Contacts of the helix formed by residues 32 - 59 (chain D) in PDB entry 2FBW
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 32 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D PRO* 1.3 79.0 - - - +
33D PRO* 1.3 70.7 - - - +
34D ALA 3.3 2.0 + - - -
35D VAL 3.5 2.2 + - - -
36D ASP* 2.8 35.7 + - - +
94D CYS* 4.1 5.9 - - - -
95D LYS* 3.5 21.1 - - - +
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Residues in contact with PRO 33 (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 PRO 4.8 0.4 - - - +
32D GLY* 1.3 83.3 - - - +
34D ALA* 1.3 65.6 + - + +
36D ASP* 3.1 7.1 + - + +
37D TYR* 3.0 45.0 + - + +
95D LYS* 5.3 0.2 - - - +
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLY 3.3 1.0 + - - -
33D PRO* 1.3 81.8 - - + +
35D VAL* 1.3 66.0 + - + +
37D TYR* 4.2 1.9 - - - +
38D SER* 2.8 30.2 + - - +
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 4.5 11.4 - - + +
26D ALA* 4.0 22.0 - - + +
27D ALA* 3.8 19.5 - - + +
30D TYR* 3.2 29.4 + - + +
32D GLY 3.5 4.5 + - - +
33D PRO 3.4 0.4 - - - -
34D ALA* 1.3 79.4 - - + +
36D ASP* 1.3 65.5 + - - +
38D SER* 3.1 5.9 + - - -
39D LEU* 2.8 35.1 + - + +
94D CYS* 3.6 22.2 - - - -
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Residues in contact with ASP 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D GLY* 2.8 31.2 + - - +
33D PRO* 3.1 8.7 + - + +
35D VAL* 1.3 76.6 - - - +
37D TYR* 1.3 59.2 + - + +
39D LEU* 3.7 5.6 + - - +
40D ALA* 3.2 17.8 + - - +
87D ASN* 2.9 27.7 + - + +
91D VAL 4.2 3.8 - - - +
92D GLY* 3.6 14.4 - - - -
93D ILE* 3.0 18.1 + - - +
94D CYS* 2.7 36.7 + - - +
95D LYS* 4.5 2.9 + - - -
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Residues in contact with TYR 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D PRO* 3.0 43.3 + - + +
34D ALA* 4.3 1.8 - - - +
36D ASP* 1.3 76.0 - - + +
38D SER* 1.3 60.6 + - - +
40D ALA* 3.2 3.9 + - - +
41D ALA* 3.0 28.4 + - - +
80D PHE* 4.9 1.7 - - - -
84D CYS* 4.1 28.5 - - + -
87D ASN* 3.5 29.3 + - + +
88D TYR* 3.4 38.7 + - + +
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Residues in contact with SER 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 5.4 3.8 - - - +
23D LEU* 3.7 25.1 - - - -
34D ALA 2.8 23.2 + - - -
35D VAL* 3.7 2.7 - - - -
37D TYR* 1.3 77.9 - - - +
39D LEU* 1.3 57.2 + - - +
41D ALA* 3.3 5.1 + - - +
42D ALA* 2.8 32.9 + - - +
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Residues in contact with LEU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LEU* 3.9 20.4 - - + -
23D LEU* 3.8 29.6 - - + +
24D LEU* 5.1 10.1 - - + -
27D ALA* 4.2 15.3 - - + -
35D VAL* 2.8 36.2 + - + +
36D ASP 3.8 4.0 - - - +
38D SER* 1.3 70.6 - - - +
40D ALA* 1.3 59.8 + - - +
42D ALA 4.5 0.2 - - - +
43D LEU* 2.8 50.6 + - + +
93D ILE* 4.3 27.4 - - + -
94D CYS* 4.8 3.6 - - - -
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ASP 3.2 13.2 + - - +
37D TYR* 3.3 11.0 - - - +
39D LEU* 1.3 79.7 - - - +
41D ALA* 1.3 59.9 + - - +
44D THR* 2.9 30.8 + - - -
80D PHE* 3.6 14.7 - - + -
83D LEU* 3.9 33.9 - - + +
84D CYS* 4.4 5.2 - - - -
87D ASN* 4.0 9.2 - - - +
93D ILE* 4.3 2.6 - - + +
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D TYR 3.0 15.8 + - - +
38D SER* 3.8 6.1 - - - +
40D ALA* 1.3 76.4 - - - +
42D ALA* 1.3 59.3 + - - +
44D THR* 3.2 2.9 + - - -
45D LEU* 2.9 31.5 + - - +
80D PHE* 3.9 19.2 - - + -
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Residues in contact with ALA 42 (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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16D VAL* 4.0 9.2 - - + +
19D LEU* 3.9 27.1 - - + -
20D LEU* 3.8 24.9 - - + +
