Contacts of the helix formed by residues 86 - 109 (chain D) in PDB entry 2POZ
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 GLY 86 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D ASN 4.0 0.4 + - - -
85D GLY* 1.3 72.1 - - - -
87D ALA* 1.3 65.6 + - - -
88D ILE 3.3 3.5 + - - -
89D ILE* 3.3 8.7 - - - +
90D PHE* 3.2 26.2 + - - +
260D TYR* 4.1 12.1 - - - -
84E ASN 5.3 0.7 - - - -
85E GLY 4.9 0.2 - - - -
86E GLY* 3.9 27.9 - - - -
87E ALA* 4.8 2.6 - - - +
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ILE* 3.9 5.3 - - + +
86D GLY* 1.3 71.8 - - - -
88D ILE* 1.3 60.2 + - + +
91D ALA* 2.9 33.3 + - - +
260D TYR* 3.4 41.1 - - + +
283D THR* 4.7 1.9 - - + +
81E TRP* 3.6 33.7 - - + +
85E GLY* 5.7 0.6 - - - -
86E GLY 4.9 3.6 - - - +
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Residues in contact with ILE 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ILE* 4.2 22.0 - - + -
43D VAL 5.4 0.4 - - - +
44D GLY* 4.1 21.8 - - - +
47D ALA* 3.8 28.5 - - + +
48D ALA* 4.2 3.2 - - - +
51D MSE 3.6 15.4 - - + +
86D GLY 3.3 1.0 - - - -
87D ALA* 1.3 81.1 - - + +
89D ILE* 1.3 65.8 + - - +
91D ALA* 3.4 3.3 + - - +
92D GLY 3.1 17.8 + - - -
47E ALA* 4.1 0.7 - - + -
51E MSE 5.5 2.5 - - - -
81E TRP* 5.3 8.1 - - + -
88E ILE* 3.7 44.9 - - + -
89E ILE* 4.7 10.3 - - + +
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Residues in contact with ILE 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D MSE 3.2 34.8 - - + +
79D SER* 3.3 18.8 - - - +
81D TRP* 3.4 25.4 - - + +
82D ALA* 3.1 34.8 - - + +
85D GLY* 3.9 4.5 - - - -
86D GLY 3.3 26.2 - - - +
88D ILE* 1.3 78.7 - - - +
90D PHE* 1.3 66.4 + - + +
92D GLY* 3.7 0.7 + - - -
93D ILE* 3.1 34.8 + - + +
43E VAL 4.8 0.2 - - - +
88E ILE* 4.9 6.1 - - + +
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Residues in contact with PHE 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D TRP* 4.3 12.8 - + - -
76D TYR* 3.8 24.0 - + - -
82D ALA* 3.1 35.0 - - + -
85D GLY* 3.4 23.8 - - - -
86D GLY 3.2 22.4 + - - +
89D ILE* 1.3 78.1 - - + +
91D ALA* 1.3 56.2 + - - +
92D GLY 3.3 0.2 - - - -
93D ILE* 3.9 16.5 - - + +
94D SER* 2.4 40.4 + - - -
260D TYR* 3.9 7.2 - - + -
261D THR* 3.6 32.1 - - + -
283D THR 3.2 19.7 - - - +
285D GLY* 4.1 4.1 - - - +
237E PHE* 3.8 7.6 - + - -
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Residues in contact with ALA 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ALA* 3.4 16.8 - - + +
38D GLY 4.1 3.6 - - - +
39D ILE* 3.7 27.4 - - + -
48D ALA* 5.1 1.6 - - + -
87D ALA 2.9 23.8 + - - +
88D ILE 3.8 3.1 - - - +
89D ILE 3.4 0.2 - - - -
90D PHE* 1.3 75.8 - - - +
92D GLY* 1.3 61.6 + - - +
94D SER* 3.5 1.4 - - - -
95D ALA 3.0 23.2 + - - -
282D GLY 3.1 19.3 - - - +
283D THR* 4.1 3.3 + - + +
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Residues in contact with GLY 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ALA* 4.6 0.4 - - - +
48D ALA* 4.9 1.5 + - - +
51D MSE 4.4 4.5 - - - -
52D ILE* 3.7 24.9 - - - +
55D LEU* 3.7 13.7 - - - -
88D ILE 3.1 14.8 + - - -
91D ALA* 1.3 76.0 - - - +
93D ILE* 1.3 63.5 + - - +
95D ALA* 3.2 4.3 + - - +
96D ILE* 3.2 26.2 + - - +
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Residues in contact with ILE 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LEU* 3.6 17.7 - - + +
72D TRP* 3.4 39.7 - - + +
75D MSE 3.9 41.6 - - + +
76D TYR* 4.5 3.6 - - + +
82D ALA* 4.5 2.2 - - + -
89D ILE* 3.1 32.9 + - + +
90D PHE* 3.9 22.9 - - + +
92D GLY* 1.3 75.3 - - - +
94D SER* 1.3 57.3 + - - +
96D ILE* 3.4 6.3 + - - +
97D GLU* 2.9 27.4 + - - +
285D GLY 4.2 1.3 - - - +
