Contacts of the helix formed by residues 33 - 64 (chain B) in PDB entry 2YF3
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 PRO 33 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 4.0 0.7 - - - +
31B PRO 4.6 1.8 - - - +
32B PRO* 1.3 90.4 - - + +
34B PRO* 1.4 73.8 - - + +
35B GLU* 3.5 17.0 - - + +
36B LEU* 3.1 33.3 + - + +
37B LEU* 3.4 8.7 + - - +
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Residues in contact with PRO 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.6 11.7 - - + +
62A GLN* 3.4 36.5 - - + +
33B PRO* 1.4 89.4 - - + +
35B GLU* 1.3 71.6 + - - +
37B LEU* 3.3 2.5 + - + -
38B ARG* 3.0 47.9 + - - +
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PRO* 3.5 21.2 - - + +
34B PRO* 1.3 87.0 - - - +
36B LEU* 1.3 58.5 + - - +
38B ARG* 3.5 28.2 + - - +
39B LEU* 3.0 27.7 + - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 4.8 10.8 - - + -
32B PRO* 3.9 20.6 - - + -
33B PRO* 3.1 29.5 + - + +
35B GLU* 1.3 80.9 - - - +
37B LEU* 1.3 58.2 + - + +
39B LEU* 3.2 14.6 + - + +
40B ARG* 2.9 49.9 + - + +
93B GLN* 3.5 52.5 - - + +
94B LEU* 5.8 1.3 - - + -
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Residues in contact with LEU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.9 21.6 - - + +
58A LEU* 3.8 28.7 - - + -
59A LEU* 3.9 12.3 - - + -
62A GLN* 3.6 24.9 - - - +
68A LEU* 4.8 0.7 - - + -
76A LEU* 3.9 27.4 - - + -
32B PRO* 3.7 32.1 - - + -
33B PRO 3.4 2.4 + - - +
34B PRO 3.3 7.9 + - - +
36B LEU* 1.3 80.3 - - + +
38B ARG* 1.3 56.8 + - - +
40B ARG* 3.3 8.8 + - + +
41B GLN* 3.0 29.6 + - - +
94B LEU* 4.6 4.0 - - + -
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.9 23.9 - - + +
34B PRO* 3.0 35.5 + - - +
35B GLU* 3.5 39.2 + - - +
37B LEU* 1.3 75.4 - - - +
39B LEU* 1.3 63.1 + - - +
41B GLN* 3.4 6.7 + - - +
42B THR* 3.0 27.3 + - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU 3.0 19.2 + - - +
36B LEU* 3.6 17.5 - - + +
38B ARG* 1.3 76.3 - - - +
40B ARG* 1.3 68.9 + - - +
42B THR* 3.3 10.0 + - + -
43B LEU* 3.1 53.9 + - + +
93B GLN* 5.7 3.4 - - - +
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Residues in contact with ARG 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 5.0 6.5 - - + -
18B HIS* 4.0 9.3 + - - -
36B LEU* 2.9 45.4 + - + +
37B LEU* 3.3 9.8 + - + +
39B LEU* 1.3 78.0 - - - +
41B GLN* 1.3 63.3 + - - +
43B LEU* 3.3 28.6 + - - +
44B LEU* 3.0 30.5 + - + +
86B VAL* 2.9 36.4 + - - +
89B GLY* 3.4 17.8 - - - -
90B ALA* 3.5 31.9 - - + +
93B GLN* 3.6 24.8 - - + +
94B LEU* 6.3 2.0 - - + -
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Residues in contact with GLN 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A SER 5.3 1.4 + - - -
51A VAL* 5.4 0.2 - - - +
52A ARG* 3.3 47.9 - - + +
55A ILE* 3.4 30.5 - - + +
56A ASP* 4.9 2.5 - - - +
59A LEU* 6.3 0.2 - - + -
37B LEU 3.0 17.4 + - - +
38B ARG* 3.7 7.2 - - - +
40B ARG* 1.3 77.4 - - - +
42B THR* 1.3 63.2 + - - +
44B LEU* 3.2 13.7 + - - +
45B ASP* 2.9 60.0 + - - +
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Residues in contact with THR 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG 3.0 15.6 + - - -
39B LEU* 3.6 14.4 - - + -
41B GLN* 1.3 77.5 - - - +
43B LEU* 1.3 60.2 + - + +
45B ASP* 3.3 9.0 + - + +
46B GLU* 2.9 50.7 + - + +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 3.1 37.7 + - + +
40B ARG* 3.5 41.3 - - - +
42B THR* 1.3 77.7 - - + +
44B LEU* 1.3 62.6 + - - +
46B GLU* 3.4 19.1 + - - +
47B GLU* 3.2 29.9 + - - +
86B VAL* 4.0 21.8 - - + -
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.8 29.2 - - + -
55A ILE* 4.3 8.3 - - + -
80A LEU* 4.2 9.4 - - + -
83A LEU* 3.7 18.6 - - + -
