Contacts of the helix formed by residues 52 - 76 (chain C) in PDB entry 1J1J
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 GLN 52 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C PHE* 1.3 106.1 - - + +
53C ASP* 1.3 58.6 + - - +
54C ILE 3.2 0.7 - - - -
55C PRO* 2.9 25.9 - - + +
56C LYS* 3.8 7.6 + - - +
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Residues in contact with ASP 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLY 4.9 1.6 - - - +
45C VAL* 4.2 8.2 - - + +
51C PHE* 2.7 23.2 - - + +
52C GLN* 1.3 80.1 - - - +
54C ILE* 1.3 65.7 + - - +
56C LYS* 2.8 22.1 + - - +
57C ARG* 2.8 57.0 + - - +
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Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C VAL* 3.2 41.7 - - + +
50C GLY* 6.1 2.2 - - - -
51C PHE 3.4 17.3 - - - +
53C ASP* 1.3 77.4 - - - +
55C PRO* 1.3 71.5 - - + +
57C ARG* 3.3 2.2 + - - +
58C CYS* 3.0 30.0 + - - -
108C LEU* 3.7 44.6 - - + +
109C GLU* 5.5 0.4 - - - -
166C ARG* 4.3 20.9 - - - +
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Residues in contact with PRO 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C PHE 4.4 0.4 - - - +
52C GLN* 2.9 30.7 - - + +
54C ILE* 1.3 90.9 - - + +
56C LYS* 1.3 61.7 + - - +
58C CYS* 3.3 6.9 + - + +
59C LEU* 3.1 34.5 + - + +
109C GLU* 6.0 1.6 - - + -
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Residues in contact with LYS 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C GLN 3.8 3.3 + - - +
53C ASP* 2.8 26.8 + - - +
55C PRO* 1.3 82.2 - - - +
57C ARG* 1.3 62.3 + - + +
59C LEU* 3.4 8.8 + - - +
60C LYS* 3.2 57.8 + - + +
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C THR* 3.9 3.8 + - - +
41C LEU* 2.5 58.2 + - + +
42C LEU* 4.2 5.8 - - + +
44C GLY* 3.2 26.6 + - - -
45C VAL* 3.1 34.8 - - + +
53C ASP* 2.8 47.0 + - - +
54C ILE* 3.9 3.4 - - - +
56C LYS* 1.3 71.4 - - + +
58C CYS* 1.3 61.0 + - - +
60C LYS* 3.8 8.0 - - + +
61C ALA* 2.8 30.0 + - - +
108C LEU* 6.2 0.7 - - + -
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Residues in contact with CYS 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 4.6 2.2 - - - -
54C ILE* 3.0 28.4 + - - +
55C PRO* 3.7 6.7 - - + +
56C LYS 3.3 0.2 - - - -
57C ARG* 1.3 77.3 - - - +
59C LEU* 1.3 57.3 + - + +
61C ALA* 3.4 8.2 + - - +
62C ARG* 2.9 32.0 + - - +
105C VAL* 4.0 10.9 - - + +
108C LEU* 3.7 37.5 - - - -
109C GLU* 3.6 33.9 - - + +
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Residues in contact with LEU 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C PRO* 3.1 25.3 + - + +
56C LYS* 3.7 8.1 - - - +
57C ARG 3.2 0.2 - - - -
58C CYS* 1.3 75.3 - - + +
60C LYS* 1.3 61.1 + - + +
62C ARG* 3.1 19.5 + - + +
63C GLU* 2.9 32.5 + - + +
109C GLU* 5.4 2.5 - - - +
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Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 3.6 28.9 - - + -
56C LYS* 3.2 49.9 + - + +
57C ARG* 3.3 5.1 + - + +
59C LEU* 1.3 73.9 - - + +
61C ALA* 1.3 66.8 + - - +
63C GLU* 3.1 21.7 + - - +
