Contacts of the helix formed by residues 49 - 76 (chain A) in PDB entry 2G7S
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 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 3.3 12.4 + - - -
44A HIS* 5.3 3.8 - - - -
47A PHE* 3.1 2.9 + - - +
48A PRO* 1.3 81.0 - - - +
50A LYS* 1.3 60.6 + - - +
51A SER* 3.0 12.9 + - - -
52A ASP* 3.0 23.9 + - - +
53A LEU* 3.0 23.4 + - - +
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Residues in contact with LYS 50 (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 TYR* 2.8 56.7 + - + +
25A ASN* 4.2 8.3 + - - +
27A PHE* 2.9 40.8 + - + -
28A SER* 4.9 2.5 - - - +
29A TYR* 3.3 29.4 + - + -
44A HIS* 6.1 0.2 - - - -
49A SER* 1.3 71.8 - - - +
51A SER* 1.3 66.2 + - - +
53A LEU* 3.2 5.4 + - + +
54A VAL* 2.9 27.4 + - + +
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Residues in contact with SER 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR* 3.3 9.8 + - - -
49A SER* 3.0 11.3 + - - -
50A LYS* 1.3 80.0 - - - +
52A ASP* 1.4 59.3 + - - +
54A VAL 3.4 0.2 + - - -
55A CYS* 2.8 34.6 + - - -
115A PRO* 3.6 32.8 - - - -
117A THR* 4.2 9.2 + - - -
118A VAL* 3.8 4.6 - - - +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A HIS 4.8 0.3 - - - +
47A PHE* 3.6 12.1 - - - -
48A PRO* 3.2 32.3 - - + +
49A SER* 3.0 21.2 + - - +
51A SER* 1.4 75.2 + - - +
53A LEU* 1.3 66.4 + - - +
55A CYS* 3.2 8.0 + - - +
56A LYS* 2.9 51.2 + - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.7 25.1 - - + -
12A LEU* 3.7 6.9 - - + +
15A ALA* 3.8 26.9 - - + -
27A PHE* 5.0 4.0 - - + -
29A TYR* 3.8 29.6 - - + +
32A ILE* 4.0 8.5 - - + -
43A ILE* 4.2 2.0 - - + -
47A PHE* 3.6 29.4 - - + -
49A SER 3.0 12.7 + - - +
50A LYS* 3.4 10.1 - - + +
52A ASP* 1.3 76.6 + - - +
54A VAL* 1.3 70.0 + - + +
56A LYS* 3.2 4.2 + - - +
57A LEU* 2.9 26.7 + - + +
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.8 22.9 - - + -
24A TYR* 3.6 27.1 - - + -
27A PHE* 4.1 23.3 - - + -
50A LYS* 2.9 21.7 + - + +
51A SER 4.0 2.2 - - - +
53A LEU* 1.3 80.9 - - + +
55A CYS* 1.3 59.8 + - - +
57A LEU* 3.5 6.9 - - + +
58A VAL* 2.8 36.0 + - + +
107A LEU* 4.4 1.3 - - + -
118A VAL* 3.9 25.1 - - + -
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Residues in contact with CYS 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A SER 2.8 24.8 + - - +
52A ASP* 3.2 9.2 + - - +
54A VAL* 1.3 71.5 - - - +
56A LYS* 1.3 60.8 + - + +
58A VAL* 3.4 2.8 + - - +
59A SER* 2.8 31.8 + - - -
117A THR* 3.4 49.4 - - - -
118A VAL* 3.6 7.6 - - - +
121A GLU* 4.2 16.4 - - + +
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.0 18.6 - - + +
47A PHE* 4.1 15.7 - - + -
52A ASP* 2.9 45.7 + - - +
53A LEU 3.5 4.0 - - - +
55A CYS* 1.3 76.6 - - + +
57A LEU* 1.3 64.0 + - - +
59A SER* 3.9 6.6 - - - -
60A GLN* 3.1 23.9 + - - +
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Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.7 14.3 - - + +
15A ALA* 3.6 41.5 - - + +
16A ARG* 4.1 27.6 + - + +
19A ILE* 4.2 20.6 - - + -
27A PHE* 5.2 0.2 - - + -
53A LEU* 2.9 22.0 + - + +
54A VAL* 3.5 7.2 - - + +
56A LYS* 1.3 78.3 - - - +
58A VAL* 1.4 63.3 + - + +
60A GLN* 3.3 9.2 + - - +
61A TYR* 2.9 28.1 + - - +
103A VAL* 3.9 26.9 - - + -
