Contacts of the helix formed by residues 50 - 79 (chain A) in PDB entry 2JWA
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 50 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA 4.6 1.1 - - - +
49A SER* 1.3 86.7 - - - +
51A LEU* 1.3 65.3 + - + +
52A THR 3.0 1.8 - - - -
53A SER* 2.7 36.3 + - - -
54A ILE* 3.6 7.1 + - - +
143B PRO 5.6 5.6 - - - +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A SER* 3.4 2.4 - - - -
50A PRO* 1.3 85.2 - - + +
52A THR* 1.3 62.2 + - - +
54A ILE* 3.5 13.0 + - + +
55A ILE* 3.0 35.6 + - + +
144B ALA* 4.2 23.8 - - + -
145B GLU 4.5 1.8 - - - +
146B GLN* 3.1 53.6 - - + +
147B ARG* 3.4 27.8 - - + +
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Residues in contact with THR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ARG* 4.6 6.8 - - - +
48A ALA* 5.8 0.9 - - - -
49A SER* 3.2 31.8 + - - -
50A PRO 3.0 0.2 - - - -
51A LEU* 1.3 79.2 - - - +
53A SER* 1.3 56.0 + - - +
55A ILE* 4.0 0.9 - - - +
56A SER* 2.9 31.0 + - - -
147B ARG* 5.3 2.3 - - - +
152B THR* 4.0 30.2 + - + +
155B ILE* 3.5 46.2 - - + -
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Residues in contact with SER 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A SER 4.1 1.7 + - - -
50A PRO* 2.7 16.2 + - - -
52A THR* 1.3 76.4 - - - +
54A ILE* 1.3 61.1 + - - -
56A SER* 2.6 23.3 + - - -
57A ALA* 2.8 22.8 + - - +
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A PRO 4.3 9.4 - - - +
51A LEU* 3.5 15.3 + - + +
53A SER* 1.3 79.2 - - - +
55A ILE* 1.3 61.5 + - + +
57A ALA* 3.5 6.0 + - + +
58A VAL* 2.9 41.7 + - + +
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LEU* 3.0 31.9 + - + +
54A ILE* 1.3 77.7 - - + +
56A SER* 1.3 66.1 + - - +
58A VAL* 3.3 7.3 + - + +
59A VAL* 3.1 38.5 + - + +
147B ARG* 4.5 18.2 - - + +
148B ALA* 5.7 0.4 - - - +
152B THR* 3.5 33.0 - - + -
156B SER* 4.5 4.3 - - - -
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Residues in contact with SER 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A THR 2.9 18.3 + - - -
53A SER* 2.6 23.4 + - - -
55A ILE* 1.3 76.6 - - - +
57A ALA* 1.3 62.7 + - - +
59A VAL* 3.4 4.2 + - - +
60A GLY 3.2 17.0 + - - -
155B ILE* 4.4 5.6 - - - +
156B SER* 3.6 31.8 - - - +
159B VAL* 3.7 30.0 - - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A SER 2.8 20.6 + - - +
54A ILE* 3.7 7.4 - - + +
56A SER* 1.3 73.4 + - - +
58A VAL* 1.3 65.4 + - + +
60A GLY* 3.1 2.4 + - - -
61A ILE* 2.9 39.5 + - + +
159B VAL* 4.8 7.2 - - - -
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE* 2.9 34.0 + - + +
55A ILE* 3.3 7.8 + - - +
57A ALA* 1.3 75.8 - - + +
59A VAL* 1.3 59.8 - - + +
61A ILE* 3.4 7.7 + - + +
62A LEU* 2.8 43.3 + - + +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 3.1 22.1 + - + +
56A SER 3.6 6.1 - - - +
57A ALA 3.2 0.2 - - - -
58A VAL* 1.3 79.6 - - + +
60A GLY* 1.3 62.2 + - - +
62A LEU* 3.2 9.9 + - + +
63A LEU* 3.0 30.4 + - + +
156B SER* 3.7 35.7 - - - +
157B ALA* 4.7 5.2 - - - +
160B GLY* 5.1 3.1 - - - -
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Residues in contact with GLY 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER 3.2 7.2 + - - -
57A ALA 3.1 6.4 + - - -
59A VAL* 1.3 80.2 - - - +
61A ILE* 1.3 59.8 + - - +
63A LEU* 3.3 3.2 + - - +
64A VAL* 2.9 32.9 + - - +
159B VAL* 4.8 3.8 - - - -
160B GLY* 3.4 28.7 - - - -
163B LEU* 4.8 7.6 - - - -
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Residues in contact with ILE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 2.9 33.6 + - + +
58A VAL* 3.9 6.1 - - + +
60A GLY* 1.3 75.7 - - - +
62A LEU* 1.3 59.7 + - - +
64A VAL* 3.6 8.0 + - + +
65A VAL* 3.0 35.8 + - + +
163B LEU* 5.4 7.6 - - + -
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A VAL* 2.8 28.5 + - + +
59A VAL* 3.5 9.6 - - + +
61A ILE* 1.3 75.7 - - - +
63A LEU* 1.3 70.8 + - + +
65A VAL* 3.9 4.3 - - - +
66A VAL* 2.9 42.9 + - + +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL* 3.0 23.0 + - + +
60A GLY* 3.8 5.8 - - - +
62A LEU* 1.3 84.0 - - + +
64A VAL* 1.3 62.6 + - - +
66A VAL* 3.6 8.8 + - + +
67A LEU* 3.1 27.9 + - + +