40B ARG* 3.0 26.9 + - + +
41B GLN* 3.7 13.2 - - - +
43B LEU* 1.3 76.7 - - - +
45B ASP* 1.3 56.7 + - - +
47B GLU* 3.4 0.5 + - - -
48B SER* 2.9 36.5 + - - -
83B LEU* 4.2 5.0 - - + +
86B VAL* 4.1 18.8 - - + +
87B THR* 3.6 31.2 - - - +
90B ALA* 5.2 2.5 - - + -
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Residues in contact with ASP 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 2.8 33.0 + - - +
41B GLN* 2.9 43.4 + - - +
42B THR* 3.5 8.9 - - + +
44B LEU* 1.3 76.2 - - - +
46B GLU* 1.3 58.4 + - + +
48B SER* 3.4 6.4 + - - -
49B ALA* 2.9 31.8 + - - +
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B THR* 2.9 35.1 + - + +
43B LEU* 3.7 23.0 - - - +
44B LEU 3.3 0.2 - - - -
45B ASP* 1.3 78.1 - - + +
47B GLU* 1.3 70.5 + - + +
49B ALA* 3.4 5.3 + - - +
50B GLU* 3.2 33.7 + - - +
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Residues in contact with GLU 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B LEU* 3.2 17.3 + - - +
46B GLU* 1.3 80.1 - - - +
48B SER* 1.3 62.6 + - - +
50B GLU* 3.0 29.4 + - - +
51B VAL* 3.0 32.3 + - - +
79B GLU* 3.4 3.5 - - - +
82B ASP* 3.3 33.5 - - + +
83B LEU* 3.9 22.7 - - + +
86B VAL* 3.7 24.6 - - + +
----------------------------------------------------------
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 5.2 1.4 + - - -
44A LEU* 6.3 2.5 - - - -
48A SER* 4.2 23.1 + - - -
52A ARG* 5.4 2.6 + - - -
44B LEU 2.9 21.1 + - - -
45B ASP* 3.4 9.0 + - - -
47B GLU* 1.3 77.0 - - - +
49B ALA* 1.3 58.8 + - - +
51B VAL* 3.4 8.3 + - - +
52B ARG* 2.9 42.0 + - - +
83B LEU* 4.1 16.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP 2.9 18.1 + - - +
46B GLU* 3.6 7.2 - - - +
48B SER* 1.3 78.4 + - - +
50B GLU* 1.3 55.7 + - + +
52B ARG* 3.3 19.0 + - - +
53B ALA* 3.0 29.1 + - - +
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B GLU* 3.2 21.2 + - - +
47B GLU* 3.0 23.4 + - - +
49B ALA* 1.3 74.4 - - + +
51B VAL* 1.3 63.8 + - - +
53B ALA* 3.5 7.3 + - - +
54B GLU* 3.2 27.8 + - - +
79B GLU* 2.9 43.2 - - + +
82B ASP* 4.2 2.3 - - - +
----------------------------------------------------------
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 5.2 1.1 - - - +
44A LEU* 3.8 28.3 - - + -
47B GLU 3.0 16.4 + - - +
48B SER* 3.7 8.3 - - - +
50B GLU* 1.3 74.4 - - - +
52B ARG* 1.3 64.6 + - - +
54B GLU* 3.1 4.2 + - - +
55B ILE* 3.0 32.8 + - + +
76B LEU* 3.9 6.7 - - + -
79B GLU* 3.4 39.9 - - + +
80B LEU* 3.7 19.5 - - + +
83B LEU* 4.3 12.1 - - + -
----------------------------------------------------------
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 3.3 27.9 - - + +
45A ASP* 2.7 35.0 + - - +
48A SER* 6.0 2.6 - - - -
48B SER* 2.9 25.0 + - - +
49B ALA* 3.6 26.1 - - - +
51B VAL* 1.3 76.5 - - - +
53B ALA* 1.3 56.7 + - - +
55B ILE* 3.4 2.3 + - - +
56B ASP* 2.9 50.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA 3.0 16.7 + - - +
50B GLU* 3.7 8.3 - - - +
51B VAL 3.3 0.2 - - - -
52B ARG* 1.3 77.0 - - - +
54B GLU* 1.3 59.7 + - - +
56B ASP* 3.3 7.2 + - - +
57B HIS* 3.0 51.6 + - + +
----------------------------------------------------------
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Residues in contact with GLU 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLU* 3.2 14.4 + - - +
51B VAL 3.1 8.4 + - - +
53B ALA* 1.3 74.4 - - - +
55B ILE* 1.3 66.0 + - - +
57B HIS* 3.4 23.5 + - - +
58B LEU* 3.1 30.1 + - + +
75B PRO* 3.5 31.8 - - - +
76B LEU* 3.8 21.1 - - + +
79B GLU* 3.8 23.1 - - + +
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.9 27.6 - - + +
40A ARG* 4.8 4.7 - - + -
41A GLN* 3.3 45.8 - - + +
44A LEU* 4.1 10.8 - - + -
51B VAL* 3.0 31.0 + - + +
54B GLU* 1.3 75.0 - - - +