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Residues in contact with SER 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D PHE 2.4 28.4 + - - -
91D ALA 3.5 0.4 - - - -
92D GLY 3.2 0.2 - - - -
93D ILE* 1.3 74.5 - - - +
95D ALA* 1.3 66.0 + - - +
97D GLU* 3.3 1.6 + - - +
98D GLN* 3.0 31.2 + - - +
281D ILE 3.4 18.4 - - - -
282D GLY* 3.4 15.3 - - - -
283D THR 3.6 4.0 - - - -
285D GLY 2.8 36.8 + - - -
286D GLY* 3.7 1.3 - - - -
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Residues in contact with ALA 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 3.5 18.8 - - + +
35D GLY* 3.4 12.0 - - - -
36D GLU* 3.8 14.6 + - - +
37D ALA* 3.6 20.2 - - - +
52D ILE* 3.9 13.7 - - + -
91D ALA 3.0 13.9 + - - +
92D GLY 3.2 9.2 + - - +
94D SER* 1.3 76.3 - - - +
96D ILE* 1.3 63.5 + - - +
98D GLN* 3.3 0.9 + - - +
99D ALA 3.2 16.1 + - - -
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Residues in contact with ILE 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 4.6 6.7 - - + -
25D ILE* 4.2 9.0 - - + -
52D ILE* 4.5 15.7 - - + +
55D LEU* 3.7 31.0 - - + -
56D SER* 4.4 5.8 - - - +
60D LEU* 3.8 33.4 - - + -
75D MSE 3.8 30.3 - - + -
92D GLY 3.2 13.6 + - - +
93D ILE 3.7 6.3 - - - +
95D ALA* 1.3 74.6 - - - +
97D GLU* 1.3 67.5 + - - +
99D ALA* 3.1 5.5 + - - +
100D LEU* 3.0 31.6 + - + +
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Residues in contact with GLU 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ILE* 4.2 10.1 - - + -
72D TRP* 3.9 22.1 - - + -
75D MSE 5.2 1.8 - - + +
93D ILE 2.9 17.8 + - - +
94D SER 3.7 3.1 - - - +
96D ILE* 1.3 76.1 - - - +
98D GLN* 1.3 68.6 + - - +
100D LEU* 3.1 20.5 + - + +
101D TRP* 3.0 42.4 + - + +
285D GLY 4.0 7.4 - - - +
286D GLY* 3.2 6.1 - - - -
287D LEU* 2.7 23.6 + - - -
288D MSE 2.8 31.5 + - - +
289D GLU 3.9 2.1 + - - -
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Residues in contact with GLN 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ALA 3.8 3.5 - - - +
35D GLY* 3.8 6.8 - - - -
36D GLU* 3.0 43.7 + - - +
94D SER 3.0 16.8 + - - +
95D ALA 3.5 7.0 - - - +
96D ILE 3.2 0.2 - - - -
97D GLU* 1.3 86.9 + - - +
99D ALA* 1.3 57.1 + - - +
101D TRP* 3.3 6.6 + - - +
102D ASP* 3.0 26.9 + - - +
281D ILE* 3.2 43.9 + - + +
282D GLY* 3.6 5.7 - - - -
287D LEU* 4.6 11.9 - - + +
313D LEU* 5.2 1.4 - - - +
314D ILE* 4.7 3.4 - - - +
317D ALA* 4.1 13.1 - - + +
366D LEU* 3.9 9.9 - - + +
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Residues in contact with ALA 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D VAL* 4.4 3.8 - - + -
25D ILE* 3.5 21.8 - - + -
33D GLY* 3.6 23.4 - - - +
34D ALA 3.3 17.7 + - - -
35D GLY 4.0 0.7 - - - +
95D ALA 3.2 7.2 + - - +
96D ILE 3.1 10.1 + - - +
98D GLN* 1.3 79.0 - - - +
100D LEU* 1.3 62.1 + - - +
102D ASP* 3.4 2.4 + - - +
103D ILE* 3.1 28.7 + - - +
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.2 9.4 - - + -
25D ILE* 3.8 18.8 - - + -
60D LEU* 5.1 0.4 - - + -
65D PRO* 3.9 31.8 - - + +
68D ILE* 3.6 29.2 - - + +
71D LEU* 3.6 32.5 - - + -
75D MSE 5.1 2.5 - - + -
96D ILE* 3.0 31.9 + - + +
97D GLU* 3.1 12.8 + - + +
99D ALA* 1.3 78.1 - - - +
101D TRP* 1.3 58.3 + - - +
103D ILE* 3.4 6.8 + - + +
104D LYS* 3.0 26.0 + - - +
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Residues in contact with TRP 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D ILE* 3.4 19.5 - - + +
69D GLU* 5.2 1.3 - - - -
97D GLU* 3.0 56.6 + - + -
98D GLN 3.3 5.6 + - - +
100D LEU* 1.3 73.3 - - - +
102D ASP* 1.3 61.8 + - - +
104D LYS* 3.5 25.0 - - + +
105D GLY 2.8 24.8 + - - -
