Contacts of the helix formed by residues 45 - 72 (chain A) in PDB entry 1RCE
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 45 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASN* 4.2 17.3 - - - -
43A ALA* 3.6 3.2 + - - +
44A LEU* 1.3 74.9 - - - +
46A ASN* 1.3 66.9 + - - +
48A ALA* 3.4 3.3 + - - +
49A LYS* 2.9 27.0 + - - +
167A ASN* 3.9 7.2 + - - +
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Residues in contact with ASN 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER* 1.3 80.3 + - - +
47A PHE* 1.3 57.7 + - - +
49A LYS* 3.6 24.0 - - - +
50A PHE* 2.9 27.5 + - - +
167A ASN* 2.9 43.3 - - - +
168A LYS* 4.5 6.2 - - - +
171A LEU* 3.5 21.5 + - + +
172A GLY* 3.5 11.4 - - - -
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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
----------------------------------------------------------
37A PHE* 3.8 16.6 - + + -
44A LEU* 2.9 26.3 + - + +
46A ASN* 1.3 74.7 - - - +
48A ALA* 1.3 65.0 + - - +
50A PHE* 3.1 4.3 + - - +
51A PHE* 3.0 45.6 + + - -
92A GLY* 3.6 34.8 - - - -
96A LEU* 4.4 8.3 - - + -
151A LEU* 4.1 13.2 - - + -
163A GLU* 3.7 28.0 - - - -
166A PHE* 3.7 18.8 - + + -
167A ASN* 3.1 34.4 - - + +
171A LEU* 3.6 18.6 - - + -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ALA* 3.3 39.9 - - - +
37A PHE* 3.8 11.8 - - + +
38A ASN* 3.7 26.7 - - - +
44A LEU 3.1 3.4 + - - +
45A SER 3.4 9.0 - - - +
47A PHE* 1.3 80.2 - - - +
49A LYS* 1.3 56.9 + - - +
51A PHE 3.3 1.0 + - - -
52A ARG* 3.0 26.1 + - - +
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Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER 2.9 18.1 + - - +
46A ASN* 3.6 24.3 + - - +
48A ALA* 1.3 75.3 - - - +
50A PHE* 1.3 73.7 + - - +
52A ARG* 3.2 16.3 + - - +
53A GLU* 3.2 40.5 + - + +
171A LEU* 2.9 31.0 + - - +
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Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ASN 2.9 15.1 + - - +
47A PHE 3.1 8.5 + - - +
49A LYS* 1.3 86.9 - - - +
51A PHE* 1.3 80.7 + + - +
53A GLU* 3.3 13.8 + - - +
54A ARG* 3.2 56.0 + - - -
96A LEU* 4.1 12.3 - - + -
143A LYS* 4.2 16.4 - - + -
144A LEU* 3.8 29.6 - - + -
147A HIS* 4.1 20.6 - + - -
171A LEU* 4.1 24.2 - - + -
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Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.5 42.3 - + + +
33A MET* 3.8 24.9 - - + -
34A ALA* 4.0 7.2 - - - +
37A PHE* 3.7 28.0 - + - -
47A PHE* 3.0 33.2 + + - +
48A ALA 4.0 1.6 - - - +
50A PHE* 1.3 93.5 - + - +
52A ARG* 1.3 60.6 + - - +
53A GLU 3.2 0.4 - - - -
54A ARG* 3.7 3.4 - - + -
55A SER* 3.0 28.4 + - - -
95A ALA* 3.9 18.6 - - + -
96A LEU* 3.8 22.0 - - + -
99A ALA* 4.2 16.6 - - + -
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Residues in contact with ARG 52 (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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31A LEU* 5.2 12.5 - - + +
34A ALA* 4.1 12.1 - - + +
48A ALA 3.0 14.3 + - - +
49A LYS* 3.2 13.6 + - - +
51A PHE* 1.3 76.5 - - - +
53A GLU* 1.3 59.2 + - + +
55A SER* 3.4 14.2 + - - -
56A ALA* 3.0 60.9 + - - +
59A LYS* 5.4 4.4 - - - +
200A BET 4.9 9.9 + - - -
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Residues in contact with GLU 53 (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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49A LYS* 3.2 41.9 + - + +
50A PHE* 3.5 11.8 - - - +
52A ARG* 1.3 75.6 - - + +
54A ARG* 1.3 86.3 + - - +
56A ALA* 3.4 6.4 + - - +
57A ALA* 3.0 25.5 + - - +
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Residues in contact with ARG 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TYR* 3.6 43.8 - - + +
50A PHE* 3.2 51.6 + - + +
51A PHE* 3.4 14.6 + - + +
53A GLU* 1.3 101.9 + - - +
55A SER* 1.3 63.5 + - - +
57A ALA* 3.4 13.6 + - - +
58A ALA* 3.1 22.9 + - - +
103A GLN* 5.1 1.8 - - - +