160B GLY* 4.6 11.2 - - - +
161B ILE* 4.9 8.7 - - + +
164B VAL* 3.9 25.4 - - + -
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLY 2.9 26.4 + - - +
61A ILE* 3.7 7.6 - - + +
63A LEU* 1.3 73.2 - - - +
65A VAL* 1.3 70.4 + - + +
67A LEU* 2.9 17.8 + - + +
68A GLY* 3.0 11.8 + - - -
163B LEU* 4.0 26.2 - - + -
164B VAL* 4.8 13.9 - - + +
167B LEU* 5.7 13.2 - - + -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ILE* 3.0 29.2 + - + +
62A LEU* 3.9 5.4 - - - +
64A VAL* 1.3 78.2 - - + +
66A VAL* 1.3 65.7 + - + +
68A GLY* 3.1 3.8 + - - +
69A VAL* 3.1 37.6 + - + +
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 2.9 37.2 + - + +
63A LEU* 3.8 9.2 - - + +
65A VAL* 1.3 78.3 - - + +
67A LEU* 1.3 60.5 + - + +
69A VAL* 3.5 7.1 + - + +
70A VAL* 2.9 41.8 + - + +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.1 16.3 + - + +
64A VAL* 2.9 13.7 + - + +
66A VAL* 1.3 75.2 - - + +
68A GLY* 1.3 66.7 + - - +
70A VAL* 3.2 8.3 + - + +
71A PHE* 2.9 37.8 + - + +
164B VAL* 5.5 15.0 - - + -
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL 3.0 12.4 + - - -
65A VAL* 3.1 3.5 + - - -
67A LEU* 1.3 76.7 - - - +
69A VAL* 1.3 62.0 + - - +
71A PHE* 3.8 5.0 - - - +
72A GLY* 2.9 22.9 + - - -
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Residues in contact with VAL 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 3.1 27.7 + - + +
66A VAL* 3.7 8.5 - - - +
68A GLY* 1.3 76.6 - - - +
70A VAL* 1.3 64.3 + - + +
72A GLY* 3.9 1.0 - - - -
73A ILE* 3.1 48.7 + - + +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL* 2.9 29.6 + - + +
67A LEU* 3.6 10.3 - - + +
69A VAL* 1.3 77.5 - - + +
71A PHE* 1.3 56.0 + - - +
73A ILE* 3.7 5.9 - - - +
74A LEU* 2.7 61.6 + - + +
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Residues in contact with PHE 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 2.9 29.0 + - + +
68A GLY* 3.8 5.6 - - - +
70A VAL* 1.3 74.6 - - - +
72A GLY* 1.3 65.7 + - - +
74A LEU* 3.1 14.7 + - + +
75A ILE* 2.9 61.3 + - + +
171B PHE* 4.9 19.5 - + - -
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Residues in contact with GLY 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A GLY 2.9 17.1 + - - -
69A VAL* 3.9 0.9 - - - -
71A PHE* 1.3 77.2 - - - +
73A ILE* 1.3 61.5 + - - +
75A ILE* 3.3 8.2 + - - +
76A LYS* 3.0 38.7 + - - +
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 3.1 37.2 + - + +
70A VAL* 3.8 4.9 - - - +
72A GLY* 1.3 74.7 - - - +
74A LEU* 1.3 63.3 + - + +
76A LYS* 3.1 13.3 + - + +
77A ARG* 2.9 33.5 + - + +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 2.7 50.0 + - + +
71A PHE* 3.1 15.0 + - + +
73A ILE* 1.3 75.6 - - + +
75A ILE* 1.3 60.6 + - + +
76A LYS 3.1 0.2 + - - -
77A ARG* 3.2 5.1 + - + +
78A ARG* 2.9 54.1 + - + +
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Residues in contact with ILE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PHE* 2.9 69.0 + - + +
72A GLY* 3.9 5.4 - - - +
74A LEU* 1.3 73.4 - - + +
76A LYS* 1.3 57.0 + - - +
78A ARG* 3.9 9.3 - - - +
79A GLN* 2.9 27.2 + - - +
82A ILE* 4.5 17.9 - - + -
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLY* 3.0 26.1 + - - +
73A ILE* 3.3 16.4 - - + +
75A ILE* 1.3 75.1 - - - +
77A ARG* 1.3 67.7 + - + +
79A GLN* 3.2 20.4 + - - +
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A ILE* 2.9 25.0 + - + +
74A LEU* 3.8 5.6 - - + +
76A LYS* 1.3 77.1 - - + +
78A ARG* 1.3 63.9 + - + +
79A GLN* 3.2 5.4 + - - +
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Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 2.9 43.2 + - + +
75A ILE* 4.1 7.6 - - - +
77A ARG* 1.3 78.3 - - + +
79A GLN* 1.3 74.9 + - - +
80A GLN 3.4 5.7 - - - +
81A LYS 4.3 3.6 - - - +
82A ILE* 3.8 34.4 - - + +
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Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A ILE* 2.9 18.6 + - - -
76A LYS* 3.2 13.2 + - - +
77A ARG 3.1 6.7 - - - +
78A ARG* 1.3 87.5 - - - +
80A GLN* 1.3 85.7 + - - +
82A ILE* 3.4 17.3 - - - +
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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