9 - - + -
105D ILE* 3.6 8.1 + - + +
106D PHE* 3.1 20.1 + - + +
108D GLY* 1.3 74.6 - - - +
110D ASP* 1.3 64.2 + - - +
112D ALA* 3.1 5.5 + - - +
113D MSE 2.9 31.5 + - + +
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Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D VAL* 3.3 19.0 - - - +
83D ILE* 4.0 13.2 - - + +
106D PHE 2.8 19.4 + - - +
107D SER 3.9 1.8 - - - +
109D ILE* 1.3 75.0 - - - +
111D MSE 1.3 64.6 + - - +
113D MSE 3.2 1.0 + - - +
114D TRP* 3.0 53.1 + - - -
276D GLY 3.9 9.6 - - - +
277D GLY* 4.0 2.5 - - - -
278D ILE* 2.7 29.1 + - - +
279D GLN* 3.1 16.6 + - - +
280D PRO* 4.2 5.5 - - - +
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Residues in contact with MSE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ILE 4.3 2.2 - - - -
49D GLY* 3.8 5.2 - - - -
50D GLU 3.7 23.8 - - - +
107D SER* 3.0 20.4 + - - +
108D GLY 3.2 10.1 - - - +
110D ASP* 1.3 78.4 + - - +
112D ALA* 1.3 63.3 + - - +
114D TRP* 3.5 2.6 + - - +
115D ASP* 3.1 21.7 + - - +
272D PRO* 5.4 7.2 - - + -
278D ILE* 4.1 15.1 - - + +
305D ILE* 3.1 45.1 - - + +
306D THR* 4.3 12.8 - - - -
309D ALA* 3.4 20.6 - - + -
356D LEU* 3.3 31.6 - - + +
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Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 3.9 6.7 - - + +
39D ILE* 3.5 22.2 - - + -
47D GLY* 3.5 19.8 - - - +
48D ILE 3.8 12.7 + - - +
49D GLY 3.8 9.4 - - - +
108D GLY 3.0 9.0 + - - +
109D ILE 3.5 7.0 - - - +
111D MSE 1.3 78.6 - - - +
113D MSE 1.3 59.6 + - - +
115D ASP* 3.2 2.3 + - - +
116D LEU* 2.8 30.9 + - - +
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Residues in contact with MSE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 3.8 23.3 - - + -
39D ILE* 3.7 23.6 - - + -
71D LEU* 4.1 9.2 - - + -
75D SER 3.7 8.7 - - - +
76D PRO* 3.7 36.8 - - + +
79D VAL* 3.7 41.7 - - + -
82D LEU* 3.9 10.3 - - + -
109D ILE* 2.9 26.8 + - + +
110D ASP 3.2 4.9 + - - +
112D ALA* 1.3 76.4 - - - +
114D TRP* 1.3 57.6 + - - +
116D LEU* 3.3 7.8 + - - +
117D GLN* 2.9 32.5 + - - +
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Residues in contact with TRP 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D VAL* 3.8 15.5 - - + +
110D ASP* 3.0 56.2 + - - +
113D MSE 1.3 75.5 - - + +
115D ASP* 1.3 66.5 + - - +
117D GLN* 3.6 31.0 - - - +
118D GLY* 2.9 19.4 + - - -
125D VAL* 3.7 19.1 - - + +
128D LEU* 4.1 26.1 - - + +
129D LEU* 4.3 23.1 - - + -
278D ILE* 4.1 24.5 - - + -
279D GLN* 3.8 37.1 - - + +
128H LEU 4.3 12.1 - - - -
129H LEU* 4.6 0.4 - - - -
130H GLY* 4.1 17.5 - - - -
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Residues in contact with ASP 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLY* 3.2 1.9 - - - -
48D ILE* 2.8 30.4 + - - +
111D MSE 3.1 15.6 + - - +
112D ALA 3.2 8.0 + - - +
114D TRP* 1.3 75.6 - - - +
116D LEU* 1.3 58.6 + - - +
118D GLY 3.2 1.4 + - - -
119D LYS* 2.8 63.9 + - - +
125D VAL* 4.3 0.6 - - - +
355D GLY* 3.5 7.8 - - - -
356D LEU* 2.8 41.3 + - + +
