Contacts of the helix formed by residues 86 - 109 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN 5.3 0.9 - - - -
85A GLY 4.9 0.4 - - - -
86A GLY* 4.0 27.1 - - - -
87A ALA 4.9 1.6 - - - +
85F GLY* 1.3 72.8 - - - -
87F ALA* 1.3 66.4 + - - -
88F ILE 3.4 2.9 - - - -
89F ILE* 3.1 21.9 - - - +
90F PHE* 3.1 13.2 + - - +
260F TYR* 4.0 13.0 - - - -
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Residues in contact with ALA 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TRP* 3.6 32.5 - - + +
86A GLY 4.9 3.4 - - - +
39F ILE* 4.1 9.3 - - + +
86F GLY* 1.3 70.7 - - - -
88F ILE* 1.3 56.6 + - + +
90F PHE 3.7 0.2 - - - -
91F ALA* 2.7 39.4 + - - +
260F TYR* 3.3 40.5 - - + +
283F THR* 4.8 1.7 - - + +
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Residues in contact with ILE 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 4.2 0.9 - - + -
51A MSE 5.5 2.7 - - - -
81A TRP* 5.2 8.7 - - + -
88A ILE* 3.7 42.2 - - + -
89A ILE* 4.7 9.0 - - + +
39F ILE* 4.2 22.2 - - + -
43F VAL 5.4 0.4 - - - +
44F GLY* 4.1 22.9 - - - +
47F ALA* 3.6 31.0 - - + +
48F ALA* 4.1 2.9 - - - +
51F MSE 3.7 14.4 - - + +
86F GLY 3.4 1.0 - - - -
87F ALA* 1.3 75.9 - - + +
89F ILE* 1.3 66.6 + - - +
91F ALA* 3.3 4.1 + - - +
92F GLY 3.1 18.2 + - - -
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL 4.7 2.9 - - - +
88A ILE* 4.8 7.4 - - + +
51F MSE 3.7 27.1 - - - -
55F LEU* 4.3 6.3 - - + +
79F SER* 4.0 26.0 - - - +
81F TRP* 3.9 12.1 - - + +
82F ALA* 3.8 21.8 - - + +
85F GLY* 3.8 9.0 - - - -
86F GLY 3.1 29.8 - - - +
88F ILE* 1.3 79.3 - - - +
90F PHE* 1.3 73.2 + - + +
92F GLY* 3.4 1.7 + - - -
93F ILE* 3.1 36.8 + - + +
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Residues in contact with PHE 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A PHE* 3.9 9.9 - + - -
72F TRP* 4.2 10.3 - + - -
76F TYR* 3.8 24.7 - + - -
82F ALA* 3.2 31.0 - - + -
85F GLY* 3.5 21.5 - - - -
86F GLY 3.1 23.5 + - - +
87F ALA 4.4 0.2 - - - +
89F ILE* 1.3 82.6 - - + +
91F ALA* 1.3 56.3 + - - +
93F ILE* 3.9 23.4 - - + +
94F SER* 2.5 39.0 + - - -
260F TYR* 4.1 6.5 - - + -
261F THR* 3.5 31.0 - - + -
283F THR 3.2 20.6 - - - +
285F GLY* 4.3 4.4 - - - +
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Residues in contact with ALA 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ALA* 3.6 14.0 - - + +
39F ILE* 3.5 29.6 - - + -
48F ALA* 5.0 2.0 - - + -
87F ALA 2.7 24.6 + - - +
88F ILE 3.3 4.2 + - - +
90F PHE* 1.3 72.9 - - - +
92F GLY* 1.3 59.1 + - - +
94F SER* 3.4 1.9 + - - -
95F ALA* 3.0 28.9 + - - +
282F GLY 3.1 20.7 - - - +
283F THR* 4.1 2.7 + - + +
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Residues in contact with GLY 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ALA* 4.8 0.4 - - - +
48F ALA* 5.0 1.5 - - - +
51F MSE 4.3 3.8 - - - -
52F ILE* 3.7 22.3 - - - +
55F LEU* 3.7 13.9 - - - -
88F ILE 3.1 13.9 + - - -
89F ILE 3.8 3.4 - - - -
91F ALA* 1.3 76.1 - - - +
93F ILE* 1.3 62.4 + - - +
95F ALA* 3.5 1.9 + - - +
96F ILE* 3.3 28.9 + - - +
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Residues in contact with ILE 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F LEU* 4.0 14.6 - - + -
72F TRP* 3.3 39.7 - - + +
75F MSE 4.0 36.5 - - + +
76F TYR* 4.5 3.4 - - + +
82F ALA* 4.4 7.6 - - + -
89F ILE* 3.1 35.4 + - + +
90F PHE* 3.9 23.3 - - + +
92F GLY* 1.3 76.1 - - - +
94F SER* 1.3 57.3 + - - +
96F ILE* 3.3 7.1 + - - +
97F GLU* 2.8 27.2 + - - +
285F GLY 4.1 1.3 - - - +
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Residues in contact with SER 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F PHE 2.5 23.9 + - - -
