Contacts of the helix formed by residues 46 - 75 (chain A) in PDB entry 2YW7
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 ASN 46 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLY 3.4 0.2 - - - -
45A PRO* 1.3 86.8 - - - +
47A PHE* 1.3 56.6 + - - +
48A ILE* 3.2 3.8 - - - -
49A GLY* 2.8 27.2 + - - +
50A VAL* 3.6 6.2 + - - +
102A VAL* 4.1 14.8 - - + +
103A GLN* 5.7 4.0 - - - +
46C ASN* 5.3 7.3 + - - +
45G PRO* 4.2 13.0 - - + +
46G ASN* 3.6 33.1 + - - +
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Residues in contact with PHE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.3 18.5 - - - +
43A VAL* 3.3 23.8 - - - +
44A GLY 3.1 26.9 + - - +
45A PRO 3.1 1.4 + - - -
46A ASN* 1.3 77.4 - - - +
48A ILE* 1.3 89.5 + - + +
50A VAL* 3.3 7.6 + - - +
51A HIS* 3.2 47.3 + + - -
102A VAL* 3.8 11.1 - - - +
150C TRP* 4.6 13.2 - + - -
151C PHE* 4.2 25.8 - + - -
154C ALA* 4.0 11.0 - - + -
155C HIS* 3.9 26.9 - + - -
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Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO 3.6 21.3 - - - +
46A ASN 4.7 0.9 - - - -
47A PHE* 1.3 101.7 - - + +
49A GLY* 1.3 59.4 + - - +
51A HIS* 2.9 22.9 - - + +
52A GLU* 2.8 38.8 + - + +
49C GLY* 5.7 3.1 - - - +
151C PHE* 4.1 18.2 - - + -
155C HIS* 3.7 22.2 - - + +
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Residues in contact with GLY 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASN* 2.8 14.3 + - - -
48A ILE* 1.3 75.3 - - - +
50A VAL* 1.3 64.4 + - - -
52A GLU* 3.0 18.7 + - - +
53A MET* 3.0 26.7 + - - +
155A HIS* 6.1 1.1 - - - -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A VAL* 5.2 0.4 - - + -
42A VAL* 3.7 28.5 - - + -
46A ASN 3.6 2.6 + - - +
47A PHE 3.3 6.5 + - - +
49A GLY* 1.3 69.9 - - - +
51A HIS* 1.3 67.6 + - - +
53A MET* 3.1 15.6 + - + +
54A ILE* 2.8 51.5 + - + +
102A VAL* 3.3 38.1 - - + -
105A HIS* 5.6 1.1 - - + -
106A LEU* 4.2 24.5 - - + -
109A LEU* 5.8 1.1 - - + -
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Residues in contact with HIS 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 3.0 64.7 + + - +
42A VAL* 4.4 4.3 - - - +
47A PHE* 3.2 46.1 + + - -
48A ILE* 2.9 28.3 - - + +
50A VAL* 1.3 80.7 - - - +
52A GLU* 1.3 56.8 + - + +
54A ILE* 3.1 9.3 + - - +
55A ASP* 2.3 27.5 + - - +
150C TRP* 5.7 4.8 - + - -
151C PHE* 5.9 3.8 - + - -
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Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 2.8 24.1 + - + +
49A GLY* 3.0 21.7 + - - +
51A HIS* 1.3 74.2 - - + +
53A MET* 1.3 57.4 + - - +
55A ASP* 3.7 4.9 - - - +
56A PRO* 3.1 24.9 - - - +
52G GLU* 5.7 1.0 - - - +
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Residues in contact with MET 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY 3.0 10.5 + - - +
50A VAL* 3.1 30.7 + - + +
52A GLU* 1.3 75.5 - - - +
