Contacts of the helix formed by residues 55 - 84 (chain A) in PDB entry 4GUP
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 ALA 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASN 3.7 4.8 + - - +
54A LEU* 1.4 76.0 - - - +
56A PRO* 1.4 68.8 - - + +
57A ASP* 3.0 29.9 + - + +
58A HIS* 3.1 19.3 + - + +
59A TRP* 3.7 3.3 - - - -
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Residues in contact with PRO 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A LEU 4.6 1.6 - - - +
55A ALA* 1.4 83.6 - - + +
57A ASP* 1.4 61.6 - - - +
58A HIS 3.3 0.2 - - - -
59A TRP* 3.5 16.0 + - + +
60A GLU* 3.2 43.7 + - - +
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Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ALA* 3.0 20.6 + - + +
56A PRO* 1.4 78.4 - - - +
58A HIS* 1.3 57.1 + - - +
60A GLU* 3.6 10.4 + - - +
61A ARG* 3.0 49.2 + - - +
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Residues in contact with HIS 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 5.7 2.4 + - - -
34A THR* 5.7 1.6 - - + -
43A LYS* 5.2 7.2 - - + -
50A MET* 5.5 0.9 - - + -
54A LEU* 3.5 39.6 - - + +
55A ALA* 3.1 14.4 + - + +
57A ASP* 1.3 78.0 - - - +
59A TRP* 1.3 78.9 + + + +
61A ARG* 4.0 15.4 - - - +
62A TYR* 3.2 67.6 + + - +
164A TRP* 3.5 33.0 - + - -
168A PHE* 5.0 6.5 - + - -
301A 6FP 5.9 0.8 - + - -
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Residues in contact with TRP 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR* 3.6 31.2 - - + -
42A GLN* 5.0 5.4 - - - +
43A LYS* 3.8 37.9 - - + +
44A GLU 3.9 9.6 - - - -
45A PRO* 3.7 34.1 - - + +
50A MET* 3.6 30.6 + - + -
51A ALA* 4.7 3.8 + - - +
54A LEU* 3.6 30.8 + - + +
55A ALA 3.7 13.2 - - - -
56A PRO* 3.5 14.5 + - + +
57A ASP 3.4 0.2 - - - -
58A HIS* 1.3 82.0 - + - +
60A GLU* 1.3 55.7 + - + +
62A TYR* 3.5 2.3 + - - +
63A THR* 2.8 41.7 + - - -
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 5.4 6.5 - - - +
56A PRO* 3.2 34.9 + - - +
57A ASP* 3.9 9.8 - - - +
59A TRP* 1.3 78.5 - - + +
61A ARG* 1.3 61.1 + - - +
63A THR* 3.4 4.9 + - - -
64A GLN* 3.1 37.9 + - - +
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Residues in contact with ARG 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 3.0 41.9 + - - +
58A HIS* 4.0 27.3 - - - +
60A GLU* 1.3 75.1 - - - +
62A TYR* 1.3 70.4 + - + +
64A GLN* 3.7 7.8 + - - +
65A LEU* 3.2 34.2 + - + +
164A TRP* 5.4 4.2 - - - -
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Residues in contact with TYR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 3.7 21.5 - - + -
58A HIS* 3.2 58.4 + + + +
59A TRP 4.2 0.7 - - - +
61A ARG* 1.3 91.8 - - + +
63A THR* 1.3 63.7 + - - +
65A LEU* 3.7 27.7 - - + +
66A LEU* 3.1 30.7 + - + +
69A TRP* 4.6 4.7 - + - -
156A TRP* 5.0 0.7 + - - -
160A GLU* 3.5 21.3 + - - -
164A TRP* 4.3 10.6 + + - -
301A 6FP 3.4 42.5 + + + -
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 4.2 1.8 - - + -
41A ARG 3.4 25.6 - - - +
42A GLN* 3.5 29.5 + - - +
43A LYS* 3.0 24.9 + - - +
59A TRP 2.8 23.4 + - - -
60A GLU 3.7 5.4 - - - -
61A ARG 3.4 0.4 - - - -
62A TYR* 1.3 76.1 - - - +
64A GLN* 1.4 67.7 + - - +
66A LEU* 3.7 3.5 - - - +
67A ARG* 3.0 41.8 + - - +
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Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 5.7 1.0 - - - +
60A GLU* 3.1 30.4 + - - +
61A ARG* 3.8 7.6 - - - +
63A THR* 1.4 82.5 - - - +
65A LEU* 1.4 64.3 + - - +
67A ARG* 3.4 39.4 + - - +
68A GLY* 3.5 8.0 + - - -
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG* 3.2 23.6 + - + +
