Contacts of the helix formed by residues 53 - 76 (chain D) in PDB entry 3PJA
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 ASP 53 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52D GLN* 1.3 76.4 + - - +
54D ILE* 1.3 62.5 + - - +
55D PRO* 4.0 8.4 - - - +
56D LYS* 3.0 41.2 + - + +
57D ARG* 3.4 30.4 + - - +
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Residues in contact with ILE 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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45D VAL* 4.2 24.0 - - + -
52D GLN* 3.4 25.7 + - + +
53D ASP* 1.3 71.5 - - - +
55D PRO* 1.3 76.9 - - + +
57D ARG* 3.0 10.2 + - + +
58D CYS* 2.9 37.0 + - - -
108D LEU* 4.0 31.6 - - + +
154D LEU* 6.2 1.1 - - + -
166D ARG* 3.6 31.0 - - - +
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Residues in contact with PRO 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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52D GLN 5.1 1.3 - - - +
53D ASP* 3.7 10.5 - - - +
54D ILE* 1.3 96.5 - - + +
56D LYS* 1.3 61.2 + - - +
58D CYS* 3.3 8.0 + - + +
59D LEU* 3.0 34.0 + - + +
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Residues in contact with LYS 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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53D ASP* 3.0 35.7 + - + +
54D ILE 3.2 0.6 - - - -
55D PRO* 1.3 76.9 - - - +
57D ARG* 1.3 63.1 + - - +
59D LEU* 3.4 10.3 + - - +
60D LYS* 3.0 57.5 + - + +
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Residues in contact with ARG 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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41D LEU* 2.9 48.1 + - + +
42D LEU* 4.2 7.9 - - + +
44D GLY* 3.7 23.1 + - - -
45D VAL* 3.7 27.4 - - + +
52D GLN* 3.6 20.4 + - - -
53D ASP* 3.4 22.0 + - - +
54D ILE* 3.0 12.7 + - + +
56D LYS* 1.3 80.6 - - - +
58D CYS* 1.3 56.8 + - - +
60D LYS* 3.2 10.0 + - - +
61D ALA* 3.0 27.4 + - - +
108D LEU* 6.0 0.7 - - + -
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Residues in contact with CYS 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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42D LEU* 4.5 2.7 - - - -
54D ILE* 2.9 21.6 + - - +
55D PRO* 3.7 10.1 - - + +
57D ARG* 1.3 73.9 - - - +
59D LEU* 1.3 62.1 + - + +
61D ALA* 3.4 8.5 + - - +
62D ARG* 3.0 31.5 + - - +
105D VAL* 4.0 8.9 - - + +
108D LEU* 3.3 41.3 - - - -
109D GLU* 3.8 33.4 - - + +
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Residues in contact with LEU 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 PRO* 3.0 27.3 + - + +
56D LYS* 3.7 8.7 - - + +
58D CYS* 1.3 77.8 - - + +
60D LYS* 1.3 64.0 + - + +
62D ARG* 3.1 15.3 + - + +
63D GLU* 3.0 23.8 + - - +
109D GLU* 4.8 9.9 - - - +
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Residues in contact with LYS 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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41D LEU* 3.9 31.0 - - + +
56D LYS* 3.0 47.3 + - + +
57D ARG* 3.6 7.6 - - - +
59D LEU* 1.3 72.8 - - + +
61D ALA* 1.3 66.5 + - - +
63D GLU* 2.9 38.2 - - - +
64D HIS* 3.1 13.0 + - - -
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Residues in contact with ALA 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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38D ILE* 4.3 11.4 - - + +
41D LEU* 3.9 12.6 - - + +
42D LEU* 3.6 33.4 - - + -
57D ARG 3.0 6.6 + - - +
58D CYS 3.5 10.3 - - - +
60D LYS* 1.3 76.1 - - - +
62D ARG* 1.3 63.5 + - - +
64D HIS* 2.9 17.2 + - - +