64C HIS* 3.1 29.8 + - + +
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ILE* 4.1 13.9 - - + +
41C LEU* 3.7 10.5 - - + +
42C LEU* 3.7 22.7 - - + -
57C ARG 2.8 17.9 + - - +
58C CYS 3.4 6.5 - - - +
60C LYS* 1.3 77.7 - - - +
62C ARG* 1.3 56.8 + - - +
64C HIS* 3.3 8.3 + - - +
65C PHE* 3.0 31.6 + - - -
105C VAL* 3.9 13.9 - - + -
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C CYS 2.9 14.1 + - - +
59C LEU* 3.1 22.6 + - + +
61C ALA* 1.3 76.7 - - - +
63C GLU* 1.3 67.6 + - - +
65C PHE* 3.0 23.1 + - + +
66C GLY* 3.3 7.1 + - - -
69C LYS* 5.4 1.7 - - - -
105C VAL* 3.8 11.5 - - + +
106C VAL* 4.1 18.0 - - - +
109C GLU* 2.9 40.0 + - - -
122C ILE* 4.1 26.6 - - + +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LEU* 2.9 18.8 + - + +
60C LYS* 3.1 27.3 + - - +
62C ARG* 1.3 74.3 - - - +
64C HIS* 1.3 60.0 + - + +
66C GLY* 2.8 23.4 + - - -
67C THR* 3.7 3.8 + - - -
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Residues in contact with HIS 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C THR* 3.8 7.0 - - + +
37C GLU* 3.5 35.5 + - + +
38C ILE* 3.5 22.9 - - + -
41C LEU* 3.3 27.0 - - + +
60C LYS* 3.1 24.6 + - + +
61C ALA 3.4 7.6 - - - +
62C ARG 3.2 0.2 - - - -
63C GLU* 1.3 79.3 - - + +
65C PHE* 1.3 56.8 + - - +
67C THR* 2.8 34.0 + - - -
68C VAL* 3.2 7.1 + - - +
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Residues in contact with PHE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 4.0 18.6 - - + -
61C ALA 3.0 26.2 + - - -
62C ARG* 3.0 17.3 + - + +
64C HIS* 1.3 75.4 - - - +
66C GLY* 1.3 61.7 + - - +
68C VAL* 3.1 19.2 + - + +
69C LYS* 3.0 32.8 + - - +
98C LEU* 4.0 14.1 - - + -
101C LEU* 4.0 11.9 - - + -
102C ALA* 3.7 28.3 - - + -
105C VAL* 4.1 24.0 - - + -
122C ILE* 3.7 29.6 - - + +
123C LEU* 3.8 22.4 - - + -
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Residues in contact with GLY 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ARG 3.3 4.9 + - - -
63C GLU 2.8 13.3 + - - -
65C PHE* 1.3 78.4 - - - +
67C THR* 1.3 59.9 + - - +
69C LYS* 3.6 19.7 + - - +
70C THR* 3.3 23.4 + - - -
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Residues in contact with THR 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C THR* 3.7 17.0 - - + +
63C GLU 3.7 3.6 + - - -
64C HIS* 2.8 21.3 + - - -
66C GLY* 1.3 77.7 - - - +
68C VAL* 1.3 62.8 + - - +
70C THR* 3.3 7.3 + - - -
71C HIS* 3.1 49.4 + - + +
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Residues in contact with VAL 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 5.3 6.7 - - + +
34C THR* 3.5 28.7 - - + -
38C ILE* 4.2 5.4 - - + -
64C HIS 3.7 5.4 - - - +
65C PHE* 3.1 23.5 + - + +
67C THR* 1.3 75.8 - - - +
69C LYS* 1.3 65.2 + - + +
71C HIS* 3.4 6.5 + - - +
72C LEU* 3.0 31.4 + - + +
98C LEU* 3.8 35.2 - - + -
123C LEU* 3.8 20.6 - - + -
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Residues in contact with LYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C ARG 5.4 1.6 - - - -
65C PHE* 3.0 20.1 + - - +