62A TYR* 3.7 36.3 - - + +
63A THR 3.3 0.2 - - - -
64A GLN* 1.4 76.2 - - - +
66A LEU* 1.3 57.6 + - - +
68A GLY* 3.3 4.9 + - - -
69A TRP* 3.1 67.0 + - + +
152A TYR* 5.2 9.4 - - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 5.5 0.9 - - - +
22A PHE* 3.8 21.1 - - + -
24A SER* 3.6 31.6 - - - +
36A TYR* 3.8 25.8 - - + -
43A LYS* 3.9 30.1 - - + -
62A TYR* 3.1 21.6 + - + +
63A THR 3.7 2.7 - - - +
65A LEU* 1.3 74.1 - - - +
67A ARG* 1.4 55.5 + - - +
68A GLY 3.1 2.5 - - - -
69A TRP* 3.0 26.9 + - + +
70A GLN* 2.7 34.5 + - - +
301A 6FP 4.1 10.8 - - + +
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.2 22.9 + - + +
41A ARG* 2.9 64.7 + - - +
42A GLN* 4.3 10.5 - - - +
63A THR* 3.0 35.7 + - - +
64A GLN* 3.5 32.1 + - - +
66A LEU* 1.4 75.2 - - - +
68A GLY* 1.3 57.0 + - - +
70A GLN* 3.4 14.7 - - - +
71A GLN* 3.7 11.1 + - - +
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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
----------------------------------------------------------
64A GLN 3.5 5.0 + - - -
65A LEU 3.3 7.7 + - - -
66A LEU 3.1 0.6 - - - -
67A ARG* 1.3 76.7 - - - +
69A TRP* 1.3 64.9 + - - +
70A GLN 3.1 1.6 - - - -
71A GLN* 3.1 10.4 + - - +
72A MET* 3.1 23.4 + - - +
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Residues in contact with TRP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.2 44.1 + - - +
22A PHE* 4.1 8.5 - - + -
62A TYR* 4.6 3.6 - + - -
65A LEU* 3.1 51.5 + - + +
66A LEU* 3.0 33.7 + - + +
68A GLY* 1.3 74.3 - - - +
70A GLN* 1.3 62.3 + - - +
72A MET* 3.9 11.8 - - + +
73A PHE* 3.1 26.7 + - - +
152A TYR* 5.0 11.0 - + - -
301A 6FP 3.5 48.7 - + - -
302A CL 4.4 5.8 - - + +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 4.9 9.3 + - - +
22A PHE* 3.8 31.0 - - + +
36A TYR* 2.7 35.7 + - - -
38A SER* 3.3 37.9 + - - +
41A ARG* 3.9 19.5 + - - +
66A LEU 2.7 14.5 + - - +
67A ARG 3.4 9.2 - - - +
69A TRP* 1.3 78.2 - - - +
71A GLN* 1.4 68.8 + - + +
73A PHE* 3.5 3.5 + - - +
74A LYS* 3.2 21.3 + - - +
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Residues in contact with GLN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 5.9 1.4 + - - -
41A ARG* 5.4 5.4 - - - +
67A ARG 3.7 11.6 + - - +
68A GLY* 3.1 11.3 + - - +
70A GLN* 1.4 86.5 - - - +
72A MET* 1.3 63.0 + - - +
74A LYS* 3.4 20.2 + - - +
75A VAL* 3.2 32.3 + - + +
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Residues in contact with MET 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 6.1 1.6 - - - +
68A GLY 3.1 15.7 + - - +
69A TRP* 3.9 14.1 - - + +
71A GLN* 1.3 72.1 - - - +
73A PHE* 1.3 57.3 + - + +
75A VAL* 3.2 18.3 + - + +
76A GLU* 2.8 59.7 + - - +
79A ARG* 5.8 4.5 - - - +
303A PO4 3.7 26.5 - - - +
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.8 32.3 - - + -
10A LEU 3.7 4.7 - - - -
11A GLY* 3.6 16.8 - - - -
22A PHE* 3.6 27.6 - + + -
69A TRP 3.1 15.6 + - - +
70A GLN 3.6 5.8 - - - +
71A GLN 3.3 0.2 - - - -
72A MET* 1.3 79.0 - - + +
74A LYS* 1.4 61.1 + - - +
76A GLU* 3.7 8.2 - - - +
77A LEU* 3.0 27.7 + - + +
92A TYR* 3.4 60.4 - + - -
93A GLN 4.2 0.2 - - - -
94A ARG* 3.8 22.7 - - + -
112A TYR* 4.3 6.1 - + - -
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.7 34.1 - - - +
70A GLN 3.2 11.0 + - - +
71A GLN* 3.6 25.6 - - - +
72A MET 3.3 0.2 - - - -
73A PHE* 1.4 76.8 - - - +
75A VAL* 1.3 57.4 + - + +
77A LEU* 3.9 4.5 - - - +
78A LYS* 3.0 44.8 + - + +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLN* 3.2 20.1 + - + +
72A MET* 3.2 18.8 + - + +