357D GLY 4.3 0.9 + - - -
358D PHE* 4.4 4.4 + - - -
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Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.7 2.2 - - + -
39D ILE* 3.8 31.9 - - + +
41D ALA* 4.2 11.0 - - + -
45D THR* 3.6 46.0 - - + +
47D GLY* 3.7 16.1 - - - +
76D PRO* 3.8 25.4 - - + -
112D ALA 2.8 17.0 + - - +
113D MSE 3.4 8.1 - - - +
115D ASP* 1.3 78.6 - - - +
117D GLN* 1.3 60.9 + - - +
119D LYS* 3.5 2.9 + - - +
120D LEU* 3.0 38.8 + - + +
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Residues in contact with GLN 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D PRO* 3.2 28.4 + - + +
77D HIS* 3.5 34.1 + - + +
79D VAL* 3.8 14.5 - - - +
113D MSE 2.9 18.6 + - - +
114D TRP* 3.2 43.4 + - - +
116D LEU* 1.3 76.9 - - - +
118D GLY* 1.3 58.2 + - - +
120D LEU* 3.5 9.0 + - - +
121D ALA* 3.0 29.6 + - - +
128D LEU* 3.9 13.7 - - + +
127H GLN 4.0 9.5 - - - +
128H LEU* 5.2 1.9 - - - -
130H GLY* 5.5 1.0 + - - -
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Residues in contact with GLY 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D TRP 2.9 10.1 + - - -
117D GLN* 1.3 75.3 - - - +
119D LYS* 1.3 54.8 + - - +
121D ALA* 3.3 1.3 + - - -
122D GLY* 2.7 30.5 + - - -
123D LEU 2.8 30.1 + - - +
128D LEU* 3.6 13.4 - - - +
355D GLY* 3.4 12.2 + - - -
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Residues in contact with LYS 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D THR* 3.6 20.6 + - + -
46D VAL 3.0 27.4 + - - +
47D GLY* 4.5 0.2 - - - -
48D ILE* 4.5 10.9 - - - +
115D ASP* 2.8 50.9 + - - +
116D LEU 3.9 0.7 - - - +
118D GLY* 1.3 75.2 - - - +
120D LEU* 1.3 62.7 + - - +
122D GLY* 3.3 10.9 + - - -
354D PRO* 3.9 25.1 - - + +
357D GLY 5.7 0.9 - - - +
358D PHE* 4.9 17.8 + - - +
359D GLN* 5.8 4.0 - - - +
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Residues in contact with LEU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 4.4 22.0 - - + -
41D ALA* 4.8 0.4 - - + -
43D ASP* 3.5 29.8 - - - +
45D THR* 3.5 18.8 - - + +
76D PRO* 4.1 28.5 - - + -
77D HIS* 4.6 15.9 - - + +
116D LEU* 3.0 32.7 + - + +
117D GLN* 3.7 6.1 - - - +
119D LYS* 1.3 76.2 - - - +
121D ALA* 1.3 58.6 + - - +
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D HIS* 6.2 2.2 - - + -
117D GLN 3.0 17.1 + - - +
118D GLY 4.0 2.0 - - - +
120D LEU* 1.3 77.8 - - - +
122D GLY* 1.3 63.4 + - - +
123D LEU* 3.8 27.6 - - + +
128D LEU* 4.5 7.6 - - + -
121H ALA* 5.4 11.4 - - + -
123H LEU* 6.2 3.4 - - + -
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Residues in contact with GLY 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D GLY 2.7 13.4 + - - -
119D LYS 3.3 11.0 + - - -
121D ALA* 1.3 75.4 - - - +
123D LEU* 1.3 64.6 + - - +
124D PRO* 4.7 1.0 - - - +
354D PRO* 4.0 20.6 - - - +
----------------------------------------------------------
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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