54A ILE* 1.3 68.8 - - + +
56A PRO* 3.3 11.2 - - - +
57A GLN* 3.9 4.0 + - - +
106A LEU* 3.8 30.5 - - + -
148A PHE* 3.6 29.9 - - + -
151A PHE* 3.5 39.1 - - + +
152A VAL* 4.6 2.9 - - - -
155A HIS* 3.3 48.2 - - + +
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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
----------------------------------------------------------
35A LEU* 3.9 24.2 - - + +
38A VAL* 3.3 28.0 - - + -
39A HIS* 4.1 25.8 - - + +
42A VAL* 4.8 0.2 - - + -
50A VAL* 2.8 45.6 + - + +
51A HIS 3.7 3.4 - - - +
53A MET* 1.3 80.0 - - + +
55A ASP* 1.3 54.6 + - - +
57A GLN* 3.1 8.3 + - - +
58A VAL* 2.8 52.2 + - + +
109A LEU* 4.8 2.7 - - + -
148A PHE* 4.6 6.5 - - + -
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Residues in contact with ASP 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 5.1 5.8 - - - +
39A HIS* 3.3 25.5 + - - -
51A HIS* 2.3 33.1 + - - +
52A GLU* 3.6 5.2 + - - +
54A ILE* 1.3 76.7 - - - +
56A PRO* 1.3 69.4 - - + +
57A GLN 3.2 0.7 + - - -
58A VAL* 3.2 17.0 + - - +
59A GLU* 3.2 16.1 + - - +
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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
----------------------------------------------------------
52A GLU 3.1 23.3 - - - +
53A MET* 3.3 11.4 - - - +
55A ASP* 1.3 92.9 - - + +
57A GLN* 1.3 58.7 + - - +
59A GLU* 4.2 4.4 - - + +
60A LEU* 3.2 24.4 + - - +
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Residues in contact with GLN 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.8 10.3 - - + -
53A MET 3.9 1.7 + - - +
54A ILE 3.3 8.3 - - - +
55A ASP 3.1 0.2 - - - -
56A PRO* 1.3 78.7 - - - +
58A VAL* 1.3 55.8 + - - +
60A LEU* 2.9 24.0 + - - +
61A VAL* 2.7 52.1 + - - +
113A TYR* 2.7 33.2 + - - +
144A GLU* 3.8 3.6 + - - +
145A LEU* 3.5 19.0 - - - +
148A PHE* 3.6 45.9 - - + +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 4.2 7.8 - - + +
35A LEU* 3.7 22.9 - - + -
36A LYS* 3.7 33.9 - - + +
54A ILE* 2.8 43.8 + - + +
55A ASP* 3.6 7.6 - - - +
57A GLN* 1.3 72.3 - - - +
59A GLU* 1.3 64.9 + - - +
61A VAL* 4.0 6.6 - - - +
62A ARG* 3.1 45.4 + - + +
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Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 5.9 0.5 - - - -
55A ASP 3.2 12.2 + - - +
56A PRO* 4.2 4.7 - - + +
57A GLN 3.2 0.6 - - - -
58A VAL* 1.3 80.1 - - - +
60A LEU* 1.3 61.6 + - - +
62A ARG* 3.4 40.3 + - - +
63A GLY* 2.9 26.0 + - - -
59E GLU* 5.3 4.5 - - - +
62E ARG* 4.2 5.5 + - - -
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO 3.2 14.7 + - - +
57A GLN* 3.0 26.5 - - - +
59A GLU* 1.3 77.6 - - - +
61A VAL* 1.3 57.0 + - - +
63A GLY* 3.1 4.7 + - - -
64A TYR* 3.0 75.8 + - + +
144A GLU* 3.5 28.3 - - + +
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.5 36.8 - - + +
31A LEU* 3.7 23.3 - - + -
32A HIS* 3.8 13.7 - - + -
35A LEU* 4.1 4.7 - - + -
