Contacts of the helix formed by residues 37 - 63 (chain D) in PDB entry 1ZOY
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 LYS 37 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B GLN* 3.2 18.6 - - - +
242B MET 5.1 4.5 - - - +
243B ALA* 5.0 11.4 + - - +
244B THR* 6.2 0.2 - - - +
245B TYR* 4.5 22.0 + - + +
246B LYS* 6.3 0.6 - - - +
35D SER 3.6 3.5 + - - +
36D SER* 1.3 73.3 + - - +
38D ALA* 1.3 61.4 + - - +
39D ALA 3.5 1.6 - - - -
40D SER* 2.8 28.9 + - - +
41D LEU* 3.1 53.3 + - + +
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Residues in contact with ALA 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN* 3.9 0.6 + - - +
36D SER* 3.4 15.9 + - - +
37D LYS* 1.3 72.8 - - - +
39D ALA* 1.3 67.1 + - - +
41D LEU* 3.2 8.2 + - - +
42D HIS* 3.0 24.7 + - - +
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN* 3.6 8.3 + - - +
208B ASP* 3.3 44.4 - - - +
209B PRO* 4.5 2.5 - - + -
213B TYR* 3.7 16.5 - - + -
37D LYS 3.5 0.4 - - - -
38D ALA* 1.3 78.3 - - - +
40D SER* 1.3 62.0 + - - +
42D HIS* 3.4 7.4 + - - +
43D TRP* 3.1 22.2 + - - +
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Residues in contact with SER 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN* 2.9 23.0 + - - -
213B TYR* 3.4 21.0 + - - -
242B MET* 3.3 27.8 + - - -
243B ALA* 4.5 3.3 - - - +
37D LYS* 2.8 25.7 + - - +
39D ALA* 1.3 79.5 - - - +
41D LEU* 1.3 61.2 + - - +
43D TRP* 3.3 5.9 + - - +
44D THR* 3.1 25.3 + - - +
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Residues in contact with LEU 41 (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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36D SER* 5.8 1.8 - - - +
37D LYS* 3.1 66.6 + - + +
38D ALA* 3.7 6.3 - - - +
40D SER* 1.3 73.9 + - - +
42D HIS* 1.3 61.4 + - - +
44D THR* 2.5 24.9 + - + +
45D GLY* 2.8 14.0 + - - -
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Residues in contact with HIS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ALA 3.0 15.9 + - - +
39D ALA* 3.7 6.6 + - - +
41D LEU* 1.3 75.1 - - - +
43D TRP* 1.3 65.9 + - - +
45D GLY* 3.1 2.8 + - - +
46D GLU* 3.0 49.2 + - - +
82D TRP* 3.6 46.5 - + + -
86D GLN* 3.5 15.1 + - - -
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Residues in contact with TRP 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B TYR* 3.5 33.0 - + + -
239B LYS* 4.1 49.8 - - + +
240B LYS* 5.0 3.4 - - + -
243B ALA* 4.2 13.7 - - + -
112C ASP* 3.9 41.7 - - + -
39D ALA 3.1 14.1 + - - +
40D SER 3.3 8.7 - - - +
41D LEU 3.2 0.2 - - - -
42D HIS* 1.3 79.6 + - - +
44D THR* 1.3 90.2 + - + +
46D GLU* 3.3 15.4 + - - +
47D ARG* 3.1 62.1 + - + +
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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
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243B ALA* 3.3 36.6 - - + +
40D SER 3.1 4.0 + - - +
41D LEU* 2.5 36.0 + - + +
43D TRP* 1.3 86.6 - - + +
45D GLY* 1.3 65.7 + - - +
47D ARG* 3.0 8.5 + - + +
48D VAL* 2.9 29.3 + - - +
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Residues in contact with GLY 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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41D LEU 2.8 16.0 + - - -
42D HIS* 3.1 5.1 + - - -
44D THR* 1.3 77.8 + - - +
46D GLU* 1.3 61.2 + - - +
48D VAL* 3.1 8.7 + - - +
49D VAL* 3.1 20.8 + - - +
82D TRP* 3.5 21.3 - - - -
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Residues in contact with GLU 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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42D HIS* 3.0 27.5 + - + +