140A THR* 4.3 21.1 + - + +
143A LYS* 3.5 25.4 - - - +
144A LEU* 5.5 2.9 - - + -
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Residues in contact with SER 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 2.8 43.4 + - - +
30A TYR* 3.7 10.5 - - - +
31A LEU* 3.8 9.0 + - - +
51A PHE 3.0 18.6 + - - -
52A ARG* 3.5 19.3 + - - -
54A ARG* 1.3 73.9 - - - +
56A ALA* 1.3 66.8 + - - +
58A ALA* 3.1 3.3 + - - +
59A LYS* 2.9 19.4 + - - +
200A BET 4.0 7.3 + - - -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.0 39.3 + - - +
53A GLU* 3.8 7.0 - - - +
55A SER* 1.3 74.2 - - - +
57A ALA* 1.3 57.3 + - - +
59A LYS* 3.3 17.0 + - - +
60A ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLU 3.0 17.7 + - - +
54A ARG* 3.6 18.8 - - - +
55A SER 3.1 0.2 - - - -
56A ALA* 1.3 76.8 - - - +
58A ALA* 1.3 56.4 + - - +
60A ALA* 3.3 8.1 + - - +
61A HIS* 3.0 45.8 + - + +
136A GLU* 5.8 2.2 - - + +
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Residues in contact with ALA 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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23A LYS* 3.7 19.2 - - + +
26A SER* 3.5 25.6 - - - +
27A SER* 3.9 8.5 - - - +
30A TYR* 4.9 4.3 - - + -
54A ARG 3.1 11.7 + - - +
55A SER* 3.1 8.3 + - - +
57A ALA* 1.3 73.3 - - - +
59A LYS* 1.3 65.1 + - - +
61A HIS* 3.2 14.1 + - - +
62A ALA* 3.0 22.7 + - - +
103A GLN* 6.0 0.7 - - - +
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Residues in contact with LYS 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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24A PHE* 4.3 14.5 - - + -
27A SER* 3.6 11.3 + - - +
52A ARG* 5.4 3.7 - - - +
55A SER 2.9 12.2 + - - +
56A ALA* 3.5 24.8 + - - +
58A ALA* 1.3 76.7 - - - +
60A ALA* 1.3 66.8 + - - +
62A ALA* 3.2 8.4 + - - +
63A GLU* 3.0 55.8 + - + +
200A BET 3.5 22.4 - - - +
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Residues in contact with ALA 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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56A ALA 3.0 14.3 + - - +
57A ALA* 3.5 11.4 - - - +
59A LYS* 1.3 78.0 - - - +
61A HIS* 1.3 68.1 + - + +
63A GLU* 3.3 12.2 + - - +
64A LYS* 3.0 29.7 + - + +
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Residues in contact with HIS 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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23A LYS* 3.1 33.1 + - - -
57A ALA* 3.0 34.3 + - + +
58A ALA* 3.2 7.2 + - - +
60A ALA* 1.3 75.4 - - + +
62A ALA* 1.3 67.7 + - - +
64A LYS* 3.2 5.6 + - + +
65A LEU* 3.0 28.7 + - + +
132A PRO* 5.5 6.6 + - + +
133A TYR* 3.9 28.1 - + + -
136A GLU* 3.2 46.3 + - + +
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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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20A VAL* 3.9 9.1 - - + +
23A LYS* 3.6 25.5 - - + +
24A PHE* 3.6 31.2 - - + -
58A ALA 3.0 8.2 + - - +
59A LYS 3.5 8.3 - - - +
61A HIS* 1.3 75.1 - - - +
63A GLU* 1.3 62.3 + - - +
65A LEU* 3.2 10.9 + - - +
66A ILE* 3.1 26.7 + - - +
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Residues in contact with GLU 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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24A PHE* 4.9 10.0 - - + -
59A LYS* 3.0 47.5 + - + +
60A ALA* 3.6 11.3 - - - +
61A HIS 3.2 0.2 - - - -
62A ALA* 1.3 77.5 - - - +
64A LYS* 1.3 62.5 - - + +
66A ILE* 3.3 13.2 + - + +
67A GLU* 3.1 30.6 + - - +
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Residues in contact with LYS 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 ALA* 3.0 23.0 + - + +
61A HIS* 3.7 4.3 - - + +
63A GLU* 1.3 75.0 - - + +
65A LEU* 1.3 59.7 + - - +
67A GLU* 3.3 33.7 + - + +
68A TYR* 2.9 27.2 + - - +
128A PHE* 4.1 4.8 - - + -
133A TYR* 2.9 27.1 - - + +