74A LYS* 1.3 74.2 - - + +
76A GLU* 1.4 65.7 + - - +
77A LEU 3.2 0.5 + - - -
78A LYS* 3.2 9.0 + - - +
79A ARG* 3.1 51.7 + - + +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET* 2.8 35.6 + - - +
73A PHE* 3.7 10.3 - - - +
75A VAL* 1.4 72.3 - - - +
77A LEU* 1.4 58.0 - - - +
79A ARG* 3.5 27.4 + - - +
80A LEU* 3.4 27.5 + - - +
92A TYR* 3.7 29.1 + - + +
112A TYR* 4.2 11.3 + - - -
139A ILE* 5.9 3.1 - - + -
143A TRP* 3.9 22.1 + - + +
303A PO4 3.0 29.9 + - - -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 4.9 7.2 - - - +
12A VAL 5.4 1.1 - - - -
13A SER* 3.4 17.3 - - - +
73A PHE* 3.0 18.0 + - + +
74A LYS* 3.9 4.7 - - - +
76A GLU* 1.4 71.9 - - - +
78A LYS* 1.4 68.8 + - - +
79A ARG 3.1 1.3 - - - -
80A LEU* 2.8 24.1 + - - +
81A GLN* 3.3 30.0 + - - +
90A HIS 4.4 10.5 - - - +
92A TYR* 3.5 36.9 - - + +
114A TYR* 3.7 29.8 - - + -
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Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 3.0 34.2 + - + +
75A VAL* 3.6 7.4 - - - +
77A LEU* 1.4 80.4 - - - +
79A ARG* 1.4 59.0 + - - +
81A GLN* 3.5 9.0 + - - +
82A ARG* 3.5 35.8 + - + +
----------------------------------------------------------
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Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET* 5.8 5.3 - - - +
75A VAL* 3.1 40.7 + - + +
76A GLU* 3.5 38.6 + - - +
78A LYS* 1.4 75.6 - - - +
80A LEU* 1.4 55.2 + - - +
82A ARG* 3.3 6.9 + - - +
83A HIS* 3.1 53.6 + - + +
139A ILE* 4.7 22.9 - - + +
143A TRP* 5.9 2.8 - - - +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU 3.5 15.7 - - - +
77A LEU* 2.8 18.7 + - - +
79A ARG* 1.4 71.7 - - - +
81A GLN* 1.3 63.1 + - - +
83A HIS* 3.3 5.1 + - - +
84A TYR* 3.1 38.5 + - + -
92A TYR* 3.7 35.2 - - + +
114A TYR* 3.8 27.6 - - + -
119A PHE* 3.2 39.9 - - + -
135A VAL* 4.1 11.4 - - + -
139A ILE* 4.6 7.6 - - + -
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Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 2.6 23.8 + - - -
77A LEU* 3.3 16.0 + - + +
78A LYS* 3.8 10.6 - - - +
79A ARG 3.4 0.4 - - - -
80A LEU* 1.3 78.4 - - - +
82A ARG* 1.3 59.5 + - + +
84A TYR 3.0 6.4 - - - +
85A ASN* 3.8 0.5 - - - -
86A HIS* 3.0 50.4 + - + +
87A SER* 4.0 2.2 - - - +
88A GLY 3.4 15.2 + - - +
90A HIS* 2.9 27.6 + - - +
114A TYR* 3.2 29.4 - - + +
----------------------------------------------------------
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Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 3.5 24.1 + - + +
79A ARG* 3.3 10.7 + - - +
80A LEU 3.2 0.8 - - - -
81A GLN* 1.3 76.7 - - + +
83A HIS* 1.3 66.2 + - + +
84A TYR 2.9 11.5 - - - +
86A HIS 6.1 0.2 - - - +
----------------------------------------------------------
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Residues in contact with HIS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 3.1 44.4 + - + +
80A LEU* 3.3 2.4 + - - +
82A ARG* 1.3 78.5 - - + +
84A TYR* 1.3 65.4 + - - +
135A VAL* 3.6 37.7 - - + +
138A THR* 4.4 16.5 + - - -
139A ILE* 4.7 7.0 - - + +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU* 3.1 36.5 + - + +
81A GLN 3.0 5.6 - - - +
82A ARG* 2.9 17.7 - - - +
83A HIS* 1.3 75.8 - - - +
85A ASN* 1.3 62.2 + - - +
86A HIS* 3.3 26.9 - + + -
114A TYR* 3.6 37.0 - + - -
119A PHE* 3.4 13.2 - + - -
132A VAL* 5.1 0.7 - - - +
133A ASP* 2.7 38.6 + - - -
135A VAL* 3.5 17.0 - - + -
----------------------------------------------------------
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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