Contacts of the helix formed by residues 86 - 109 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ASN 4.1 0.2 + - - -
85A GLY* 1.3 72.6 - - - -
87A ALA* 1.3 66.0 + - - -
88A ILE 3.3 2.7 - - - -
89A ILE* 3.2 8.2 - - - +
90A PHE* 3.1 26.3 + - - +
260A TYR* 4.0 14.4 - - - -
84F ASN 5.3 0.4 - - - -
85F GLY 4.9 0.7 - - - -
86F GLY* 4.0 26.3 - - - -
87F ALA 4.9 1.4 - - - +
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Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.2 6.5 - - + -
86A GLY* 1.3 71.6 - - - -
88A ILE* 1.3 59.9 + - + +
91A ALA* 2.8 35.1 + - - +
260A TYR* 3.3 41.9 - - + +
283A THR* 4.8 1.8 - - - -
81F TRP* 3.5 33.4 - - + +
85F GLY* 5.7 0.4 - - - -
86F GLY 4.9 3.6 - - - +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.2 23.8 - - + -
43A VAL 5.5 0.2 - - - +
44A GLY* 4.0 24.0 - - - +
47A ALA* 3.9 26.7 - - + +
48A ALA* 4.3 3.8 - - - +
51A MSE 3.7 15.3 - - + +
86A GLY 3.3 0.4 - - - -
87A ALA* 1.3 77.3 - - + +
89A ILE* 1.3 67.2 + - - +
91A ALA* 3.9 2.7 - - - +
92A GLY* 3.1 17.5 + - - -
47F ALA* 4.1 0.7 - - + -
51F MSE 5.5 2.9 - - - -
81F TRP* 5.3 8.1 - - + -
88F ILE* 3.7 44.0 - - + -
89F ILE* 4.8 10.5 - - + +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A MSE 3.5 29.8 - - - -
55A LEU* 4.3 11.0 - - + +
79A SER* 4.0 24.7 - - - +
81A TRP* 4.0 13.2 - - + +
82A ALA* 3.9 17.9 - - - +
85A GLY* 3.8 7.4 - - - -
86A GLY 3.2 28.3 - - - +
88A ILE* 1.3 77.8 - - - +
90A PHE* 1.3 76.1 + - + +
92A GLY* 3.3 3.3 + - - -
93A ILE* 3.0 36.5 + - + +
43F VAL 4.6 3.1 - - - +
88F ILE* 4.7 7.1 - - + +
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Residues in contact with PHE 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TRP* 4.2 11.0 - + - -
76A TYR* 3.8 21.5 - + - -
82A ALA* 3.2 30.7 - - + -
85A GLY* 3.5 23.1 - - - -
86A GLY 3.1 22.6 + - - +
89A ILE* 1.3 83.4 - - + +
91A ALA* 1.3 55.8 + - - +
93A ILE* 3.7 26.7 - - + +
94A SER* 2.6 39.1 + - - -
260A TYR* 4.1 5.4 - - + -
261A THR* 3.4 35.7 - - + -
283A THR 3.2 20.0 - - - +
285A GLY* 4.3 4.8 - - - +
237F PHE* 3.8 5.8 - + - -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 3.4 20.2 - - + +
39A ILE* 3.6 29.2 - - + -
48A ALA* 5.1 1.3 - - + -
87A ALA 2.8 22.1 + - - +
88A ILE* 3.9 3.1 - - - +
90A PHE* 1.3 75.8 - - - +
92A GLY* 1.3 63.7 + - - +
94A SER* 3.7 0.3 - - - -
95A ALA* 3.0 18.5 + - - +
282A GLY 3.1 20.6 - - - +
283A THR* 4.0 4.2 + - + +
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Residues in contact with GLY 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ALA* 4.9 0.2 - - - -
48A ALA* 5.1 1.7 - - - +
51A MSE 4.3 4.7 - - - -
52A ILE* 3.8 22.5 - - - +
55A LEU* 3.7 12.8 - - - -
88A ILE 3.1 13.6 + - - -
89A ILE 3.7 3.1 - - - -
91A ALA* 1.3 75.3 - - - +
93A ILE* 1.3 65.4 + - - +
95A ALA* 3.3 3.6 + - - +
96A ILE* 3.2 26.7 + - - +
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.6 15.7 - - + +
72A TRP* 3.2 40.8 - - + +
75A MSE 4.0 43.6 - - + +
76A TYR* 4.6 2.7 - - + +
82A ALA* 4.5 3.4 - - + -
89A ILE* 3.0 34.9 + - + +
90A PHE* 3.9 24.5 - - + +
92A GLY* 1.3 76.6 - - - +
94A SER* 1.3 56.9 + - - +
96A ILE* 3.3 4.0 + - - +
97A GLU* 2.9 26.7 + - - +
285A GLY 4.2 1.3 - - - +
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Residues in contact with SER 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A PHE 2.6 28.1 + - - -
