Contacts of the helix formed by residues 55 - 77 (chain A) in PDB entry 2CUY
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 LEU 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU 3.3 7.6 + - - +
52A ALA* 3.3 21.3 - - + +
53A LEU 3.1 1.2 - - - +
54A THR* 1.3 74.3 - - - +
56A THR* 1.3 67.0 + - - +
57A GLU* 3.1 7.2 - - + +
58A ASN* 2.7 28.6 + - - +
59A GLN 2.8 11.6 + - - -
119A GLN* 6.6 0.2 - - + -
133B LEU* 3.8 16.2 - - + -
134B LYS* 4.9 4.3 - - - +
183B ARG* 3.6 49.4 - - + +
184B VAL 4.4 10.5 - - - +
185B VAL* 4.1 20.2 - - + -
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Residues in contact with THR 56 (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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9A GLN* 3.3 35.4 + - - +
54A THR 3.1 6.6 + - - -
55A LEU* 1.3 70.9 - - - +
57A GLU* 1.3 61.5 + - - +
58A ASN 3.2 1.0 + - - -
59A GLN* 4.3 1.3 - - - -
60A GLN* 3.2 37.4 + - - +
115A GLY* 3.6 21.9 - - - +
119A GLN* 3.0 29.9 + - + +
193A PHE* 4.0 15.8 - - + -
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Residues in contact with GLU 57 (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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55A LEU* 2.9 4.9 + - + +
56A THR* 1.3 79.4 - - - +
58A ASN* 1.3 74.1 + - - +
61A PRO* 3.3 12.0 - - - +
112A ARG* 3.2 54.2 + - + +
115A GLY* 4.2 1.3 - - - -
116A ARG* 3.5 39.8 - - + +
119A GLN* 6.4 0.2 - - + -
183B ARG* 2.9 33.3 + - - +
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Residues in contact with ASN 58 (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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41A LEU* 4.3 2.9 - - + +
44A LEU* 3.5 27.7 - - + +
52A ALA* 2.8 23.1 + - - +
53A LEU* 3.6 11.9 - - + +
55A LEU* 2.7 26.4 + - - +
57A GLU* 1.3 84.7 + - - +
59A GLN* 1.3 68.4 + - - +
60A GLN 3.3 1.1 - - - -
61A PRO* 3.0 18.3 - - - +
62A ALA* 3.0 14.5 + - - +
112A ARG* 3.0 23.6 + - - +
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Residues in contact with GLN 59 (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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9A GLN* 2.8 32.7 - - - +
10A GLY 2.6 29.3 + - - -
12A HIS* 3.4 37.3 - - + +
53A LEU* 3.1 14.5 + - - +
54A THR* 3.0 23.2 + - - +
55A LEU 2.8 8.8 + - - +
56A THR* 3.9 3.5 - - - +
58A ASN* 1.3 78.0 - - - +
60A GLN* 1.3 57.4 + - - +
62A ALA* 3.2 6.8 + - - +
63A LEU* 2.9 40.7 + - + +
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Residues in contact with GLN 60 (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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9A GLN* 3.0 33.6 + - + +
56A THR* 3.2 23.5 + - - +
59A GLN* 1.3 80.2 - - - +
61A PRO* 1.3 70.3 - - + +
63A LEU* 3.4 1.3 + - - -
64A LEU* 3.2 19.8 + - - +
90A LEU* 3.7 34.9 - - + +
111A VAL* 3.3 19.6 - - + +
114A ARG* 2.8 41.8 + - - +
115A GLY* 3.5 12.2 - - - -
118A MET* 3.6 5.5 - - - -
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Residues in contact with PRO 61 (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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38A LEU* 3.6 31.9 - - + -
41A LEU* 4.3 9.4 - - + -
57A GLU 3.3 24.2 - - - +
58A ASN* 3.0 21.5 - - - +
60A GLN* 1.3 91.2 - - + +
62A ALA* 1.3 59.5 + - - +
64A LEU* 4.5 0.4 - - + -
65A ALA* 3.0 21.8 + - - +
108A LEU* 3.2 19.8 - - + +
111A VAL* 3.7 16.4 - - + -
112A ARG* 4.2 11.4 - - + +
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Residues in contact with ALA 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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12A HIS* 5.5 0.2 - - + -
16A MET* 3.6 11.0 - - + +
41A LEU* 4.1 4.4 - - + +
45A MET* 3.6 36.9 - - + +
53A LEU* 3.9 15.5 - - + -
58A ASN 3.0 18.5 + - - +
59A GLN* 3.4 5.4 - - - +
