Contacts of the helix formed by residues 49 - 73 (chain A) in PDB entry 3N3B
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 THR 49 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A THR 3.8 3.1 + - - +
48A LEU* 1.3 76.8 - - - +
50A VAL* 1.3 60.3 + - - +
51A VAL* 3.9 10.6 + - - +
52A GLU* 3.0 37.8 + - - +
53A GLN* 2.9 28.9 + - - +
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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
----------------------------------------------------------
49A THR* 1.3 73.1 - - - +
51A VAL* 1.3 59.4 + - + +
53A GLN* 3.4 17.2 + - - +
54A GLN* 2.9 40.7 + - + +
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 3.9 9.2 + - - +
50A VAL* 1.3 79.5 - - + +
52A GLU* 1.3 58.7 + - + +
54A GLN* 3.4 7.0 + - - +
55A LEU* 2.9 29.5 + - + +
243A GLU* 3.5 56.5 - - + +
244A THR* 4.0 15.5 - - + -
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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
----------------------------------------------------------
47A THR 4.9 0.5 - - - +
48A LEU* 3.6 27.7 - - + +
49A THR* 3.0 41.6 + - - +
51A VAL* 1.3 81.2 - - + +
53A GLN* 1.3 53.1 + - - +
55A LEU* 3.5 8.1 + - - +
56A THR* 2.6 37.1 + - - -
171A TYR* 5.2 1.4 - - - -
172A PHE* 3.8 17.3 - - + -
177A LYS* 5.3 5.8 - - - +
244A THR* 5.6 0.2 - - + -
246A TRP* 3.7 33.2 - - + -
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 3.0 62.9 + - + +
46A GLN* 4.8 2.4 - - - +
48A LEU* 4.0 20.1 + - + +
49A THR 2.9 15.3 + - - +
50A VAL* 3.7 23.5 - - - +
52A GLU* 1.3 74.7 - - - +
54A GLN* 1.3 64.7 - - - +
56A THR* 3.3 4.2 + - - -
57A MET* 3.1 34.4 + - + +
117A ASP* 5.8 1.8 + - - -
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 2.9 27.3 + - + +
51A VAL* 3.7 7.8 - - - +
53A GLN* 1.3 76.0 - - - +
55A LEU* 1.3 61.9 + - - +
57A MET* 3.5 12.5 + - + +
58A ARG* 3.1 74.6 + - + +
121A ALA* 5.3 0.2 - - - +
243A GLU* 4.0 15.1 - - - +
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Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 2.9 19.0 + - + +
52A GLU* 3.7 7.6 - - - +
53A GLN 3.3 0.2 - - - -
54A GLN* 1.3 74.9 - - - +
56A THR* 1.3 63.8 + - - +
58A ARG* 3.5 6.2 + - - +
59A VAL* 3.0 38.7 + - + +
168A LEU* 3.8 17.7 - - + -
240A LEU* 3.3 37.2 - - + +
241A TYR* 3.7 31.2 - - + -
244A THR* 3.9 12.6 - - + -
246A TRP* 3.8 25.1 - - + -
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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
----------------------------------------------------------
45A TRP* 3.7 25.5 - - + -
48A LEU* 4.7 0.7 - - - +
52A GLU 2.6 24.6 + - - -
53A GLN 3.5 6.1 - - - -
55A LEU* 1.3 76.1 - - - +
57A MET* 1.3 62.0 + - + +
59A VAL* 3.4 3.1 + - - +
60A PHE* 3.2 53.4 + - + -
108A ILE* 5.6 3.4 - - + -
112A LEU* 6.4 0.7 - - + -
113A CYS* 6.0 0.9 - - - -
168A LEU* 3.6 11.7 - - + +
172A PHE* 3.6 20.1 - - + -
178A LEU* 4.9 8.7 - - + -
181A THR* 6.1 0.4 - - + -
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Residues in contact with MET 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 4.3 12.1 - - + -
53A GLN* 3.1 32.3 + - + +
54A GLN* 4.1 9.0 - - + +
56A THR* 1.3 80.4 - - + +
58A ARG* 1.3 56.5 + - - +
60A PHE 3.5 0.3 + - - -
61A THR* 3.0 35.5 + - - +
109A PHE* 3.9 16.8 - - + -
113A CYS* 3.8 26.9 - - - -
114A GLN 6.0 0.2 - - - +