43D TRP* 3.4 17.5 - - - +
44D THR 3.1 0.2 - - - -
45D GLY* 1.3 75.9 - - - +
47D ARG* 1.3 90.0 + - - +
49D VAL* 3.4 3.9 + - - +
50D SER* 2.9 28.7 + - - +
79D HIS* 4.7 1.2 + - + +
82D TRP* 3.6 37.2 - - + +
86D GLN* 3.0 40.4 + - - +
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Residues in contact with ARG 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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108C HIS* 5.8 0.8 - - - +
109C LEU* 4.3 11.7 - - + -
112C ASP* 2.8 44.6 + - + -
1305C HEM 3.7 40.0 + - - +
43D TRP* 3.1 58.7 + - + +
44D THR* 3.0 12.5 + - - +
46D GLU* 1.3 103.9 + - - +
48D VAL* 1.3 59.1 + - + +
50D SER* 2.8 25.4 + - - -
51D VAL* 2.8 21.2 + - + +
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Residues in contact with VAL 48 (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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44D THR* 2.9 22.6 + - - +
45D GLY* 3.1 11.2 + - - +
47D ARG* 1.3 75.4 - - + +
49D VAL* 1.3 63.6 + - + +
51D VAL* 2.9 16.9 - - + +
52D LEU* 2.9 38.7 + - + +
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Residues in contact with VAL 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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45D GLY 3.1 11.1 + - - +
46D GLU 3.5 9.6 - - - +
48D VAL* 1.3 80.6 - - + +
50D SER* 1.3 59.7 + - - +
51D VAL 3.3 0.2 - - - -
52D LEU* 3.6 14.4 - - + -
53D LEU* 2.8 33.1 + - - +
75D ALA* 4.9 9.2 - - + +
78D LEU* 3.7 25.4 - - + -
79D HIS* 4.1 27.8 + - + +
82D TRP* 3.8 22.4 - - + -
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Residues in contact with SER 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 4.4 13.5 - - - -
1305C HEM 3.7 29.3 - - - +
46D GLU* 2.9 18.3 + - - +
47D ARG* 2.8 18.7 + - - -
49D VAL* 1.3 79.4 - - - +
51D VAL* 1.3 59.9 + - - +
53D LEU* 3.7 2.9 + - - +
54D LEU* 3.3 20.4 + - - +
79D HIS* 3.2 29.2 - - - -
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 3.5 25.6 - - + -
47D ARG* 2.8 18.7 + - + +
48D VAL* 2.9 26.7 + - + +
50D SER* 1.3 74.1 - - - +
52D LEU* 1.3 66.4 + - + +
54D LEU* 3.1 12.4 + - + +
55D GLY* 3.0 24.3 + - - -
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Residues in contact with LEU 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 VAL* 2.9 30.4 + - + +
49D VAL* 3.6 14.8 - - + +
50D SER 3.3 0.2 - - - -
51D VAL* 1.3 79.9 - - + +
53D LEU* 1.3 59.0 + - - +
54D LEU 2.9 4.5 - - - -
55D GLY* 3.0 4.1 + - - -
56D LEU* 3.0 39.8 + - + +
75D ALA* 5.2 7.0 - - + -
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Residues in contact with LEU 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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1305C HEM 3.6 38.2 - - + +
49D VAL 2.8 21.9 + - - +
50D SER* 4.1 4.5 - - - +
52D LEU* 1.3 72.4 - - - +
54D LEU* 1.3 59.2 + - - +
56D LEU* 3.9 6.7 - - - -
57D LEU* 3.4 26.5 + - + +
72D LEU* 4.2 16.4 - - + -
75D ALA* 4.2 19.9 - - + +
76D LEU* 3.4 34.8 - - + +
79D HIS* 4.0 26.5 - - + -
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Residues in contact with LEU 54 (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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102C THR* 4.4 4.9 - - + -
106C ILE* 4.0 39.0 - - + -
109C LEU* 4.5 17.7 - - + -
1305C HEM 4.1 25.6 - - + -
50D SER 3.3 13.9 + - - +
51D VAL* 3.1 15.9 - - + +
52D LEU 2.9 0.4 - - - -
53D LEU* 1.3 79.7 - - - +
55D GLY* 1.3 56.6 + - - +
57D LEU* 4.5 1.5 - - + +
58D PRO* 3.0 24.4 - - + +