61A PRO* 1.3 78.8 - - - +
63A LEU* 1.3 57.6 + - - +
65A ALA* 3.4 2.1 + - - +
66A ALA* 3.0 30.0 + - - +
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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
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7A PRO* 4.5 15.3 - - + +
8A GLY* 3.4 32.8 - - - +
9A GLN* 3.9 3.1 - - + +
11A SER* 3.7 9.9 - - - -
12A HIS* 3.4 36.1 - - + +
16A MET* 3.8 5.4 - - + -
59A GLN* 2.9 38.8 + - + +
60A GLN* 3.8 7.9 - - - +
62A ALA* 1.3 75.2 - - - +
64A LEU* 1.3 59.9 + - - +
66A ALA* 3.9 1.1 - - - +
67A GLY* 2.9 26.3 + - - -
90A LEU* 3.9 13.2 - - + -
94A THR* 4.5 1.6 + - - +
269A GLY* 5.3 0.5 - - - -
270A SER* 3.8 11.0 - - - +
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Residues in contact with LEU 64 (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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60A GLN 3.2 15.9 + - - +
61A PRO* 3.8 4.9 - - + +
63A LEU* 1.3 76.0 - - - +
65A ALA* 1.3 66.4 + - - +
67A GLY 3.3 0.7 + - - -
68A TYR* 2.9 22.3 + - + +
90A LEU* 4.1 3.1 - - + +
93A TRP* 3.8 17.9 - - + +
94A THR* 3.4 45.2 - - - +
97A VAL* 4.2 10.3 - - + -
104A LEU* 3.7 26.9 - - + -
107A ALA* 4.0 16.4 - - + -
108A LEU* 3.9 13.9 - - + -
111A VAL* 4.2 13.0 - - + -
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Residues in contact with ALA 65 (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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30A VAL* 3.6 11.0 - - + +
31A LEU* 4.0 13.4 - - + +
34A ALA* 3.9 28.3 - - + -
41A LEU* 4.4 5.6 - - + -
45A MET* 4.7 1.3 - - - -
61A PRO 3.0 18.5 + - - +
62A ALA* 3.8 3.8 - - - +
64A LEU* 1.3 81.9 - - - +
66A ALA* 1.3 58.1 + - - +
68A TYR* 4.9 0.2 - - - -
69A ALA* 2.9 29.8 + - - +
104A LEU* 4.9 2.9 - - + -
108A LEU* 4.0 5.6 - - + -
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Residues in contact with ALA 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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16A MET* 3.9 24.5 - - + -
17A GLY* 4.9 10.9 - - - +
20A LEU* 5.5 0.3 - - - +
31A LEU* 4.5 5.5 - - + +
45A MET* 5.5 1.8 - - - -
62A ALA 3.0 17.0 + - - +
63A LEU 3.9 3.4 - - - +
65A ALA* 1.3 73.8 - - - +
67A GLY* 1.3 68.3 + - - +
69A ALA* 3.3 6.3 + - - +
70A ALA* 2.9 26.0 + - - +
269A GLY* 3.6 20.0 - - - +
270A SER* 4.9 0.2 - - - +
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Residues in contact with GLY 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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6A PHE* 4.0 9.4 - - - -
7A PRO* 5.5 0.9 - - - -
63A LEU 2.9 18.0 + - - -
64A LEU 3.7 0.9 - - - -
66A ALA* 1.3 79.1 - - - +
68A TYR* 1.3 61.6 - - - +
70A ALA* 3.3 2.4 + - - +
71A TYR* 3.0 22.5 + - - +
94A THR* 4.0 8.3 - - - -
268A PHE* 3.7 12.8 - - - +
269A GLY* 3.6 15.0 - - - -
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Residues in contact with TYR 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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6A PHE* 4.9 0.9 - - - -
30A VAL* 3.8 25.6 - - + -
33A ARG* 4.4 13.6 + - - -
64A LEU 2.9 17.1 + - - +
65A ALA 4.1 2.5 - - - +
67A GLY* 1.3 75.1 - - - +
69A ALA* 1.3 62.3 + - - +
71A TYR* 3.2 10.6 + + - +
72A ARG* 2.9 72.1 + - + +
94A THR* 3.8 7.5 - - + +
97A VAL* 3.8 30.7 + - + -
98A ALA* 3.7 36.0 + - + -
104A LEU* 4.0 14.4 - - + -
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Residues in contact with ALA 69 (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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17A GLY* 6.1 1.8 - - - -
20A LEU* 5.8 2.0 - - + -
27A ALA* 3.7 18.6 - - + +
30A VAL* 3.7 17.2 - - + +
31A LEU* 3.9 26.9 - - + -
65A ALA 2.9 20.1 + - - +
66A ALA* 3.6 6.1 - - - +
68A TYR* 1.3 77.6 - - - +
70A ALA* 1.3 58.3 + - - +