65D PHE* 3.0 17.6 + - + -
105D VAL* 3.7 13.2 - - + -
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Residues in contact with ARG 62 (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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58D CYS 3.0 15.1 + - - +
59D LEU* 3.1 18.4 + - + +
61D ALA* 1.3 76.1 - - - +
63D GLU* 1.3 61.0 + - - +
65D PHE* 3.4 25.8 - - + +
66D GLY* 3.8 2.4 + - - -
69D LYS* 4.7 4.3 + - - -
105D VAL* 4.0 11.5 - - + +
106D VAL* 4.2 18.8 - - - +
109D GLU* 3.1 39.8 + - - -
122D ILE* 4.3 30.6 - - + +
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Residues in contact with GLU 63 (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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59D LEU 3.0 10.3 + - - +
60D LYS* 2.9 41.1 - - - +
62D ARG* 1.3 73.8 - - - +
64D HIS* 1.3 61.1 + - - +
65D PHE 3.1 1.1 - - - -
66D GLY* 3.0 19.8 + - - -
67D THR* 4.1 3.8 + - - +
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Residues in contact with HIS 64 (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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34D THR* 4.1 9.1 - - + +
37D GLU* 3.1 36.3 + - + +
38D ILE* 3.5 20.9 - - + -
41D LEU* 3.7 24.6 - - + +
60D LYS* 3.1 9.0 + - - +
61D ALA* 2.9 9.7 + - - +
63D GLU* 1.3 73.5 - - - +
65D PHE* 1.3 59.0 + - - +
66D GLY 2.9 9.7 + - - -
67D THR* 2.7 38.0 + - + -
68D VAL* 3.1 8.8 + - - +
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Residues in contact with PHE 65 (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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38D ILE* 3.7 25.8 - - + +
61D ALA 3.0 27.8 + - - -
62D ARG* 3.4 16.8 - - + +
63D GLU 3.1 0.2 - - - -
64D HIS* 1.3 74.8 - - - +
66D GLY* 1.3 56.8 + - - +
68D VAL* 3.3 16.8 - - + +
69D LYS* 3.0 36.4 + - - +
98D LEU* 4.4 9.4 - - + -
101D LEU* 3.9 11.0 - - + -
102D ALA* 3.6 36.3 - - + -
105D VAL* 4.4 13.7 - - + -
122D ILE* 4.0 27.5 - - + +
123D LEU* 3.7 31.6 - - + -
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Residues in contact with GLY 66 (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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62D ARG 3.8 2.2 + - - -
63D GLU* 3.0 12.7 + - - -
64D HIS 2.9 2.4 + - - -
65D PHE* 1.3 74.8 - - - +
67D THR* 1.3 63.6 + - - +
68D VAL 3.0 1.1 - - - -
69D LYS* 3.0 24.1 + - - +
70D THR* 3.1 19.5 + - - +
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Residues in contact with THR 67 (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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34D THR* 3.8 18.8 + - - +
63D GLU 4.1 3.5 + - - +
64D HIS* 2.7 29.0 + - + +
66D GLY* 1.3 74.1 - - - +
68D VAL* 1.3 60.2 + - - +
70D THR* 2.9 22.9 + - - +
71D HIS* 3.0 26.1 + - - -
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Residues in contact with VAL 68 (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 LEU* 4.2 16.8 - - + -
34D THR* 3.4 28.0 - - + -
38D ILE* 4.0 11.2 - - + -
64D HIS 3.1 8.8 + - - +
65D PHE* 3.3 20.2 - - + +
66D GLY 3.0 0.6 - - - -
67D THR* 1.3 76.2 - - - +
69D LYS* 1.3 67.1 + - - +
71D HIS* 3.1 4.0 + - - +
72D LEU* 3.0 39.8 + - + +
98D LEU* 4.2 19.1 - - + -
123D LEU* 4.2 15.0 - - + +
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Residues in contact with LYS 69 (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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62D ARG 4.7 4.0 + - - -
65D PHE* 3.0 32.7 + - - +
66D GLY* 3.0 13.1 + - - +
68D VAL* 1.3 75.7 - - - +
70D THR* 1.3 59.5 + - + +