91A ALA 3.7 0.2 - - - -
93A ILE* 1.3 74.0 - - - +
95A ALA* 1.3 63.8 + - - +
97A GLU* 3.3 1.7 + - - +
98A GLN* 2.9 29.5 + - - +
281A ILE 3.2 21.3 + - - -
282A GLY* 3.5 15.3 - - - -
283A THR 3.6 4.5 - - - -
285A GLY 2.8 35.7 + - - -
286A GLY* 3.6 1.0 - - - -
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Residues in contact with ALA 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.5 20.3 - - + +
35A GLY* 3.3 12.5 - - - -
36A GLU* 3.6 14.3 + - - +
37A ALA 3.6 20.6 - - - +
52A ILE* 3.9 13.7 - - + -
91A ALA 3.0 16.6 + - - +
92A GLY 3.7 4.9 - - - +
94A SER* 1.3 76.6 - - - +
96A ILE* 1.3 62.1 + - - +
98A GLN* 3.4 1.2 + - - +
99A ALA 3.2 15.9 + - - -
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Residues in contact with ILE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.4 10.1 - - + -
25A ILE* 4.3 5.4 - - + -
52A ILE* 4.4 15.7 - - + -
55A LEU* 3.8 28.9 - - + -
56A SER* 4.1 7.4 - - - +
60A LEU* 3.8 35.4 - - + -
75A MSE 3.8 26.5 - - + -
92A GLY 3.2 14.6 + - - +
93A ILE 3.6 7.0 - - - +
95A ALA* 1.3 77.4 - - - +
97A GLU* 1.3 62.9 + - - +
99A ALA* 3.1 5.5 + - - +
100A LEU* 3.0 33.4 + - + +
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 4.2 11.2 - - + -
72A TRP* 3.9 24.0 - - + -
75A MSE 5.6 1.3 - - + -
93A ILE 2.9 17.0 + - - +
94A SER 3.6 3.8 - - - +
96A ILE* 1.3 76.6 - - - +
98A GLN* 1.3 67.7 + - - +
100A LEU* 3.2 12.9 + - + +
101A TRP* 3.0 47.4 + - - +
285A GLY 4.0 7.6 - - - +
286A GLY* 3.4 4.8 - - - -
287A LEU* 2.8 22.7 + - - +
288A MSE 2.8 32.2 + - - +
289A GLU 3.9 2.6 + - - -
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Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA 3.8 2.9 - - - +
35A GLY* 3.6 5.6 - - - -
36A GLU* 2.9 45.2 + - - +
94A SER 2.9 19.2 + - - +
95A ALA 3.5 5.2 - - - +
97A GLU* 1.3 83.4 + - - +
99A ALA* 1.3 64.1 + - - +
101A TRP* 3.2 4.7 + - - +
102A ASP* 3.0 22.0 + - - +
281A ILE* 3.3 35.6 + - + +
282A GLY* 3.6 5.5 - - - -
287A LEU* 4.3 25.1 - - + +
313A LEU* 5.3 1.0 - - - +
314A ILE* 4.5 2.5 - - - +
317A ALA* 4.3 11.4 - - + +
366A LEU* 3.9 9.7 - - + +
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Residues in contact with ALA 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 4.4 3.6 - - + -
25A ILE* 3.4 29.2 - - + -
33A GLY* 3.5 21.2 - - - +
34A ALA 3.4 19.3 + - - +
35A GLY 3.9 0.9 - - - +
95A ALA 3.2 7.4 + - - +
96A ILE 3.1 4.1 + - - +
98A GLN* 1.3 79.0 - - - +
100A LEU* 1.3 62.3 + - - +
102A ASP* 3.4 2.2 - - - +
103A ILE* 3.1 28.1 + - - +
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ILE* 4.3 9.6 - - + -
25A ILE* 4.2 15.5 - - + -
60A LEU* 5.4 1.3 - - + -
65A PRO* 3.7 36.7 - - + +
68A ILE* 3.7 32.7 - - + +
71A LEU* 4.2 27.4 - - + -
72A TRP 5.7 0.2 - - - +
75A MSE 5.3 1.8 - - + -
96A ILE* 3.0 32.5 + - + +
97A GLU* 3.4 11.0 - - - +
98A GLN 3.1 0.4 - - - -
99A ALA* 1.3 77.6 - - - +
101A TRP* 1.3 57.6 + - - +
103A ILE* 3.2 8.7 + - + +
104A LYS* 3.0 26.2 + - - +
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Residues in contact with TRP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ILE* 3.5 22.5 - - + +
69A GLU* 5.8 1.1 - - + -
97A GLU* 3.0 56.3 + - + -
98A GLN 3.2 5.8 + - - +
100A LEU* 1.3 74.0 - - - +
102A ASP* 1.3 60.7 + - - +
104A LYS* 3.7 17.7 - - + +