117A ASP* 3.7 47.1 - - + +
118A VAL* 3.8 13.7 - - + -
121A ALA* 3.7 15.0 - - + -
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLN* 3.1 60.6 + - + +
55A LEU* 3.9 6.3 - - - +
57A MET* 1.3 74.3 - - - +
59A VAL* 1.3 64.9 + - - +
61A THR* 3.1 16.2 + - - -
62A GLY* 3.3 9.4 + - - -
121A ALA* 4.3 12.9 - - + +
124A TRP* 3.3 67.6 - - + +
125A SER* 3.8 4.5 + - - -
236A TYR* 4.4 2.6 + - - -
239A GLU 5.1 4.2 + - - -
240A LEU* 3.9 26.2 + - + +
243A GLU* 5.3 2.8 + - - -
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 3.0 33.0 + - + +
56A THR 3.5 5.6 - - - +
57A MET 3.3 0.2 - - - -
58A ARG* 1.3 77.8 - - - +
60A PHE* 1.3 69.1 + - + +
62A GLY* 3.3 3.3 + - - -
63A LEU* 3.1 35.2 + - + +
165A GLY* 3.4 36.1 - - - +
168A LEU* 3.9 18.4 - - + -
236A TYR* 4.9 2.5 + - - -
240A LEU* 4.5 14.8 - - + -
241A TYR* 4.2 12.8 - - - +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.2 42.5 + - + +
59A VAL* 1.3 81.9 - - + +
61A THR* 1.3 55.1 + - - +
63A LEU* 3.8 15.3 - - + +
64A THR* 2.5 39.0 + - - -
105A TYR* 3.6 27.9 - + + -
108A ILE* 4.3 22.2 - - + -
109A PHE* 3.5 22.4 - + + -
168A LEU* 5.9 0.9 - - + -
169A PRO* 4.4 18.2 - - + -
181A THR* 4.2 18.4 - - + -
185A ILE* 3.6 33.7 - - + -
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Residues in contact with THR 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET 3.0 22.0 + - - +
58A ARG* 3.1 7.6 + - - -
60A PHE* 1.3 76.2 - - - +
62A GLY* 1.3 60.4 + - - +
64A THR* 3.6 8.8 + - - -
65A LEU* 3.4 19.4 + - - +
109A PHE* 3.7 15.9 - - + -
118A VAL 4.3 0.7 - - - +
121A ALA* 3.3 14.6 + - + -
122A TYR* 3.7 43.9 - - + +
125A SER* 2.7 28.2 + - - -
8B ALA* 4.2 6.2 - - - +
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Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG 3.3 6.9 + - - -
59A VAL 3.3 4.7 + - - -
60A PHE 3.2 0.4 - - - -
61A THR* 1.3 82.3 + - - +
63A LEU* 1.3 62.3 + - - +
65A LEU* 3.3 13.4 + - - +
66A LEU* 3.4 19.8 + - - +
125A SER* 3.7 0.6 + - - -
131A LEU* 3.9 27.5 - - - +
236A TYR* 3.9 12.1 - - - -
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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
----------------------------------------------------------
59A VAL* 3.1 28.1 + - + +
60A PHE* 3.4 26.7 + - + +
62A GLY* 1.3 74.4 - - - +
64A THR* 1.3 58.5 - - - +
66A LEU* 3.6 8.2 + - + +
67A ASP* 3.1 32.2 + - - +
105A TYR* 3.5 29.0 - - + +
162A PHE* 3.6 44.9 - - + +
164A SER* 5.9 0.4 - - - +
165A GLY* 4.4 9.2 - - - +
166A PHE* 4.1 20.4 - - + -
236A TYR* 6.1 1.6 - - + +
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE 2.5 24.7 + - - -
61A THR* 3.7 10.3 - - - -
62A GLY 3.2 0.2 - - - -
63A LEU* 1.3 75.5 - - - +
65A LEU* 1.3 58.8 + - - +
67A ASP* 4.0 1.9 - - - +
68A THR* 2.5 35.0 + - - -
102A ALA* 3.9 17.7 - - + +
105A TYR* 3.4 22.1 - - + +
106A SER* 5.3 0.4 - - - +
109A PHE* 4.4 4.0 - - - -
122A TYR* 4.2 6.5 - - - +
8B ALA* 4.3 3.8 - - + -
9B ILE* 3.2 39.0 - - + +
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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
----------------------------------------------------------
61A THR 3.4 6.4 + - - +
62A GLY* 3.3 9.3 + - - +
63A LEU 3.3 0.8 - - - -
64A THR* 1.3 79.8 - - - +
66A LEU* 1.3 59.8 + - + +
68A THR* 3.5 3.5 + - - -
69A LEU* 3.1 25.9 + - + +
125A SER* 5.3 1.6 - - - +
