Contacts of the helix formed by residues 54 - 81 (chain D) in PDB entry 4GCK
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 SER 54 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D TYR* 3.7 4.5 - - - -
52D PHE* 3.1 13.7 - - - +
53D PRO* 1.3 83.4 - - - +
55D LYS* 1.3 63.9 + - - +
56D THR* 3.4 11.2 + - - -
57D ARG* 3.1 32.6 + - - +
58D MET* 3.5 13.9 - - - +
34Z C 3.6 23.3 - - - -
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Residues in contact with LYS 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 6.1 1.1 - - + -
31D ARG* 4.0 6.3 - - - +
32D ILE* 2.4 36.7 + - + +
34D THR* 4.0 17.9 - - + -
37D LEU* 5.3 4.0 - - + -
54D SER* 1.3 72.2 - - - +
56D THR* 1.3 66.0 + - - +
57D ARG 3.1 0.2 - - - -
58D MET* 2.9 39.2 + - + +
59D PHE* 3.2 31.5 + - + -
116D PHE* 5.4 0.4 - - - +
117D GLU* 3.3 29.7 + - - +
33Z A 2.6 35.2 + - - -
34Z C 2.9 18.0 + - - +
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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
----------------------------------------------------------
54D SER* 3.2 10.8 + - - -
55D LYS* 1.3 80.1 - - - +
57D ARG* 1.3 59.3 + - - +
59D PHE* 3.2 2.8 + - - -
60D ASP* 3.0 31.4 + - - +
117D GLU* 4.9 3.1 - - - +
118D GLN* 3.6 28.2 + - + +
120D ARG* 2.9 34.8 - - - +
121D LEU* 3.7 19.3 - - + +
34Z C 5.2 2.8 + - - -
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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
----------------------------------------------------------
12D ARG* 5.4 3.1 + - - +
52D PHE* 4.0 9.9 - - + -
53D PRO* 3.3 33.2 - - + -
54D SER* 3.1 26.1 + - - +
55D LYS 3.1 0.6 - - - -
56D THR* 1.3 75.3 - - - +
58D MET* 1.3 67.2 + - - +
60D ASP* 2.4 39.1 + - - +
61D SER* 3.0 26.2 + - - -
120D ARG* 2.7 27.9 - - - +
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Residues in contact with MET 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 4.0 13.7 - - - -
16D LEU* 3.4 16.7 - - + +
19D LEU* 3.8 17.5 - - + -
34D THR* 4.8 7.2 - - + -
37D LEU* 3.4 31.4 - - + -
48D LEU* 5.3 9.2 - - + +
49D TYR* 5.1 4.7 - - + +
52D PHE* 3.6 30.7 - - + -
54D SER 3.5 7.2 - - - +
55D LYS* 2.9 49.3 + - + +
57D ARG* 1.3 77.5 - - - +
59D PHE* 1.3 59.0 + - + +
61D SER* 3.3 4.9 + - - -
62D LEU* 3.0 23.9 + - - +
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Residues in contact with PHE 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 4.1 25.4 - - + -
23D LEU* 3.9 25.6 - - + -
32D ILE* 5.5 5.4 - - + -
55D LYS* 3.2 28.8 + - + -
56D THR 3.2 3.3 + - - +
58D MET* 1.3 76.5 - - - +
60D ASP* 1.3 56.0 + - - +
62D LEU* 3.1 6.5 + - + +
63D ILE* 2.7 41.9 + - + +
108D ILE* 3.9 21.1 - - + -
113D ALA* 4.3 15.5 - - + -
114D LEU* 4.0 14.1 - - + -
117D GLU* 3.6 35.7 - - + -
121D LEU* 3.8 21.1 - - + -
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Residues in contact with ASP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D THR* 3.0 17.8 + - - +
57D ARG* 2.4 45.0 + - - +
59D PHE* 1.3 76.0 - - - +
61D SER* 1.3 52.3 + - - +
63D ILE* 3.2 1.8 + - - -
64D GLU* 2.8 33.2 + - - +
120D ARG* 2.5 29.7 + - - -
121D LEU* 3.6 9.6 - - - +
124D ARG* 2.8 38.7 + - - +
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ARG* 3.6 24.1 + - - -
16D LEU* 3.7 25.4 - - - -
52D PHE* 3.7 5.0 - - - -
57D ARG 3.0 15.2 + - - -
58D MET 3.4 9.6 - - - -
60D ASP* 1.3 76.9 - - - +
62D LEU* 1.3 62.3 + - - +
64D GLU* 3.2 10.4 + - - +
65D PHE* 3.0 22.2 + - - +
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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