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 2.8 30.8 + - + +
55A CYS 4.0 2.5 - - - +
57A LEU* 1.4 71.5 - - + +
59A SER* 1.4 61.3 + - - +
61A TYR* 3.1 7.2 + - - +
62A ARG* 2.9 33.8 + - - +
103A VAL* 4.0 9.2 - - + -
104A CYS* 3.7 26.2 - - - -
107A LEU* 3.6 29.8 - - + -
118A VAL* 4.8 5.2 - - + -
121A GLU* 3.6 28.9 - - + -
122A VAL* 4.4 1.3 - - + +
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A CYS 2.8 18.4 + - - -
56A LYS* 3.9 10.1 - - - -
57A LEU 3.3 0.2 - - - -
58A VAL* 1.4 76.6 - - - +
60A GLN* 1.3 57.1 + - - +
62A ARG* 3.4 4.5 + - - +
63A GLN* 2.9 39.9 + - - +
121A GLU* 3.6 22.9 + - - -
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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
----------------------------------------------------------
9A ASP* 5.0 7.5 + - - +
12A LEU* 4.0 36.2 - - + +
13A GLN* 5.2 1.6 + - - -
16A ARG* 3.2 19.0 + - - +
56A LYS 3.1 16.8 + - - +
57A LEU* 3.6 5.0 - - - +
58A VAL 3.2 0.2 - - - -
59A SER* 1.3 73.8 - - - +
61A TYR* 1.3 67.9 + - - +
63A GLN* 3.3 16.3 + - - +
64A GLU* 3.0 45.4 + - + +
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Residues in contact with TYR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.7 33.4 - - - +
20A ILE* 5.8 1.8 - - + -
57A LEU* 2.9 17.8 + - + +
58A VAL* 3.1 7.4 + - - +
60A GLN* 1.3 77.6 - - - +
62A ARG* 1.3 60.8 + - + +
64A GLU* 3.3 4.5 + - + +
65A ALA* 2.8 35.4 + - + +
89A TYR* 5.3 5.7 + - - -
90A TRP* 3.6 15.7 - + - -
101A PHE 5.5 0.7 - - - -
102A CYS* 2.9 43.7 - - - +
103A VAL* 3.7 28.5 - - + -
104A CYS* 3.9 26.2 - - - -
125A HIS* 4.2 13.6 - + - -
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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
----------------------------------------------------------
58A VAL* 2.9 22.1 + - - +
59A SER 3.7 4.0 - - - +
61A TYR* 1.3 77.7 - - + +
63A GLN* 1.3 65.3 + - + +
65A ALA* 2.8 5.9 + - - -
66A GLU* 2.8 47.5 + - + +
104A CYS* 4.2 7.6 - - - -
121A GLU* 3.3 39.1 + - - -
124A ALA* 3.0 47.3 + - - +
125A HIS* 3.4 30.7 + - + +
127A ARG* 5.5 0.6 - - - +
128A SER* 4.2 10.3 - - - -
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Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A SER* 2.9 26.3 + - - +
60A GLN* 3.6 19.2 + - + +
62A ARG* 1.3 75.9 - - + +
64A GLU* 1.3 58.8 + - + +
66A GLU* 3.8 7.6 - - - +
67A ALA* 2.9 30.2 + - - +
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Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG* 3.0 43.4 + - - +
60A GLN* 3.0 27.8 + - + +
61A TYR* 3.6 4.5 - - + +
63A GLN* 1.3 74.6 - - + +
65A ALA* 1.3 63.6 + - - +
67A ALA* 3.3 7.1 + - - +
68A GLY* 3.0 20.8 + - - -
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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
----------------------------------------------------------
61A TYR* 2.8 30.3 + - + +
62A ARG* 2.8 8.5 + - - +
64A GLU* 1.3 75.9 - - - +
66A GLU* 1.3 64.4 + - + +
68A GLY* 3.3 2.5 + - - -
69A ILE* 3.1 32.0 + - + +
89A TYR* 5.8 4.9 - - - +
125A HIS* 4.4 20.2 - - + +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 2.8 41.7 + - + +
63A GLN* 3.8 5.9 - - - +
65A ALA* 1.3 75.9 - - + +
67A ALA* 1.3 57.4 + - - +
69A ILE* 3.5 14.9 + - + +
70A ALA* 2.9 31.4 + - - +
125A HIS* 6.1 1.8 - - - +