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Residues in contact with GLY 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 VAL 3.0 12.5 + - - -
52D LEU* 3.0 3.5 + - - -
54D LEU* 1.3 77.1 - - - +
56D LEU* 1.3 63.7 + - - +
58D PRO* 3.3 7.3 - - - +
59D ALA* 3.2 22.6 + - - +
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Residues in contact with LEU 56 (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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52D LEU* 3.0 25.0 + - + +
53D LEU* 4.0 5.8 - - - +
54D LEU 3.3 0.4 - - - -
55D GLY* 1.3 76.7 - - - +
57D LEU* 1.3 57.7 + - - +
59D ALA* 3.0 4.5 + - + -
60D ALA* 2.6 38.5 + - - +
68D MET* 4.3 15.9 - - - +
71D SER* 3.7 43.1 - - - +
72D LEU* 3.5 24.7 - - + -
75D ALA* 3.9 18.8 - - + -
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Residues in contact with LEU 57 (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 LEU* 4.4 16.6 - - + -
99C MET* 5.3 3.6 - - + -
102C THR* 4.4 7.9 - - + +
1305C HEM 3.4 32.8 - - + -
53D LEU* 3.4 23.1 + - + +
54D LEU* 4.5 2.0 - - + +
56D LEU* 1.3 78.5 - - - +
58D PRO* 1.3 70.8 - - + +
60D ALA* 3.4 6.3 + - - +
61D TYR* 3.4 15.1 + - - +
72D LEU* 4.2 14.4 - - + -
76D LEU* 5.2 2.0 - - + -
1306D EPH 4.0 36.6 - - + +
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Residues in contact with PRO 58 (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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54D LEU* 3.0 28.9 - - + +
55D GLY* 3.3 10.5 - - - +
57D LEU* 1.3 87.6 - - + +
59D ALA* 1.3 53.5 + - - +
61D TYR* 2.7 30.5 + - + +
62D LEU* 3.1 22.2 + - + +
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Residues in contact with ALA 59 (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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55D GLY 3.2 17.3 + - - +
56D LEU* 3.0 9.4 + - + +
58D PRO* 1.3 79.1 - - - +
60D ALA* 1.3 57.5 + - - +
62D LEU* 3.4 6.8 + - - +
63D ASN* 2.9 28.4 + - - +
68D MET* 3.6 27.4 - - + +
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Residues in contact with ALA 60 (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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56D LEU 2.6 20.3 + - - +
57D LEU 3.8 4.9 - - - +
59D ALA* 1.3 72.2 - - - +
61D TYR* 1.3 60.5 + - - +
63D ASN 4.1 1.3 - - - -
64D PRO* 3.4 23.6 - - - +
68D MET* 3.4 26.8 - - + +
72D LEU* 4.0 22.0 - - + -
127D CYS* 3.9 7.8 - - - -
1306D EPH 3.4 17.1 - - + +
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Residues in contact with TYR 61 (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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143C MET* 3.2 33.2 - - + +
57D LEU 3.4 8.3 + - - +
58D PRO* 2.7 19.4 + - + +
60D ALA* 1.3 72.0 - - - +
62D LEU* 1.3 87.0 + - + +
63D ASN 3.3 0.5 + - - -
64D PRO* 3.3 15.2 - - - +
1306D EPH 3.3 88.1 + - + +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D PRO* 3.1 19.6 + - + +
59D ALA* 4.1 5.8 - - - +
61D TYR* 1.3 101.0 - - + +
63D ASN* 1.3 61.5 + - + +
64D PRO* 3.7 3.3 - - - +
1306D EPH 4.1 9.5 + - - -
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Residues in contact with ASN 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ALA 2.9 14.0 + - - +
60D ALA 4.0 0.2 - - - -
62D LEU* 1.3 82.4 - - + +
64D PRO* 1.3 62.6 - - - +
65D CYS* 3.4 24.7 + - - +
68D MET* 3.2 25.8 - - + +
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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) + - + + + + + -
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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