72A ARG* 3.3 1.6 + - - +
73A ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 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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20A LEU* 3.5 25.9 - - + +
66A ALA 2.9 11.8 + - - +
67A GLY 3.7 1.1 - - - +
69A ALA* 1.3 76.4 - - - +
71A TYR* 1.3 63.0 + - - +
73A ALA* 3.3 3.7 + - - +
74A PHE* 3.0 22.7 + - - +
268A PHE* 3.8 6.2 - - + -
269A GLY* 3.4 29.6 - - - +
290A VAL* 3.5 18.6 - - + +
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Residues in contact with TYR 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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2A TYR* 4.0 8.7 - - - -
4A ALA* 5.1 0.9 - - + -
6A PHE* 4.2 15.0 - + + -
67A GLY 3.0 13.9 + - - +
68A TYR* 3.5 19.5 - + - +
70A ALA* 1.3 76.7 - - - +
72A ARG* 1.3 68.7 + - - +
74A PHE* 3.1 6.6 + + - +
75A LEU* 3.0 50.3 + - + +
81A PRO* 3.6 10.9 - - - +
82A PRO* 3.5 33.7 - - + +
98A ALA* 3.8 34.2 + - + -
218A ARG* 5.7 0.7 - - - -
219A PHE* 3.6 13.6 - + - -
268A PHE* 3.6 28.4 - + + -
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Residues in contact with ARG 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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26A ALA* 3.6 20.3 + - + +
30A VAL* 3.7 22.1 - - + +
33A ARG* 4.7 8.7 - - - +
68A TYR* 2.9 61.6 + - + +
69A ALA 3.8 3.4 - - - +
71A TYR* 1.3 81.8 - - - +
73A ALA* 1.3 59.3 + - - +
75A LEU* 3.2 16.0 + - - +
76A GLU* 2.8 30.8 + - - +
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Residues in contact with ALA 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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20A LEU* 4.5 6.7 - - + -
24A SER* 3.2 35.4 - - - +
26A ALA* 4.1 2.4 - - - +
27A ALA* 4.1 4.7 - - + -
69A ALA 2.9 17.2 + - - +
70A ALA* 3.5 9.4 - - - +
72A ARG* 1.3 76.4 - - - +
74A PHE* 1.3 56.6 + - - +
76A GLU* 3.3 4.5 + - - +
77A ALA* 2.9 29.8 + - - +
296A LEU* 4.2 15.7 - - + +
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Residues in contact with PHE 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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2A TYR* 3.6 28.9 - + - -
70A ALA 3.0 13.5 + - - +
71A TYR* 3.1 10.3 + + - +
73A ALA* 1.3 74.2 - - - +
75A LEU* 1.3 66.8 + - + +
77A ALA* 3.3 9.0 + - - +
78A GLY 3.5 0.3 + - - -
79A GLY* 2.8 44.5 + - - -
80A LYS 3.7 7.6 - - - -
266A LEU* 3.7 16.2 - - + -
268A PHE* 3.7 21.3 - + + -
290A VAL* 4.7 0.2 - - + -
296A LEU* 3.4 26.0 - - + +
299A ALA* 3.7 26.2 - - + -
300A LEU* 3.7 18.2 - - + -
303A GLU* 4.4 15.5 - - + -
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Residues in contact with LEU 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 TYR* 3.0 54.3 + - + +
72A ARG* 3.6 21.5 - - - +
74A PHE* 1.3 77.9 - - + +
76A GLU* 1.3 57.7 + - - +
78A GLY* 2.9 21.3 + - - -
79A GLY 3.4 20.8 + - - +
80A LYS 3.8 20.9 - - - +
81A PRO* 3.8 9.4 - - + -
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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
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23A ALA 4.8 0.3 - - - +
24A SER* 2.8 23.0 + - - -
25A PRO* 3.1 28.7 - - - +
26A ALA* 2.8 33.8 + - + +
72A ARG 2.8 18.5 + - - +
73A ALA 3.5 3.9 - - - +
75A LEU* 1.3 77.5 - - - +
77A ALA* 1.3 58.5 + - - +
78A GLY* 3.0 4.9 + - - -
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Residues in contact with ALA 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 ALA 2.9 16.3 + - - +
74A PHE* 3.8 4.3 - - - +
75A LEU 3.2 0.8 - - - -
76A GLU* 1.3 75.8 - - - +
78A GLY* 1.3 57.8 + - - +
79A GLY 3.6 1.3 - - - -
296A LEU* 4.6 6.7 - - + -
297A ARG* 4.0 19.9 + - - +
300A LEU* 3.5 33.4 - - + +
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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