23D LEU* 4.0 5.8 - - + -
38D SER 2.8 20.7 + - - +
41D ALA* 1.3 71.2 - - - +
43D LEU* 1.3 61.1 + - - +
45D LEU* 4.8 2.0 - - - -
46D HIS* 2.9 35.0 + - - +
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Residues in contact with LEU 43 (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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53C VAL* 4.5 29.2 - - + -
20D LEU* 4.0 28.9 - - + -
39D LEU* 2.8 46.3 + - + +
40D ALA 4.3 2.0 - - - +
42D ALA* 1.3 73.6 - - - +
44D THR* 1.3 55.3 + - - +
46D HIS* 4.2 0.9 - - + +
47D GLY* 2.9 27.2 + - - -
83D LEU* 4.7 11.0 - - + -
93D ILE* 4.7 14.4 - - + -
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Residues in contact with THR 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C VAL* 6.1 0.4 - - - -
40D ALA 2.9 20.9 + - - -
41D ALA 3.2 4.1 + - - -
43D LEU* 1.3 78.3 - - - +
45D LEU* 1.3 60.3 + - - +
47D GLY* 3.8 0.3 - - - -
48D HIS* 2.8 29.3 + - + +
76D SER* 3.7 26.7 + - - +
79D THR* 4.2 8.7 - - - +
80D PHE* 3.5 38.9 + - + +
83D LEU* 4.2 7.4 - - - +
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Residues in contact with LEU 45 (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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16D VAL* 3.8 17.5 - - + -
41D ALA 2.9 16.8 + - - +
42D ALA* 4.2 2.5 - - - +
44D THR* 1.3 76.9 - - - +
46D HIS* 1.3 65.3 + - - +
48D HIS* 3.8 9.1 - - + +
49D TRP* 3.1 79.1 + - + +
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Residues in contact with HIS 46 (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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98C HIS* 4.0 24.2 + + - -
13D GLU 4.8 1.6 + - - -
16D VAL* 3.7 14.9 - - + +
17D SER* 3.0 35.9 + - - -
20D LEU* 3.6 26.8 - - + +
42D ALA 2.9 19.1 + - - +
43D LEU 4.2 1.1 - - - +
45D LEU* 1.3 76.3 - - - +
47D GLY* 1.3 60.9 + - - +
49D TRP* 3.6 6.0 + - - +
50D GLY* 3.0 25.3 + - - -
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Residues in contact with GLY 47 (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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50C SER* 3.6 20.6 - - - -
43D LEU 2.9 18.0 + - - -
44D THR* 3.8 0.4 - - - -
46D HIS* 1.3 79.5 - - - +
48D HIS* 1.3 63.6 + - - +
50D GLY* 3.8 1.1 - - - -
51D LEU* 3.0 33.7 + - - +
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Residues in contact with HIS 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D THR* 2.8 23.6 + - + +
45D LEU* 3.3 11.4 + - + +
47D GLY* 1.3 74.0 - - - +
49D TRP* 1.3 76.8 + + - +
51D LEU* 5.4 0.2 - - - -
52D GLY* 3.0 22.0 + - - -
69D ASN* 5.3 0.4 - - - -
72D LEU* 3.4 37.3 - - + +
73D TYR* 4.0 44.7 + + - -
76D SER* 2.7 31.1 + - - +
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Residues in contact with TRP 49 (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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9D HIS* 3.2 34.7 + + - -
12D SER* 3.8 30.3 - - - -
13D GLU* 3.8 29.4 - - + +
16D VAL* 3.6 28.5 - - + -
45D LEU* 3.1 50.0 + - + +
46D HIS* 4.1 3.8 - - - +
48D HIS* 1.3 93.7 - + - +
50D GLY* 1.3 58.2 + - - +
52D GLY* 3.1 3.1 + - - +
53D GLN* 2.9 31.9 + - - +
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Residues in contact with GLY 50 (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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46D HIS* 3.0 20.1 + - - -
47D GLY* 3.3 1.8 + - - -
49D TRP* 1.3 77.0 - - - +
51D LEU* 1.3 62.7 + - - +
53D GLN* 3.0 19.5 + - - +
54D VAL* 3.1 16.7 + - - +
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Residues in contact with LEU 51 (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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46C GLY 5.4 0.7 - - - +