126A GLU* 4.6 7.9 - - - +
131A LEU* 3.9 26.2 - - + -
132A GLN* 3.7 24.0 - - - +
135A ALA* 4.5 19.3 - - + -
6B ILE* 3.5 32.7 - - + +
7B SER* 4.2 0.2 - - - -
8B ALA* 3.7 30.4 - - + +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLY 3.4 19.4 + - - +
63A LEU* 3.6 7.6 + - + +
64A THR 3.3 0.2 - - - -
65A LEU* 1.3 76.4 - - + +
67A ASP* 1.3 60.3 + - - +
69A LEU* 3.4 13.8 - - + +
70A GLN* 3.1 30.3 + - - +
131A LEU* 4.3 10.1 - - + -
134A LYS* 3.7 41.1 - - + +
135A ALA* 4.6 20.4 - - + -
157A LEU* 4.2 18.6 - - + +
162A PHE* 3.5 35.4 - - + +
236A TYR* 6.0 0.2 - - + -
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Residues in contact with ASP 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU 3.1 12.3 + - - +
66A LEU* 1.3 73.9 - - - +
68A THR* 1.3 59.8 + - - +
70A GLN* 3.3 4.1 + - - +
71A ASN* 3.0 27.4 + - - +
98A GLU* 3.0 21.1 - - - +
101A HIS* 3.5 13.8 + - - +
102A ALA* 3.9 13.5 - - + +
105A TYR* 3.0 29.1 + - - -
158A GLU* 3.0 2.6 - - - +
162A PHE* 3.3 15.6 - - - -
188A ILE* 4.9 0.3 - - - +
320A MN 2.2 34.7 + - - -
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR 2.5 24.0 + - - -
65A LEU 3.6 5.4 - - - -
67A ASP* 1.3 75.8 - - - +
69A LEU* 1.3 58.9 + - - +
71A ASN* 3.3 7.5 + - - +
72A VAL* 3.0 43.6 + - + +
102A ALA* 4.0 4.2 - - - +
6B ILE* 4.5 7.9 - - + -
7B SER 3.6 21.3 - - - +
9B ILE* 3.5 37.4 + - + +
85B PRO* 6.2 2.0 - - + -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU 3.1 13.7 + - - +
66A LEU* 3.4 15.7 - - + +
68A THR* 1.3 78.1 - - - +
70A GLN* 1.3 51.1 + - - +
72A VAL 4.8 0.2 - - - +
73A ILE* 3.0 21.0 + - + +
74A GLY 2.7 28.6 + - - -
135A ALA* 4.2 22.7 - - + +
138A ILE* 4.1 24.7 - - + -
139A GLN* 3.8 37.7 - - + +
142A TYR* 4.4 10.3 - - + -
157A LEU* 4.3 11.2 - - + -
6B ILE* 4.2 20.1 - - + +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU 3.1 19.0 + - - +
67A ASP 3.6 8.1 - - - +
68A THR 3.3 0.2 - - - -
69A LEU* 1.3 75.6 - - - +
71A ASN* 1.3 61.1 + - - +
74A GLY* 3.4 5.3 + - - -
75A ALA* 2.9 33.4 + - + +
98A GLU* 3.7 21.4 - - - +
142A TYR* 2.6 39.0 + - - -
154A SER* 3.4 21.2 + - - +
157A LEU* 3.5 18.5 - - + +
158A GLU* 2.9 36.0 - - + +
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Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP 3.0 17.3 + - - +
68A THR* 3.6 8.4 - - - +
69A LEU 3.3 0.2 - - - -
70A GLN* 1.3 77.0 - - - +
72A VAL* 1.3 74.9 + - - +
76A PRO* 3.5 9.5 - - - +
95A SER* 2.9 39.5 + - - +
98A GLU* 3.7 13.6 - - + +
99A ALA* 3.7 22.1 - - - +
9B ILE* 6.1 1.2 - - - +
85B PRO 5.7 0.2 + - - -
88B GLU* 4.5 2.4 + - - +
89B ALA* 4.1 15.0 - - - +
92B SER* 2.8 30.2 + - - -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A THR* 3.0 30.3 + - + +
71A ASN* 1.3 89.0 - - - +
73A ILE* 1.3 72.1 + - + +
76A PRO* 3.4 16.8 - - - +
6B ILE* 4.1 16.8 - - + -
79B MET* 6.0 1.6 - - - +
88B GLU* 4.0 35.4 - - + +
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Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 3.0 10.8 + - + +
72A VAL* 1.3 90.5 - - + +
74A GLY* 1.3 71.2 - - - +
76A PRO* 3.4 3.6 - - - +
77A SER* 3.1 26.4 + - - -
139A GLN* 3.4 36.1 - - + +
142A TYR* 3.7 28.3 - - + +
143A ARG* 3.6 37.9 - - - +
5B ARG* 4.9 1.8 - - + -
6B ILE* 3.8 21.3 - - + -
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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