Contacts of the helix formed by residues 55 - 77 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ARG* 4.1 29.6 - - + +
184A VAL 5.1 1.8 - - - +
185A VAL* 3.4 33.4 - - + -
51B GLU 3.2 16.0 + - - +
52B ALA* 3.4 18.2 - - + +
53B LEU 3.2 1.5 - - - +
54B THR* 1.3 74.5 - - - +
56B THR* 1.3 60.4 + - - +
57B GLU* 3.2 13.9 - - + +
58B ASN* 2.8 33.0 + - - +
59B GLN 2.8 10.4 + - - -
119B GLN* 5.1 15.3 - - + +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 3.6 21.8 - - + +
54B THR 3.1 9.4 + - - +
55B LEU* 1.3 70.3 - - - +
57B GLU* 1.3 59.7 + - - +
58B ASN 3.1 0.2 - - - -
59B GLN* 4.1 7.2 - - - +
60B GLN* 3.1 31.1 + - - +
115B GLY* 2.7 32.6 + - - -
118B MET* 5.1 0.2 - - - -
119B GLN* 3.6 18.2 + - - +
193B PHE* 3.6 33.9 - - + -
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 5.5 5.1 + - - -
55B LEU* 3.0 14.2 + - + +
56B THR* 1.3 80.6 + - - +
58B ASN* 1.3 73.7 + - - +
61B PRO* 3.2 11.5 - - - +
112B ARG* 3.0 51.2 + - + +
115B GLY* 3.8 0.6 - - - -
116B ARG* 3.5 53.2 + - + +
119B GLN* 5.1 8.4 - - + +
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Residues in contact with ASN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 4.1 4.6 - - + +
44B LEU* 4.3 22.3 - - + +
52B ALA* 2.7 30.1 + - - +
53B LEU* 3.9 9.9 - - + +
55B LEU* 2.8 21.0 + - - +
57B GLU* 1.3 87.0 - - - +
59B GLN* 1.3 64.3 + - - +
61B PRO* 2.8 20.8 - - - +
62B ALA* 3.0 17.9 + - - +
112B ARG* 3.0 24.2 + - - +
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Residues in contact with GLN 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 2.8 23.6 - - - +
10B GLY 2.8 28.8 + - - -
12B HIS* 3.4 37.7 - - + -
53B LEU* 3.1 13.1 + - - +
54B THR* 2.6 34.7 + - - +
55B LEU 2.8 11.1 + - - +
56B THR* 4.1 9.2 - - - +
58B ASN* 1.3 78.7 - - - +
60B GLN* 1.3 57.4 + - + +
62B ALA* 3.7 5.3 - - - +
63B LEU* 3.0 39.0 + - + +
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 2.9 34.0 + - + +
56B THR* 3.1 18.6 + - - +
59B GLN* 1.3 74.2 - - + +
61B PRO* 1.3 70.1 - - + +
63B LEU* 3.3 3.3 + - + +
64B LEU* 3.0 23.6 + - - +
90B LEU* 3.7 29.9 - - + +
111B VAL* 3.2 21.3 - - + +
114B ARG* 2.7 41.3 + - - +
115B GLY* 3.5 14.8 + - - -
118B MET* 3.5 13.3 - - - -
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Residues in contact with PRO 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 3.6 22.2 - - + -
41B LEU* 4.0 9.6 - - + -
57B GLU 3.2 22.7 - - - +
58B ASN* 2.8 23.8 - - - +
60B GLN* 1.3 88.0 - - + +
62B ALA* 1.3 56.2 + - - +
64B LEU* 3.2 1.2 + - - +
65B ALA* 2.8 31.4 + - - +
108B LEU* 3.6 10.9 - - + +
111B VAL* 3.7 11.9 - - + -
112B ARG* 3.8 27.4 - - + +
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Residues in contact with ALA 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 3.8 9.9 - - - -
41B LEU* 3.9 5.3 - - + +
45B MET* 3.3 44.7 - - + +
53B LEU* 4.0 13.7 - - + -
58B ASN 3.0 18.3 + - - +
59B GLN* 3.7 4.9 - - - +
61B PRO* 1.3 78.5 - - - +