91F ALA 3.5 0.2 - - - -
93F ILE* 1.3 78.1 - - - +
95F ALA* 1.3 63.4 + - - +
97F GLU* 3.3 1.9 + - - +
98F GLN* 2.9 30.2 + - - +
281F ILE 3.2 20.4 + - - -
282F GLY* 3.5 19.1 - - - -
283F THR 3.6 0.2 - - - -
285F GLY 2.8 36.9 + - - -
286F GLY* 3.1 1.3 + - - -
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Residues in contact with ALA 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F VAL 5.3 0.2 - - - +
23F VAL* 3.5 20.6 - - + +
35F GLY* 3.4 12.3 - - - -
36F GLU* 3.6 14.3 + - - +
37F ALA 3.6 21.1 - - - +
52F ILE* 3.8 16.2 - - + -
91F ALA 3.0 16.9 + - - +
92F GLY 3.9 1.1 - - - +
93F ILE 3.4 0.2 - - - -
94F SER* 1.3 76.5 - - - +
96F ILE* 1.3 62.7 + - - +
98F GLN* 3.4 1.0 + - - +
99F ALA 3.2 16.1 + - - -
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Residues in contact with ILE 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 4.5 8.7 - - + -
25F ILE* 3.9 7.6 - - + +
52F ILE* 4.4 16.2 - - + -
55F LEU* 3.8 28.9 - - + -
56F SER* 4.2 6.3 - - - +
60F LEU* 3.7 39.5 - - + -
75F MSE 3.8 27.6 - - + -
92F GLY 3.3 15.6 + - - +
93F ILE 3.6 6.3 - - - +
94F SER 3.2 0.2 - - - -
95F ALA* 1.3 78.3 - - - +
97F GLU* 1.3 62.2 + - - +
99F ALA* 3.2 5.0 + - - +
100F LEU* 3.1 28.6 + - + +
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Residues in contact with GLU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F ILE* 4.1 12.1 - - + +
72F TRP* 4.0 21.3 - - + -
75F MSE 5.2 2.0 - - + +
93F ILE 2.8 17.4 + - - +
94F SER 3.7 2.9 - - - +
96F ILE* 1.3 77.4 - - - +
98F GLN* 1.3 66.7 + - - +
100F LEU* 3.2 12.4 + - + +
101F TRP* 3.0 49.4 + - - +
285F GLY 4.1 7.9 - - - +
286F GLY* 3.2 5.8 - - - -
287F LEU* 2.7 24.5 + - - -
288F MSE 2.8 31.2 + - - +
289F GLU 3.8 2.4 + - - -
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Residues in contact with GLN 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34F ALA 3.9 3.1 - - - +
35F GLY* 3.5 6.1 - - - -
36F GLU* 2.9 44.7 + - - +
94F SER 2.9 18.8 + - - +
95F ALA 3.6 3.4 - - - +
96F ILE 3.3 0.2 - - - -
97F GLU* 1.3 81.8 + - - +
99F ALA* 1.3 63.4 + - - +
101F TRP* 3.2 5.4 + - - +
102F ASP* 3.0 21.5 + - - +
281F ILE* 3.3 39.2 + - + +
282F GLY* 3.6 6.5 - - - +
287F LEU* 4.3 24.9 - - + +
313F LEU* 5.3 1.0 - - - +
314F ILE* 4.4 2.7 - - - +
317F ALA* 4.3 10.3 - - + +
366F LEU* 4.0 10.6 - - + +
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Residues in contact with ALA 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 4.5 3.1 - - + -
25F ILE* 3.6 21.3 - - + -
33F GLY* 3.5 20.5 - - - +
34F ALA 3.4 19.9 + - - +
35F GLY 3.9 1.6 - - - +
95F ALA 3.2 8.3 + - - +
96F ILE 3.2 9.7 + - - +
98F GLN* 1.3 77.9 - - - +
100F LEU* 1.3 63.7 + - - +
102F ASP* 3.2 3.9 + - - +
103F ILE* 3.0 27.2 + - - +
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Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 4.2 10.1 - - + -
25F ILE* 4.0 16.6 - - + -
60F LEU* 5.3 0.2 - - + -
65F PRO* 3.9 33.9 - - + +
68F ILE* 3.8 32.8 - - + +
71F LEU* 3.8 30.1 - - + -
72F TRP 5.7 0.2 - - - +
75F MSE 5.2 2.7 - - + -
96F ILE* 3.1 32.4 + - + +
97F GLU* 3.2 11.2 + - + +
99F ALA* 1.3 76.6 - - - +
101F TRP* 1.3 57.9 + - - +
103F ILE* 3.3 8.2 + - + +
104F LYS* 3.0 26.0 + - - +
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Residues in contact with TRP 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU 3.6 25.1 - - - -
117B GLY* 3.6 22.0 - - - -
68F ILE* 3.4 27.7 - - + +
69F GLU* 5.8 1.1 - - + -
97F GLU* 3.0 56.8 + - + -
98F GLN 3.2 6.0 + - - +
100F LEU* 1.3 73.9 - - - +
102F ASP* 1.3 60.7 + - - +
104F LYS* 3.2 16.0 + - + +
105F GLY 2.8 26.2 + - - -