----------------------------------------------------------
16D LEU* 3.9 38.4 - - + +
19D LEU* 3.5 38.8 - - + -
20D ALA* 4.5 5.4 - - + +
23D LEU* 4.0 6.5 - - + -
58D MET 3.0 7.8 + - - +
59D PHE* 3.1 9.2 + - + +
61D SER* 1.3 78.5 - - - +
63D ILE* 1.3 59.6 + - - +
65D PHE* 3.3 11.9 + - + +
66D ILE* 3.1 28.5 + - - +
105D LEU* 3.7 20.6 - - + +
108D ILE* 3.9 24.7 - - + -
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D PHE 2.7 23.9 + - - +
60D ASP* 3.6 6.3 - - - +
62D LEU* 1.3 69.6 - - - +
64D GLU* 1.3 67.1 + - - +
66D ILE* 3.2 8.9 + - + +
67D GLU* 2.9 26.7 + - + +
108D ILE* 3.8 25.1 - - + -
114D LEU* 4.6 3.1 - - + -
121D LEU* 3.7 47.3 - - + +
124D ARG* 3.9 31.0 - - + +
125D ILE* 3.9 22.2 - - + -
128D LEU* 5.9 3.1 - - + -
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Residues in contact with GLU 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ASP* 2.8 16.0 + - - +
61D SER* 3.2 8.8 + - - +
63D ILE* 1.3 72.3 - - - +
65D PHE* 1.3 64.2 + - - +
67D GLU* 3.2 5.7 + - - +
68D ASP* 2.8 39.2 + - - +
124D ARG* 2.9 40.4 + - - +
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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
----------------------------------------------------------
61D SER 3.0 12.6 + - - +
62D LEU* 3.4 14.8 - - + +
63D ILE 3.2 0.2 - - - -
64D GLU* 1.3 76.8 - - - +
66D ILE* 1.3 59.8 + - - +
68D ASP* 3.2 7.3 + - + +
69D SER* 2.7 49.7 + - - -
73D ARG* 5.7 3.8 - - - -
98D PHE* 4.1 9.9 - + - -
102D ASN* 4.8 5.4 - - - -
105D LEU* 3.6 31.2 - - + -
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Residues in contact with ILE 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 LEU 3.1 18.5 + - - +
63D ILE* 3.2 14.1 + - + +
65D PHE* 1.3 76.0 - - - +
67D GLU* 1.3 63.6 + - - +
69D SER* 3.5 0.5 + - - -
70D LEU* 3.0 32.3 + - + +
98D PHE* 3.8 24.9 - - + -
105D LEU* 4.0 47.1 - - + +
108D ILE* 4.2 16.6 - - + -
109D LEU* 4.3 14.4 - - + -
125D ILE* 5.0 3.4 - - + -
128D LEU* 3.9 20.2 - - + -
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D ILE* 2.9 17.4 + - + +
64D GLU* 3.5 5.3 - - - +
66D ILE* 1.3 75.5 - - - +
68D ASP* 1.3 69.5 + - - +
70D LEU* 5.0 0.2 - - - -
71D ILE* 2.8 36.2 + - + +
124D ARG* 3.9 27.8 + - - +
128D LEU* 3.7 39.4 - - + +
131D ARG* 4.1 21.4 + - - +
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Residues in contact with ASP 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D GLU* 2.8 35.1 + - - +
65D PHE* 3.7 7.0 - - + +
67D GLU* 1.3 75.2 - - - +
69D SER* 1.3 63.0 + - - +
71D ILE* 5.0 2.0 - - - -
72D THR* 2.6 38.3 + - - +
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Residues in contact with SER 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D PHE* 2.7 46.6 + - - -
66D ILE 3.7 1.8 - - - -
68D ASP* 1.3 77.3 - - - +
70D LEU* 1.3 58.2 + - - +
73D ARG* 2.7 59.7 + - - +
98D PHE* 3.5 25.4 - - - -
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Residues in contact with LEU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ILE* 3.0 35.5 + - + +
67D GLU* 4.1 2.5 - - - +
69D SER* 1.3 81.3 - - - +
71D ILE* 1.3 59.7 + - + +
73D ARG* 3.4 1.7 + - - -
74D ILE* 2.8 36.9 + - + +
94D LEU* 3.8 24.0 - - + +
95D ILE* 4.6 15.3 - - + +
98D PHE* 3.7 37.9 - - + -
109D LEU* 4.8 9.9 - - + -
128D LEU* 4.2 6.7 - - + -
132D ILE* 4.1 28.3 - - + -
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Residues in contact with ILE 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D GLU* 2.8 32.9 + - + +
68D ASP* 4.3 2.2 - - - +
70D LEU* 1.3 75.8 - - - +
72D THR* 1.3 64.1 + - - +
74D ILE* 3.2 10.4 + - + +