63B LEU* 1.3 57.2 + - - +
65B ALA* 3.4 0.6 + - - +
66B ALA* 3.0 26.5 + - - +
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Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PRO* 4.5 15.6 - - + +
8B GLY* 3.1 36.3 - - - +
9B GLN* 3.7 9.9 - - + +
10B GLY 4.7 0.2 - - - +
11B SER* 3.8 7.2 - - - -
12B HIS* 3.7 20.9 - - + +
16B MET* 3.7 21.5 - - + -
59B GLN* 3.0 35.6 + - + +
60B GLN* 3.8 4.7 - - - +
62B ALA* 1.3 74.0 - - - +
64B LEU* 1.3 61.3 + - - +
66B ALA* 3.9 1.5 - - + +
67B GLY* 2.9 25.5 + - - -
90B LEU* 3.8 14.6 - - + -
94B THR* 4.3 1.9 + - - +
270B SER* 3.8 9.9 - - - +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLN 3.0 17.2 + - - +
61B PRO 3.6 3.1 - - - +
63B LEU* 1.3 77.6 - - - +
65B ALA* 1.3 57.6 + - - +
67B GLY* 3.3 0.5 + - - -
68B TYR* 2.9 30.4 + - + +
90B LEU* 4.1 3.1 - - + +
93B TRP* 3.9 29.4 - - + -
94B THR* 3.4 29.1 - - - +
97B VAL* 4.5 4.9 - - + -
104B LEU* 3.5 29.4 - - + -
107B ALA* 3.9 19.5 - - + -
108B LEU* 4.0 12.8 - - + -
111B VAL* 3.9 20.9 - - + -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.9 5.7 - - + +
31B LEU* 3.9 13.0 - - + +
34B ALA* 3.8 28.7 - - + -
41B LEU* 4.3 7.4 - - + -
45B MET* 4.6 1.3 - - + -
61B PRO 2.8 18.0 + - - +
62B ALA* 3.7 3.8 - - - +
64B LEU* 1.3 81.7 - - - +
66B ALA* 1.3 57.6 + - - +
68B TYR* 3.6 2.6 + - - -
69B ALA* 2.9 31.2 + - - +
104B LEU* 5.0 3.6 - - - -
108B LEU* 4.2 4.0 - - + -
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 4.1 17.0 - - + -
17B GLY* 4.8 13.0 - - - -
20B LEU* 5.6 0.3 - - - +
31B LEU* 4.2 6.0 - - - +
45B MET* 4.2 7.4 - - + -
62B ALA 3.0 16.8 + - - +
63B LEU* 4.0 2.7 - - - +
65B ALA* 1.3 73.6 - - - +
67B GLY* 1.3 67.0 + - - +
69B ALA* 3.3 6.1 + - - +
70B ALA* 3.0 25.6 + - - +
269B GLY* 3.5 21.1 - - - +
270B SER* 4.8 1.1 - - - +
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PHE* 4.2 2.5 - - - -
7B PRO* 5.4 1.1 - - - -
63B LEU 2.9 18.5 + - - -
64B LEU 3.7 0.9 - - - -
66B ALA* 1.3 78.2 - - - +
68B TYR* 1.3 61.5 + - - +
70B ALA 3.3 0.5 + - - -
71B TYR* 3.1 19.4 + - - +
94B THR* 4.0 13.2 - - - -
268B PHE* 3.5 31.6 - - - +
269B GLY* 3.6 1.5 - - - -
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Residues in contact with TYR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B PHE* 5.0 0.7 - - - -
30B VAL* 3.6 25.4 - - + -
33B ARG* 4.8 10.8 + - - -
64B LEU* 2.9 17.9 + - + +
65B ALA 4.1 2.2 - - - +
67B GLY* 1.3 74.4 - - - +
69B ALA* 1.3 57.1 + - - +
71B TYR* 3.3 9.2 + + - -
72B ARG* 2.9 71.3 + - + +
94B THR* 3.8 8.4 - - + +
97B VAL* 3.8 28.2 + - + -
98B ALA* 3.8 32.1 - - + -
104B LEU* 4.0 29.2 - - + -
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Residues in contact with ALA 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 5.9 1.1 - - + -
27B ALA* 3.6 32.7 - - + +
30B VAL* 3.8 17.9 - - + +
31B LEU* 4.0 13.2 - - + -
65B ALA 2.9 19.9 + - - +
66B ALA* 3.6 5.6 - - - +
67B GLY 3.2 0.2 - - - -