112D VAL* 3.6 28.1 - - + +
115D LEU* 4.0 15.7 - - + +
116D PHE* 3.7 25.8 - + - -
287D LEU* 4.4 10.1 - - + -
288D MSE 3.8 28.3 - - + +
115G LEU 3.5 26.0 - - - -
116G PHE 4.4 0.2 - - - -
117G GLY* 3.5 25.4 - - - -
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Residues in contact with ASP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D GLY* 3.2 8.0 - - - -
34D ALA* 2.9 24.6 + - - +
98D GLN 3.0 13.0 + - - +
99D ALA 3.5 6.7 - - - +
101D TRP* 1.3 77.7 - - - +
103D ILE* 1.3 57.5 + - - +
106D LYS* 3.1 54.4 + - - +
365D GLY* 3.4 7.0 - - - -
366D LEU* 2.6 57.1 + - + +
367D GLY 4.2 0.9 + - - -
368D ALA 5.2 4.7 + - - +
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Residues in contact with ILE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 4.0 19.7 - - + -
25D ILE* 4.0 24.9 - - + -
27D THR* 4.0 15.0 - - + -
31D ILE* 3.9 22.7 - - + +
32D THR 3.8 4.0 - - - -
33D GLY 3.5 24.7 - - - +
65D PRO* 4.4 20.6 - - + -
99D ALA 3.1 19.5 + - - +
100D LEU* 3.7 7.4 - - + +
101D TRP 3.2 0.2 - - - -
102D ASP* 1.3 75.0 - - - +
104D LYS* 1.3 66.9 + - - +
105D GLY 3.2 0.2 + - - -
106D LYS* 3.2 3.9 + - - +
107D CYS* 3.0 24.8 + - - -
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Residues in contact with LYS 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D PRO 5.6 2.0 + - - +
66D SER* 3.1 31.2 + - - +
68D ILE* 3.4 23.8 - - + -
100D LEU 3.0 16.9 + - - +
101D TRP* 3.5 28.0 - - + +
103D ILE* 1.3 77.5 - - - +
105D GLY* 1.3 61.8 + - - +
107D CYS* 3.6 5.8 + - - +
108D LEU* 3.3 33.8 + - + +
115D LEU* 3.9 11.0 - - + -
114G GLU* 2.8 45.6 + - - +
115G LEU* 4.8 0.7 - - - +
117G GLY* 4.1 4.0 - - - -
118G GLY 3.8 1.8 - - - +
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Residues in contact with GLY 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D TRP 2.8 17.8 + - - -
104D LYS* 1.3 75.4 - - - +
106D LYS* 1.3 59.7 + - - +
108D LEU* 3.0 4.2 + - - +
109D GLY 2.8 24.1 + - - -
110D VAL 3.1 22.7 + - - -
112D VAL* 5.0 0.7 - - - -
115D LEU* 4.0 11.6 - - - +
365D GLY* 3.5 12.8 - - - -
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Residues in contact with LYS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE* 4.1 16.6 - - + -
32D THR* 2.7 38.8 + - - +
33D GLY* 4.6 0.2 - - - -
34D ALA* 5.3 0.6 - - - +
102D ASP* 3.1 38.5 + - - +
103D ILE 3.2 4.0 + - - +
105D GLY* 1.3 74.1 - - - +
107D CYS* 1.3 63.0 + - - +
109D GLY* 3.0 12.0 + - - -
364D PRO* 3.9 23.5 - - + +
365D GLY* 3.6 7.8 - - - +
367D GLY 6.1 0.2 - - - +
368D ALA 5.0 10.5 + - - +
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Residues in contact with CYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 3.7 23.1 - - - -
31D ILE* 3.4 32.3 - - - -
103D ILE* 3.0 23.0 + - - +
104D LYS* 3.8 8.3 - - - +
106D LYS* 1.3 78.6 - - - +
108D LEU* 1.3 66.9 + - + +
109D GLY 3.5 0.2 + - - -
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LYS* 3.3 25.8 + - + +
105D GLY 3.0 4.6 + - - +
107D CYS* 1.3 84.0 - - + +
109D GLY* 1.3 63.4 + - - +
110D VAL* 3.3 20.5 + - + +
115D LEU* 3.5 26.5 - - + -
108G LEU* 3.9 23.0 - - + +
110G VAL* 3.9 31.0 - - + -
114G GLU* 5.6 3.1 - - + +
115G LEU* 4.1 13.5 - - + -
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Residues in contact with GLY 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D GLY 2.8 8.2 + - - -
106D LYS 3.0 12.2 + - - -
107D CYS 3.2 1.4 + - - -
108D LEU* 1.3 77.3 - - - +
110D VAL* 1.3 63.0 + - - +
111D PRO* 4.8 0.2 - - - +
364D PRO* 3.8 15.6 - - - +
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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