66C GLY* 3.7 17.9 - - - +
67C THR 3.3 0.2 - - - -
68C VAL* 1.3 75.5 - - - +
70C THR* 1.3 57.4 + - - +
72C LEU* 3.9 1.9 - - - +
73C THR* 3.0 31.7 + - - -
121C GLU 3.1 18.8 + - - -
122C ILE* 2.6 34.3 + - - +
123C LEU 3.6 19.1 - - - +
124C GLY* 4.1 9.5 - - - +
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Residues in contact with THR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLY 3.3 11.4 + - - -
67C THR* 3.3 11.4 + - - -
68C VAL 3.2 0.4 - - - -
69C LYS* 1.3 77.0 - - - +
71C HIS* 1.3 68.7 + - + +
73C THR* 3.0 10.9 + - + -
74C SER* 2.9 27.1 + - - -
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 3.3 11.3 - - + +
30C SER* 3.0 36.8 + - - +
31C LEU* 3.1 24.5 + - + +
34C THR* 4.1 8.6 + - - -
67C THR* 3.1 37.8 + - + +
68C VAL* 4.0 3.7 - - - +
70C THR* 1.3 87.5 - - + +
72C LEU* 1.3 50.7 + - - +
74C SER* 3.1 10.9 + - - -
75C LEU 2.7 30.3 + - - -
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Residues in contact with LEU 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LEU* 3.5 27.1 - - + -
68C VAL* 3.0 28.6 + - + +
69C LYS 3.9 3.8 - - - +
71C HIS* 1.3 72.3 - - - +
73C THR* 1.3 67.4 + - - +
75C LEU* 3.0 19.3 + - + +
76C LYS* 2.9 29.7 + - + +
91C TRP* 6.3 0.4 - - + -
95C LEU* 5.5 5.8 - - + -
98C LEU* 4.8 5.4 - - + -
123C LEU* 3.4 41.7 - - + +
124C GLY 6.0 0.2 - - - -
125C ILE* 3.6 21.5 - - + -
133C PHE* 4.3 14.3 - - + -
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Residues in contact with THR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LYS* 3.0 19.6 + - - +
70C THR* 3.2 13.1 - - + +
72C LEU* 1.3 77.1 - - - +
74C SER* 1.3 64.1 + - - +
76C LYS* 3.3 23.3 + - + +
77C THR* 3.5 11.8 + - - +
124C GLY 5.1 5.7 + - - -
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C VAL* 4.1 7.6 - - - +
70C THR* 2.9 14.6 + - - -
71C HIS* 3.3 14.1 - - - -
73C THR* 1.3 77.2 - - - +
75C LEU* 1.3 60.1 + - - +
77C THR* 2.9 30.2 + - - -
78C LYS* 3.6 25.1 + - - -
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Residues in contact with LEU 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 4.1 34.8 - - + +
27C VAL* 3.7 22.9 - - + -
28C VAL* 4.9 2.0 - - + -
31C LEU* 4.4 9.4 - - + -
71C HIS 2.7 15.9 + - - +
72C LEU* 3.0 22.6 + - + +
74C SER* 1.3 70.6 - - - +
76C LYS* 1.3 62.1 + - - +
77C THR 2.9 6.4 + - - -
78C LYS* 3.1 14.1 + - + +
79C PHE* 3.5 10.8 - - + -
91C TRP* 3.8 20.9 - - + +
133C PHE* 3.6 34.5 - - + -
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Residues in contact with LYS 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 2.9 19.5 + - + +
73C THR* 3.6 16.1 - - + +
74C SER 3.3 0.4 - - - -
75C LEU* 1.3 76.4 - - - +
77C THR* 1.3 59.4 - - - +
78C LYS 3.5 0.2 - - - -
79C PHE* 3.5 25.0 - - - +
81C ALA* 5.4 8.3 + - + +
124C GLY 5.8 1.3 - - - +
125C ILE* 5.4 4.9 - - + -
126C GLU* 3.0 38.6 + - - +
132C GLY* 3.7 12.5 + - - -
133C PHE* 3.7 24.7 - - + -
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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