105A GLY 2.9 26.3 + - - -
112A VAL* 3.5 26.4 - - + +
115A LEU* 3.9 20.2 - - + -
116A PHE* 3.8 23.6 - + - -
287A LEU* 4.3 12.6 - - + -
288A MSE 3.6 29.6 - - + +
115E LEU 3.6 16.8 - - - -
117E GLY* 3.5 32.8 - - - -
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 3.6 4.1 - - - -
34A ALA* 3.0 27.5 + - - +
98A GLN 3.0 13.4 + - - +
99A ALA 3.4 10.3 - - - +
101A TRP* 1.3 78.9 - - - +
103A ILE* 1.3 56.9 + - - +
106A LYS* 3.0 56.7 + - - +
112A VAL* 4.4 0.6 - - - +
364A PRO 4.2 0.2 - - - +
365A GLY* 3.5 3.5 - - - -
366A LEU* 2.7 53.0 + - + +
367A GLY 4.4 1.0 + - - -
368A ALA 4.7 6.3 - - - +
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Residues in contact with ILE 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.9 27.4 - - + -
25A ILE* 3.9 28.3 - - + +
27A THR* 4.0 13.0 - - + -
31A ILE* 4.2 13.0 - - + +
32A THR 3.7 4.9 - - - -
33A GLY* 3.5 26.0 - - - +
65A PRO* 4.2 22.7 - - + -
99A ALA 3.1 19.9 + - - +
100A LEU* 3.2 9.2 + - + +
102A ASP* 1.3 76.6 - - - +
104A LYS* 1.3 59.2 + - - +
106A LYS* 3.3 2.3 + - - +
107A CYS* 2.9 30.5 + - - -
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Residues in contact with LYS 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO 5.7 0.4 - - - +
66A SER* 3.0 39.3 + - - +
68A ILE* 3.5 17.5 - - - -
100A LEU 3.0 16.0 + - - +
101A TRP* 3.3 26.4 + - + +
103A ILE* 1.3 77.3 - - - +
105A GLY* 1.3 64.1 + - - +
107A CYS* 3.2 8.9 + - + +
108A LEU* 3.0 34.2 + - + +
115A LEU* 3.9 11.2 - - + -
114E GLU* 3.0 46.7 + - - +
115E LEU* 4.9 0.9 - - - +
117E GLY* 4.3 5.4 - - - -
118E GLY 4.0 0.6 - - - +
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A TRP 2.9 16.5 + - - -
104A LYS* 1.3 75.8 - - - +
106A LYS* 1.3 51.9 + - - +
108A LEU* 3.3 2.7 + - - -
109A GLY* 2.8 30.5 + - - -
110A VAL* 3.0 28.1 + - - -
112A VAL* 4.9 0.7 - - - -
115A LEU* 4.0 14.0 - - - +
365A GLY* 3.6 8.5 + - - -
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 3.9 19.3 - - + +
32A THR* 2.8 40.7 + - - +
34A ALA* 5.5 0.6 - - - +
102A ASP* 3.0 38.3 + - - +
103A ILE 3.7 4.3 - - - +
104A LYS 3.3 0.2 - - - -
105A GLY* 1.3 75.3 - - - +
107A CYS* 1.3 63.1 + - - +
109A GLY* 3.3 10.6 + - - -
364A PRO* 4.2 29.4 - - + +
365A GLY 3.8 0.4 - - - +
368A ALA 4.8 11.2 + - - -
369A VAL* 6.1 1.5 - - - +
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Residues in contact with CYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.4 35.2 - - - -
31A ILE* 3.6 17.9 - - - -
103A ILE* 2.9 26.2 + - - +
104A LYS* 3.5 8.3 - - + +
105A GLY 3.2 0.2 - - - -
106A LYS* 1.3 79.3 - - - +
108A LEU* 1.3 65.9 + - + +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LYS* 3.0 28.4 + - + +
105A GLY 4.1 2.0 - - - +
107A CYS* 1.3 81.4 - - + +
109A GLY* 1.3 63.2 + - - +
110A VAL* 3.4 17.8 + - + +
115A LEU* 3.5 26.9 - - + -
108E LEU* 3.9 27.0 - - + +
110E VAL* 3.5 32.8 - - + -
114E GLU* 5.4 2.9 - - + +
115E LEU* 3.9 16.2 - - + -
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Residues in contact with GLY 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY 2.8 9.2 + - - -
106A LYS 3.3 7.5 + - - -
107A CYS 3.3 4.0 + - - -
108A LEU* 1.3 75.0 - - - +
110A VAL* 1.3 68.1 + - - +
364A PRO* 3.9 14.1 - - - +
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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