72D LEU* 3.4 3.1 + - - +
73D THR* 2.9 34.9 + - + +
121D GLU 3.6 15.0 - - - -
122D ILE* 2.9 36.3 + - - +
123D LEU 3.3 19.6 - - - +
124D GLY* 3.8 8.1 - - - +
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Residues in contact with THR 70 (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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66D GLY 3.1 15.0 + - - +
67D THR* 2.9 19.0 + - - +
69D LYS* 1.3 74.4 - - + +
71D HIS* 1.3 74.3 + - - +
72D LEU 3.1 1.6 - - - -
73D THR* 2.8 25.5 + - - -
74D SER* 3.0 11.5 + - - -
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Residues in contact with HIS 71 (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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27D VAL* 3.3 19.4 - - + +
30D SER* 2.7 34.6 + - - -
31D LEU* 3.5 27.4 - - + -
34D THR* 4.1 18.3 + - - -
67D THR* 3.0 24.5 + - - +
68D VAL 3.1 0.4 + - - +
70D THR* 1.3 87.2 + - - +
72D LEU* 1.3 57.7 + - - +
74D SER* 3.4 7.9 - - - -
75D LEU 3.0 20.4 + - - -
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Residues in contact with LEU 72 (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 LEU* 3.4 29.4 - - + -
68D VAL* 3.0 25.0 + - + +
69D LYS 3.7 4.5 - - - +
70D THR 3.1 0.2 - - - -
71D HIS* 1.3 74.3 - - - +
73D THR* 1.3 64.5 + - - +
74D SER 3.0 1.6 - - - -
75D LEU* 3.2 18.9 + - + +
76D LYS* 3.0 29.6 + - - +
95D LEU* 5.8 5.8 - - + -
98D LEU* 5.2 4.7 - - + -
123D LEU* 3.0 44.4 - - + +
124D GLY 4.9 2.2 - - - +
125D ILE* 3.9 24.0 - - + -
133D PHE* 4.9 8.1 - - + -
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Residues in contact with THR 73 (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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69D LYS* 2.9 19.8 + - + +
70D THR* 2.8 19.3 + - - -
72D LEU* 1.3 76.9 - - - +
74D SER* 1.3 60.1 + - - +
76D LYS* 3.3 40.2 - - - +
77D THR* 3.6 13.7 - - - +
124D GLY* 4.5 7.4 - - - +
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Residues in contact with SER 74 (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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27D VAL* 4.2 10.5 - - - +
70D THR 3.0 12.1 + - - -
71D HIS* 3.4 15.7 - - - -
72D LEU 3.0 0.2 - - - -
73D THR* 1.3 75.5 + - - +
75D LEU* 1.3 63.5 + - - +
76D LYS 3.1 1.6 - - - -
77D THR* 2.8 24.8 + - - -
78D LYS* 3.3 22.1 + - - +
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Residues in contact with LEU 75 (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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24D ILE* 4.1 33.4 - - + +
27D VAL* 3.5 36.3 - - + +
28D VAL* 4.5 5.2 - - + -
31D LEU* 5.0 2.2 - - + -
71D HIS 3.0 9.6 + - - +
72D LEU* 3.2 21.5 + - + +
74D SER* 1.3 75.2 - - - +
76D LYS* 1.3 58.7 + - - +
77D THR 2.9 5.8 + - - -
78D LYS* 3.0 16.5 + - + +
79D PHE* 3.5 14.6 - - + -
91D TRP* 4.0 19.7 - - + -
133D PHE* 3.6 33.7 - - + -
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Residues in contact with LYS 76 (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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72D LEU 3.0 14.1 + - - +
73D THR* 3.3 38.6 - - - +
74D SER 3.1 0.4 - - - -
75D LEU* 1.3 75.2 - - - +
77D THR* 1.3 61.8 + - + +
78D LYS 3.5 0.4 - - - -
79D PHE* 3.3 27.1 - - - +
81D ALA* 5.2 4.7 + - - +
124D GLY 3.7 13.4 + - - +
125D ILE* 5.3 1.1 - - + -
126D GLU* 2.9 39.9 + - - +
132D GLY* 5.6 1.8 - - - -
133D PHE* 3.9 26.9 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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