47C VAL* 3.9 41.3 - - + -
50C SER* 4.1 22.4 - - - +
51C LEU* 5.5 5.6 - - + -
47D GLY 3.0 20.7 + - - +
50D GLY* 1.3 75.8 - - - +
52D GLY* 1.3 56.5 + - - +
54D VAL* 3.2 9.2 + - + +
55D ILE* 2.9 33.1 + - + +
72D LEU* 3.7 32.1 - - + -
75D LEU* 4.5 15.7 - - + -
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Residues in contact with GLY 52 (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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48D HIS 3.0 16.5 + - - -
49D TRP* 3.4 6.1 - - - -
50D GLY 3.1 0.4 - - - -
51D LEU* 1.3 74.9 - - - +
53D GLN* 1.3 64.5 + - - +
55D ILE* 3.3 6.0 + - - +
56D THR* 2.9 28.9 + - - -
69D ASN* 4.8 6.5 + - - -
72D LEU* 3.6 11.6 - - - +
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Residues in contact with GLN 53 (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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213B TYR* 5.4 2.5 + - - +
214B ARG* 2.7 45.4 + - - +
216B HIS* 3.9 10.6 - - + +
43C ARG* 4.3 13.0 - - - +
9D HIS* 4.4 8.1 + - - -
13D GLU* 2.9 32.4 + - - +
49D TRP 2.9 18.3 + - - +
50D GLY* 3.0 11.0 + - - +
52D GLY* 1.3 75.3 - - - +
54D VAL* 1.3 63.2 + - - +
56D THR* 3.3 3.6 + - - -
57D ASP* 3.0 28.2 + - - +
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Residues in contact with VAL 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ARG* 3.7 34.1 - - + +
47C VAL* 4.3 22.7 - - + -
50D GLY 3.1 14.3 + - - +
51D LEU* 3.2 13.4 + - + +
53D GLN* 1.3 74.6 - - - +
55D ILE* 1.3 65.8 + - + +
57D ASP* 3.2 2.1 + - - +
58D TYR* 3.2 44.9 + - + +
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Residues in contact with ILE 55 (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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51D LEU* 2.9 21.9 + - + +
52D GLY* 3.6 4.9 - - - +
54D VAL* 1.3 78.6 - - + +
56D THR* 1.3 65.4 + - - +
59D VAL* 2.9 42.2 + - + +
65D ILE* 4.9 5.4 - - + +
68D ALA* 3.8 44.6 - - + +
69D ASN* 3.9 24.5 - - - +
72D LEU* 3.8 25.1 - - + -
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Residues in contact with THR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ASN* 3.8 10.2 - - - +
209B PRO* 4.8 6.1 - - + -
210B PHE* 3.6 35.7 - - + -
214B ARG* 3.6 28.9 + - - +
52D GLY 2.9 17.5 + - - -
53D GLN* 3.7 6.2 + - - -
55D ILE* 1.3 79.2 - - - +
57D ASP* 1.3 62.8 + - - +
59D VAL 4.0 8.4 - - - +
60D HIS* 4.7 0.5 + - - -
65D ILE* 6.3 3.6 - - - -
69D ASN* 5.7 1.4 + - - -
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Residues in contact with ASP 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B SER* 4.8 3.5 + - - -
173B TRP* 3.8 8.5 - - + +
174B ASN* 3.0 26.1 + - - +
214B ARG* 2.9 32.4 + - - +
216B HIS* 2.8 27.9 + - - -
43C ARG* 2.8 32.4 + - - +
53D GLN 3.0 11.0 + - - -
54D VAL 3.6 7.9 - - - +
56D THR* 1.3 78.7 - - - +
58D TYR* 1.3 67.0 + - + +
60D HIS* 3.2 14.0 + - - -
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Residues in contact with TYR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B TRP* 3.5 38.4 + + - -
43C ARG* 3.0 39.2 + - - -
54D VAL* 3.2 33.6 + - + +
55D ILE* 5.4 0.2 - - - -
57D ASP* 1.3 85.0 - - + +
59D VAL* 1.3 66.2 + - + +
60D HIS* 3.1 21.4 + + - -
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Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ILE* 2.9 40.8 + - + +
56D THR* 4.0 5.5 - - - +
58D TYR* 1.3 82.2 - - + +
60D HIS* 1.3 69.2 + - - +
64D PRO* 3.6 40.8 - - + +
65D ILE* 3.5 21.5 - - + +
68D ALA* 4.3 9.2 - - + -
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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