112F VAL* 3.5 26.6 - - + +
115F LEU* 3.8 21.3 - - + -
116F PHE* 3.7 27.1 - + - -
287F LEU* 4.2 12.1 - - + -
288F MSE 3.7 27.6 - - + +
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Residues in contact with ASP 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F GLY* 3.4 7.7 - - - -
34F ALA* 2.9 26.5 + - - +
98F GLN 3.0 12.0 + - - +
99F ALA 3.2 11.7 - - - +
101F TRP* 1.3 77.2 - - - +
103F ILE* 1.3 57.9 + - - +
105F GLY 3.4 0.2 + - - -
106F LYS* 2.9 53.7 + - - +
112F VAL* 4.3 0.6 - - - +
364F PRO 4.4 0.5 - - - +
365F GLY* 3.5 7.1 - - - -
366F LEU* 2.8 46.5 + - + +
367F GLY 4.5 0.9 + - - -
368F ALA* 5.1 6.4 + - - +
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Residues in contact with ILE 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LEU* 3.8 28.7 - - + -
25F ILE* 4.0 21.5 - - + +
27F THR* 3.9 21.1 - - + -
31F ILE* 4.1 13.2 - - + +
32F THR 3.7 3.8 - - - -
33F GLY* 3.5 26.7 - - - +
65F PRO* 4.3 19.5 - - + -
99F ALA 3.0 18.4 + - - +
100F LEU* 3.5 9.9 - - + +
101F TRP 3.2 0.2 - - - -
102F ASP* 1.3 73.9 - - - +
104F LYS* 1.3 60.3 + - - +
106F LYS* 3.1 2.3 + - - +
107F CYS* 2.8 30.6 + - - +
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Residues in contact with LYS 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B GLU* 2.9 53.3 + - - +
115B LEU* 4.9 0.4 - - - +
117B GLY 4.3 4.0 - - - -
118B GLY 3.9 0.8 - - - +
66F SER* 3.0 33.8 + - - +
68F ILE* 3.5 17.7 - - - -
100F LEU 3.0 13.1 + - - +
101F TRP* 3.6 28.9 - - + +
103F ILE* 1.3 77.8 - - - +
105F GLY* 1.3 64.3 + - - +
107F CYS* 3.3 5.4 + - + +
108F LEU* 3.0 39.1 + - + +
115F LEU* 3.8 13.7 - - + -
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Residues in contact with GLY 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101F TRP 2.8 12.7 + - - -
104F LYS* 1.3 77.8 - - - +
106F LYS* 1.3 57.0 + - - +
108F LEU* 3.2 2.3 + - - -
109F GLY 2.8 25.6 + - - -
110F VAL 3.1 27.8 + - - -
112F VAL* 4.9 1.1 - - - -
115F LEU* 4.1 12.9 - - - +
365F GLY* 3.6 12.1 - - - -
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Residues in contact with LYS 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ILE* 3.8 19.6 - - + +
32F THR* 2.7 42.2 + - - +
102F ASP* 2.9 39.6 + - - +
103F ILE 3.6 4.0 - - - +
105F GLY* 1.3 75.7 - - - +
107F CYS* 1.3 63.8 + - - +
109F GLY* 3.2 11.4 + - - -
364F PRO* 4.1 27.1 - - + +
365F GLY 3.8 0.4 - - - +
368F ALA 5.0 10.7 + - - -
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Residues in contact with CYS 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F LEU* 3.3 36.3 - - - -
31F ILE* 3.5 19.1 - - - -
103F ILE* 2.8 20.8 + - - +
104F LYS* 3.5 8.1 - - - +
105F GLY 3.3 0.2 - - - -
106F LYS* 1.3 77.9 - - - +
108F LEU* 1.3 69.4 + - + +
109F GLY 3.7 0.2 + - - -
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Residues in contact with LEU 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 4.1 24.0 - - + +
110B VAL* 3.7 31.0 - - + -
114B GLU* 5.6 3.4 - - + +
115B LEU* 3.9 17.5 - - + -
104F LYS* 3.0 28.8 + - + +
105F GLY 4.1 1.8 - - - +
107F CYS* 1.3 85.0 - - + +
109F GLY* 1.3 62.1 + - - +
110F VAL* 3.4 18.2 + - + +
115F LEU* 3.8 24.0 - - + -
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Residues in contact with GLY 109 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105F GLY 2.8 8.6 + - - -
106F LYS 3.2 10.8 + - - -
107F CYS 3.4 0.6 + - - -
108F LEU* 1.3 78.7 - - - +
110F VAL* 1.3 63.1 + - - +
111F PRO* 4.8 0.5 - - - +
364F PRO* 3.8 15.1 - - - +
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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