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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
----------------------------------------------------------
16A LEU* 3.9 22.6 - - + +
19A THR* 4.1 21.3 - - + -
20A VAL* 3.8 20.4 - - + +
23A LYS* 4.1 24.7 - - + -
61A HIS* 3.0 18.4 + - + +
62A ALA* 3.2 8.9 + - - +
64A LYS* 1.3 75.3 - - - +
66A ILE* 1.3 64.6 + - - +
68A TYR* 3.2 6.0 + - - +
69A GLN* 3.0 22.3 + - - +
110A LEU* 5.6 2.7 - - + -
113A LEU* 5.8 0.2 - - + -
128A PHE* 3.8 26.2 - - + -
129A LEU* 4.7 7.2 - - + -
133A TYR* 4.4 13.5 - - + -
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Residues in contact with ILE 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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20A VAL* 4.3 15.3 - - + -
24A PHE* 4.3 19.3 - - + -
62A ALA 3.1 14.6 + - - +
63A GLU* 3.5 13.5 - - + +
64A LYS 3.3 0.2 - - - -
65A LEU* 1.3 75.3 - - - +
67A GLU* 1.3 66.1 + - + +
69A GLN* 3.2 17.1 + - - +
70A ASN* 3.2 19.7 + - - +
76A VAL* 3.9 26.8 - - + +
78A LEU* 4.2 22.7 - - + -
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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
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63A GLU* 3.1 21.9 + - - +
64A LYS* 3.5 40.9 + - + +
65A LEU 3.2 0.2 - - - -
66A ILE* 1.3 79.4 - - + +
68A TYR* 1.3 57.2 + - - +
70A ASN* 3.2 10.5 + - - +
71A GLN* 2.9 28.9 + - - +
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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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8A PHE* 4.4 1.3 - + - -
16A LEU* 3.5 22.7 - - + -
64A LYS 2.9 8.9 + - - +
65A LEU* 3.6 5.6 - - - +
66A ILE 3.2 0.2 - - - -
67A GLU* 1.3 72.9 - - - +
69A GLN* 1.3 67.0 + - - +
71A GLN* 3.2 19.1 + - - +
72A ARG* 2.7 62.0 + - + +
124A HIS* 2.8 33.1 + + - -
125A MET* 3.1 33.5 - - + -
128A PHE* 3.4 55.4 - + + -
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Residues in contact with GLN 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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8A PHE* 3.3 30.1 - - - -
13A GLU* 3.1 36.3 + - - +
16A LEU* 3.8 15.7 - - + +
17A ASN* 3.2 25.0 + - - +
65A LEU 3.0 12.4 + - - +
66A ILE* 3.3 10.8 - - - +
68A TYR* 1.3 79.8 - - - +
70A ASN* 1.3 58.9 + - - +
72A ARG* 3.5 2.9 + - - +
73A GLY 3.3 2.4 + - - -
74A GLY* 2.9 38.9 + - - -
75A ARG 3.9 4.3 - - - -
76A VAL* 3.7 23.1 - - + -
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Residues in contact with ASN 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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4A VAL* 4.8 2.6 - - - +
66A ILE* 3.2 20.6 + - - +
67A GLU* 3.6 10.9 - - - +
68A TYR 3.2 0.2 - - - -
69A GLN* 1.3 78.4 - - - +
71A GLN* 1.3 64.8 + - - +
73A GLY* 3.1 13.3 + - - -
74A GLY 4.1 11.1 - - - +
75A ARG* 4.4 11.0 + - - +
76A VAL* 4.4 11.6 + - - +
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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
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4A VAL* 3.8 12.6 - - - +
67A GLU 2.9 15.7 + - - +
68A TYR* 3.2 36.2 + - - +
70A ASN* 1.3 77.6 - - - +
72A ARG* 1.3 61.7 + - - +
73A GLY 3.7 0.3 + - - -
124A HIS* 3.9 17.1 + - - -
128A PHE* 5.6 0.4 - - - -
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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
----------------------------------------------------------
4A VAL* 3.9 5.2 - - - +
5A ARG* 3.5 24.3 - - - +
6A GLN 3.1 19.0 + - - +
7A ASN* 3.1 31.3 + - - +
8A PHE* 3.8 33.6 - - + +
68A TYR* 2.7 66.9 + - + +
69A GLN 4.1 0.7 - - - +
70A ASN 3.2 0.2 - - - -
71A GLN* 1.3 82.8 - - - +
73A GLY* 1.3 61.3 + - - +
122A ASP* 3.1 28.4 + - - -
124A HIS* 3.8 22.7 + - - +
125A MET* 4.2 0.2 - - - +
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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