57A GLN* 2.7 51.7 + - + +
58A VAL 4.0 3.6 - - - +
60A LEU* 1.3 69.2 - - + +
62A ARG* 1.3 66.1 + - - +
64A TYR* 3.0 11.3 + - + +
65A ALA* 2.9 21.7 + - - +
145A LEU* 4.6 4.3 - - + -
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS* 3.8 34.0 + - + -
36A LYS* 3.9 30.9 - - - +
58A VAL* 3.1 30.9 + - - +
59A GLU* 3.4 34.4 + - - +
61A VAL* 1.3 78.9 - - - +
63A GLY* 1.3 60.7 + - - +
65A ALA* 3.3 4.8 - - - +
66A ASP* 3.2 28.3 + - - +
32E HIS* 5.0 5.1 + - - -
62E ARG* 3.4 66.7 + - - +
66E ASP* 5.0 1.4 + - - -
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU 2.9 15.1 + - - -
60A LEU* 3.4 5.4 - - - -
61A VAL 3.0 0.4 - - - -
62A ARG* 1.3 73.3 - - - +
64A TYR* 1.3 60.4 + - - +
66A ASP* 3.0 13.6 + - - +
67A GLU* 2.8 33.5 + - - +
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Residues in contact with TYR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR* 3.6 20.2 - + + -
60A LEU* 3.0 52.0 + - + +
61A VAL* 3.0 15.2 + - + +
63A GLY* 1.3 72.9 - - - +
65A ALA* 1.3 66.2 + - - +
67A GLU* 2.8 22.7 + - - +
68A VAL* 2.8 16.3 + - - +
140A ALA 5.2 0.6 - - - -
141A HIS* 3.2 65.3 - + + +
144A GLU* 3.0 32.7 - - - +
145A LEU* 4.3 16.8 - - + -
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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
----------------------------------------------------------
25A LEU* 3.6 18.5 - - + +
28A TYR* 3.7 20.0 - - + -
29A ASN* 3.8 22.2 - - - +
32A HIS* 4.6 4.5 - - + +
61A VAL 2.9 11.4 + - - +
62A ARG* 3.3 15.0 - - - +
64A TYR* 1.3 75.0 - - - +
66A ASP* 1.3 62.8 + - - +
68A VAL* 3.6 0.7 + - - +
69A ALA* 3.2 20.6 + - - +
40E TRP* 4.1 5.8 - - + -
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Residues in contact with ASP 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 3.2 16.6 + - - +
63A GLY* 3.0 11.6 + - - +
65A ALA* 1.3 74.9 - - - +
67A GLU* 1.3 65.2 - - - +
69A ALA* 3.3 1.7 + - - +
70A GLU* 3.0 38.4 + - + +
36E LYS* 2.9 36.6 + - - +
40E TRP* 3.4 22.9 + - - +
62E ARG* 5.5 1.2 + - - -
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Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLY 2.8 15.6 + - - +
64A TYR* 2.8 24.0 + - - +
66A ASP* 1.3 72.3 - - + +
68A VAL* 1.3 60.9 + - - +
70A GLU* 3.6 8.4 - - - +
71A ARG* 3.1 21.0 + - - +
137A LEU* 3.2 26.0 - - + +
141A HIS* 2.4 37.7 + - + -
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.4 38.4 - - + +
24A GLN* 4.5 2.5 - - + -
25A LEU* 3.5 27.6 - - + -
28A TYR* 4.2 13.2 - - + -
64A TYR 2.8 16.3 + - - +
65A ALA 4.1 1.3 - - - +
67A GLU* 1.3 71.5 - - - +
69A ALA* 1.3 70.2 + - - +
71A ARG* 3.0 7.9 + - - +
72A ILE* 3.0 24.5 + - + +
137A LEU* 3.8 19.1 - - + -
138A LEU* 4.0 18.6 - - + -
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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
----------------------------------------------------------