56B ASP* 1.3 59.4 + - - +
58B LEU* 3.2 8.4 + - - +
59B LEU* 2.9 44.4 + - + +
76B LEU* 3.7 22.4 - - + -
80B LEU* 5.8 0.7 - - + -
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Residues in contact with ASP 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLN* 4.9 4.9 - - - +
52B ARG* 2.9 39.1 + - - +
53B ALA* 3.7 7.4 - - - +
55B ILE* 1.3 78.1 - - - +
57B HIS* 1.3 60.8 + - + +
59B LEU* 3.4 13.6 + - - +
60B ALA* 2.9 30.5 + - - +
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Residues in contact with HIS 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 3.0 41.0 + - + +
54B GLU* 3.7 25.7 + - - +
56B ASP* 1.3 79.8 - - + +
58B LEU* 1.3 66.7 + - + +
60B ALA* 3.4 6.2 + - - +
61B ARG* 3.2 36.1 + - - +
122C LYS* 4.4 21.1 + - - -
124C LEU* 5.8 0.2 - - - +
125C LYS* 6.1 0.8 + - - -
----------------------------------------------------------
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Residues in contact with LEU 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.8 22.2 - - + -
54B GLU* 3.1 20.0 + - + +
55B ILE* 3.7 5.4 - - - +
57B HIS* 1.3 78.4 - - + +
59B LEU* 1.3 62.2 + - - +
61B ARG* 3.3 18.1 + - - +
62B GLN* 3.0 27.6 + - - +
68B LEU* 4.0 27.7 - - + +
72B ASP 3.6 24.2 - - - +
73B LEU* 4.1 16.4 - - + -
76B LEU* 3.7 35.4 - - + -
----------------------------------------------------------
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 3.5 46.0 - - + +
37A LEU* 3.9 9.9 - - + -
38A ARG* 4.0 28.5 - - + +
41A GLN* 6.0 1.1 - - + -
55B ILE* 2.9 35.2 + - + +
56B ASP* 3.9 12.6 - - - +
58B LEU* 1.3 75.0 - - - +
60B ALA* 1.3 57.4 + - - +
62B GLN* 3.4 8.1 + - - +
63B ALA* 2.8 30.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ASP 2.9 19.3 + - - +
57B HIS* 3.7 7.4 - - - +
58B LEU 3.3 0.2 - - - -
59B LEU* 1.3 76.1 - - - +
61B ARG* 1.3 57.5 + - - +
63B ALA* 3.3 8.9 + - - +
64B ALA* 3.1 22.0 + - - +
118C ARG* 4.5 19.2 - - - +
122C LYS* 6.3 0.2 - - - +
124C LEU* 3.6 31.1 - - + +
----------------------------------------------------------
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Residues in contact with ARG 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B HIS* 3.2 22.9 + - - +
58B LEU* 3.3 22.3 + - - +
60B ALA* 1.3 74.1 - - - +
62B GLN* 1.3 62.9 + - - +
64B ALA* 3.3 10.3 + - - +
65B GLY 3.5 0.2 + - - -
66B GLU* 3.0 50.5 + - - +
68B LEU* 4.3 9.1 - - + +
72B ASP* 3.0 41.6 + - - +
124C LEU* 4.3 19.7 - - + -
125C LYS* 3.6 35.0 + - - +
126C PRO 3.0 25.0 + - - -
129C TRP* 4.5 3.2 - - - +
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Residues in contact with GLN 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PRO 2.8 28.7 + - - -
33A PRO* 4.1 0.4 - - - +
34A PRO* 3.4 43.6 - - + +
37A LEU* 3.5 14.5 - - - +
58B LEU 3.0 15.5 + - - +
59B LEU* 3.7 8.8 - - - +
61B ARG* 1.3 72.5 - - - +
63B ALA* 1.3 66.2 + - - +
65B GLY* 3.0 14.7 + - - -
66B GLU 3.9 14.2 + - - +
68B LEU* 3.5 31.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU 2.8 21.6 + - - +
60B ALA* 3.3 10.3 + - - +
62B GLN* 1.3 74.1 - - - +
64B ALA* 1.3 59.0 - - - +
65B GLY* 3.2 1.6 + - - -
----------------------------------------------------------
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA 3.1 11.9 + - - +
61B ARG* 3.5 9.9 - - - +
62B GLN 3.1 0.6 - - - -
63B ALA* 1.3 76.6 - - - +
65B GLY* 1.3 58.1 + - - +
66B GLU* 3.6 0.6 - - - +
116C PRO* 3.7 34.7 - - + +
117C ARG 5.2 3.6 - - - +
118C ARG* 6.0 0.7 - - - -
124C LEU* 3.8 11.4 - - + -
----------------------------------------------------------
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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