128A SER* 3.3 25.0 + - - +
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Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN 2.9 18.1 + - - +
64A GLU* 3.7 8.1 - - - +
65A ALA 3.3 0.2 - - - -
66A GLU* 1.3 75.5 - - - +
68A GLY* 1.3 56.6 + - - +
70A ALA* 3.5 6.3 + - - +
71A GLU* 3.0 28.9 + - - +
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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 GLU 3.0 14.3 + - - -
65A ALA* 3.3 3.1 + - - -
67A ALA* 1.3 76.9 - - - +
69A ILE* 1.3 61.5 + - - +
71A GLU* 3.3 8.3 + - - +
72A LEU* 3.1 25.4 + - - +
89A TYR* 6.5 0.9 - - - -
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Residues in contact with ILE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 3.1 17.6 + - + +
66A GLU* 3.5 20.2 - - + +
68A GLY* 1.3 72.7 - - - +
70A ALA* 1.3 62.4 + - - +
72A LEU* 3.3 12.7 + - + +
73A GLU* 3.0 28.1 + - - +
86A TYR* 4.0 31.2 - - + -
89A TYR* 6.2 3.1 - - + -
128A SER* 5.5 1.8 - - - +
129A LEU* 4.5 14.1 - - + -
132A TRP* 3.5 56.8 - - + -
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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
----------------------------------------------------------
66A GLU 2.9 19.6 + - - +
67A ALA* 3.6 8.5 - - - +
69A ILE* 1.3 77.1 - - + +
71A GLU* 1.3 54.6 + - - +
73A GLU* 3.2 12.6 + - - +
74A LYS* 2.8 34.5 + - - +
132A TRP* 5.1 0.9 - - - +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA 3.0 17.4 + - - +
68A GLY* 3.3 8.3 + - - +
70A ALA* 1.3 72.5 - - - +
72A LEU* 1.3 66.9 + - + +
74A LYS* 3.0 36.8 + - - +
75A ASN* 3.0 41.8 + - - +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLY 3.1 13.8 + - - +
69A ILE* 3.4 20.2 - - + +
70A ALA 3.2 0.2 - - - -
71A GLU* 1.3 78.3 - - + +
73A GLU* 1.3 62.3 + - - +
75A ASN* 5.0 1.1 - - - +
76A ILE* 3.0 43.9 + - + +
82A GLN* 4.1 7.9 - - - +
85A ALA* 3.9 21.3 - - + +
86A TYR* 3.7 39.5 - - + +
89A TYR* 5.2 6.3 - - + -
132A TRP* 4.5 8.1 - - + -
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Residues in contact with GLU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ILE 3.0 8.5 + - - +
70A ALA* 3.2 12.5 + - - +
72A LEU* 1.3 80.0 - - - +
74A LYS* 1.3 62.2 + - - +
76A ILE 3.2 15.2 - - - +
82A GLN* 3.4 16.9 + - - +
132A TRP* 2.9 29.0 + - + +
139A ARG* 3.5 38.7 + - - +
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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
----------------------------------------------------------
70A ALA 2.8 19.5 + - - +
71A GLU* 3.0 27.8 + - - +
72A LEU 3.3 0.2 - - - -
73A GLU* 1.3 76.7 - - - +
75A ASN* 1.4 79.2 + - - +
76A ILE 4.8 1.4 - - - +
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A GLU* 3.0 43.0 + - - +
72A LEU* 4.2 2.2 - - - +
74A LYS* 1.4 94.8 - - - +
76A ILE* 1.3 65.1 + - + +
77A SER 4.0 1.6 + - - -
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Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.0 31.4 + - + +
73A GLU 3.2 6.2 - - - +
74A LYS 3.4 1.1 - - - -
75A ASN* 1.3 86.0 - - + +
77A SER* 1.3 62.5 + - - +
78A ASP 3.8 4.5 - - - +
81A GLU* 3.6 32.5 - - + +
82A GLN* 2.9 38.2 + - + +
85A ALA* 3.4 33.7 - - + -
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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