25A LEU* 4.4 3.1 - - + -
65A ALA 3.2 10.6 + - - +
66A ASP 3.7 1.3 - - - +
68A VAL* 1.3 79.2 - - - +
70A GLU* 1.3 65.9 + - - +
71A ARG 2.7 1.7 + - - -
72A ILE* 2.8 18.8 + - - +
73A ALA* 2.9 12.4 + - - +
79A PRO* 3.8 22.5 - - + +
40E TRP* 3.5 45.3 - - + -
----------------------------------------------------------
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 3.0 25.5 + - + +
67A GLU* 3.6 7.8 - - - +
69A ALA* 1.3 77.1 - - - +
71A ARG* 1.3 51.5 + - - +
73A ALA* 3.5 8.7 - - - +
74A THR* 2.6 38.4 + - - +
147D LYS* 3.1 41.3 + - + +
150D TRP* 5.3 11.2 - - + -
40E TRP* 4.8 12.2 - - + -
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Residues in contact with ARG 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.4 24.5 - - + -
67A GLU 3.1 14.2 + - - +
68A VAL* 3.0 16.6 + - - +
69A ALA 2.7 4.6 + - - -
70A GLU* 1.3 70.2 - - - +
72A ILE* 1.3 54.2 + - - -
74A THR* 2.8 34.5 + - - +
75A LEU* 2.8 36.2 + - - +
131A ASP* 2.8 27.6 + - - -
133A VAL* 3.7 23.1 - - - +
134A SER* 3.1 16.1 + - - +
137A LEU* 4.8 9.9 - - + -
121D ARG* 5.3 0.8 - - - +
143D GLY* 5.0 5.3 + - - -
146D GLU* 2.7 40.6 + - - +
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 3.8 13.2 - - + +
21A LEU* 3.5 29.8 - - + +
22A GLN* 3.7 30.3 - - + +
25A LEU* 4.4 4.3 - - + -
68A VAL* 3.0 19.2 + - + +
69A ALA* 2.8 11.5 + - - +
71A ARG* 1.3 70.5 - - - +
73A ALA* 1.3 62.1 + - - +
75A LEU* 2.9 17.0 + - - +
77A LYS* 3.1 44.8 + - + +
78A SER 4.3 1.3 - - - +
79A PRO* 3.8 29.6 - - + -
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA 2.9 10.3 + - - +
70A GLU* 3.5 14.4 - - - +
72A ILE* 1.3 76.3 - - - +
74A THR* 1.3 56.0 + - - +
76A GLY 3.3 0.2 + - - -
77A LYS 3.2 12.8 + - - +
79A PRO* 3.9 15.6 - - + +
150D TRP* 3.0 30.2 + - + -
40E TRP* 4.3 7.9 - - + +
41E ASN* 5.4 0.2 - - - +
99E ARG* 2.6 34.2 + - + +
----------------------------------------------------------
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Residues in contact with THR 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLU* 2.6 21.3 + - - +
71A ARG* 2.8 29.8 + - - +
73A ALA* 1.3 68.1 - - - +
75A LEU* 1.3 52.0 + - + +
76A GLY* 2.8 16.4 + - - -
146D GLU* 3.9 42.6 - - + +
147D LYS* 4.2 10.9 - - - +
150D TRP* 3.7 27.3 - - + +
153D ARG* 5.9 0.7 + - - -
99E ARG* 4.4 0.5 + - - -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA* 4.2 38.0 - - + +
15A SER 5.1 0.2 + - - -
17A VAL* 3.5 23.3 - - + -
18A ALA* 4.5 4.0 - - + +
21A LEU* 3.4 34.1 - - + -
71A ARG* 2.8 50.6 + - + +
72A ILE* 2.9 7.5 + - - +
74A THR* 1.3 70.8 - - + +
76A GLY* 1.3 60.0 + - - +
77A LYS* 3.3 7.2 + - - +
131A ASP* 4.6 3.6 - - - +
121D ARG* 5.2 9.2 - - - +
146D GLU* 4.9 1.6 - - + +
----------------------------------------------------------
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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