68B TYR* 1.3 74.3 - - - +
70B ALA* 1.3 59.8 + - - +
72B ARG* 3.7 0.5 - - - +
73B ALA* 2.9 30.1 + - - +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 3.7 23.7 - - + +
66B ALA 3.0 11.2 + - - +
67B GLY 3.7 1.3 - - - +
69B ALA* 1.3 77.7 - - - +
71B TYR* 1.3 63.7 + - - +
73B ALA* 3.3 3.5 + - - +
74B PHE* 3.0 22.7 + - - +
268B PHE* 3.8 7.5 - - + -
269B GLY* 3.4 20.0 - - - +
290B VAL* 3.3 30.4 - - + +
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B TYR* 4.1 6.5 - - - -
4B ALA* 5.0 1.6 - - + -
6B PHE* 4.1 14.6 - + + -
67B GLY 3.1 13.8 + - - +
68B TYR* 3.5 17.7 - + - +
70B ALA* 1.3 77.4 - - - +
72B ARG* 1.3 60.7 + - - +
74B PHE* 3.1 5.4 + + - +
75B LEU* 2.9 64.8 + - + +
81B PRO* 3.7 6.6 - - - +
82B PRO* 3.2 35.9 - - + +
98B ALA* 3.6 36.5 + - + -
219B PHE* 3.5 13.5 - + - -
268B PHE* 3.6 30.9 - + + -
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Residues in contact with ARG 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA* 4.0 9.6 - - + +
30B VAL* 3.6 25.5 - - + +
68B TYR* 2.9 57.3 + - + +
69B ALA 3.3 4.2 + - - +
71B TYR* 1.3 76.1 - - - +
73B ALA* 1.3 66.5 + - - +
75B LEU* 3.7 24.1 - - - +
76B GLU* 2.9 65.6 + - - +
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Residues in contact with ALA 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 4.7 5.2 - - + -
24B SER* 3.4 30.9 + - - +
26B ALA* 3.9 5.8 - - - +
27B ALA* 3.9 8.5 - - + -
69B ALA 2.9 17.5 + - - +
70B ALA* 3.4 9.2 - - - +
72B ARG* 1.3 75.9 - - - +
74B PHE* 1.3 62.1 - - - +
76B GLU* 4.0 1.7 - - - +
77B ALA* 3.2 24.3 + - - +
296B LEU* 4.2 16.9 - - + +
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B TYR* 3.4 11.4 - + - -
70B ALA 3.0 13.3 + - - +
71B TYR* 3.3 8.3 - + - +
73B ALA* 1.3 74.9 - - - +
75B LEU* 1.3 70.5 + - + +
77B ALA 3.4 5.5 + - - -
78B GLY 3.6 0.5 + - - -
79B GLY* 2.8 38.0 + - - -
80B LYS 3.3 23.1 - - - -
266B LEU* 4.0 13.5 - - + -
268B PHE* 3.7 25.1 - + + -
290B VAL* 5.3 0.2 - - + -
296B LEU* 3.7 15.9 - - + +
299B ALA* 4.0 28.9 - - + -
300B LEU* 3.5 34.0 - - + +
303B GLU* 3.6 16.2 - - + -
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B TYR* 2.9 63.1 + - + +
72B ARG* 3.8 26.0 - - - +
74B PHE* 1.3 77.7 - - + +
76B GLU* 1.3 62.8 + - - +
78B GLY* 2.9 21.7 + - - -
79B GLY 3.4 20.5 + - - +
80B LYS 4.0 3.1 - - - -
81B PRO* 3.9 19.7 - - + -
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.1 29.6 - - + +
72B ARG* 2.9 55.5 + - - +
73B ALA 4.0 1.8 - - - +
75B LEU* 1.3 73.9 - - - +
77B ALA* 1.3 57.4 + - - +
78B GLY 3.2 3.6 + - - -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA 3.2 17.6 + - - +
74B PHE 3.8 3.6 - - - +
75B LEU 3.1 1.4 - - - -
76B GLU* 1.3 75.1 - - - +
78B GLY* 1.3 57.6 + - - +
79B GLY 3.4 1.6 - - - -
296B LEU* 5.2 4.0 - - + -
300B LEU* 3.6 27.1 - - + -
304B ARG* 3.2 24.1 + - - +
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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