75D ASN* 3.0 39.0 + - - +
128D LEU* 4.3 12.1 - - + -
131D ARG* 3.7 58.8 - - + +
132D ILE* 4.4 12.1 - - + -
135D GLN* 5.7 6.5 - - + -
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Residues in contact with THR 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D ASP* 2.6 30.8 + - - +
69D SER 3.8 2.7 - - - -
71D ILE* 1.3 78.7 - - - +
73D ARG* 1.3 71.9 + - - +
75D ASN* 3.4 9.2 + - - +
76D LEU* 3.1 39.9 + - + +
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Residues in contact with ARG 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D PHE* 5.7 3.8 - - - -
69D SER* 2.7 57.1 + - - +
72D THR* 1.3 85.7 - - - +
74D ILE* 1.3 65.8 + - - +
76D LEU* 3.3 14.7 + - - +
77D ILE* 3.0 26.2 + - + +
94D LEU* 3.5 37.5 - - + +
98D PHE* 5.3 6.4 - - + -
101D ARG* 5.2 10.0 - - - +
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Residues in contact with ILE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D LEU* 2.8 30.6 + - + +
71D ILE* 3.2 13.7 + - + +
73D ARG* 1.3 77.1 - - - +
75D ASN* 1.3 65.1 + - - +
77D ILE* 3.0 9.9 + - + +
78D LEU* 3.0 32.7 + - + +
91D ILE* 3.4 53.2 - - + +
94D LEU* 3.2 23.1 - - + -
95D ILE* 5.3 3.4 - - + -
132D ILE* 5.5 7.6 - - + -
135D GLN* 4.2 19.5 - - + -
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Residues in contact with ASN 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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71D ILE* 3.0 33.2 + - - +
72D THR* 3.7 9.2 - - - +
73D ARG 3.3 0.2 - - - -
74D ILE* 1.3 75.8 - - - +
76D LEU* 1.3 66.3 + - + +
78D LEU* 3.2 11.4 + - - +
79D LYS* 3.1 39.4 + - - +
135D GLN* 4.1 18.2 + - - -
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D THR* 3.1 29.5 + - + +
73D ARG* 3.5 17.3 - - + +
74D ILE 3.2 0.2 - - - -
75D ASN* 1.3 76.8 - - + +
77D ILE* 1.3 62.6 + - + +
79D LYS* 3.0 13.7 + - + +
80D ASP* 2.9 38.3 + - - +
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Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ARG* 3.0 20.7 + - + +
74D ILE* 3.0 13.8 + - + +
76D LEU* 1.3 75.1 - - + +
78D LEU* 1.3 64.6 + - + +
80D ASP* 3.1 4.5 + - + -
81D GLU* 2.8 31.9 + - + +
87D ARG* 4.2 21.8 - - - +
90D LEU* 3.5 52.5 - - + +
91D ILE* 4.3 11.4 - - + -
94D LEU* 5.3 4.9 - - + -
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ILE* 3.0 19.4 + - + +
75D ASN* 3.2 13.9 + - - +
77D ILE* 1.3 77.6 - - - +
79D LYS* 1.3 62.7 + - + +
81D GLU 3.2 6.6 - - - +
87D ARG* 2.9 50.0 + - + +
91D ILE* 4.4 8.7 - - + -
135D GLN* 3.5 35.2 - - - +
138D GLN* 4.7 6.7 - - - +
139D VAL* 3.5 27.8 - - + -
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Residues in contact with LYS 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ASN* 3.1 26.5 + - - +
76D LEU* 3.0 17.2 + - + +
78D LEU* 1.3 79.0 - - + +
80D ASP* 1.3 66.7 + - - +
81D GLU 5.2 0.3 - - - -
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Residues in contact with ASP 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D LEU* 2.9 35.6 + - - +
77D ILE* 4.1 3.8 - - + +
79D LYS* 1.3 85.1 - - - +
81D GLU* 1.3 60.3 + - + +
82D LYS 4.3 0.4 + - - -
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Residues in contact with GLU 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ILE* 2.8 14.8 + - + +
78D LEU 3.2 9.0 - - - +
79D LYS 3.5 1.4 - - - -
80D ASP* 1.3 83.0 - - + +
82D LYS* 1.3 57.4 + - - +
83D ASP* 2.8 29.6 + - - +
86D ALA* 3.4 32.4 - - + +
87D ARG* 2.6 44.5 + - + +
90D LEU* 4.1 20.5 - - + +
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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