Contacts of the helix formed by residues 42 - 69 (chain A) in PDB entry 3DVA
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 42 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU 4.3 0.2 - - - -
41A LEU* 1.3 75.6 - - - +
43A ASP* 1.3 61.7 + - - +
44A GLU* 3.6 6.6 + - - +
45A GLN* 2.8 37.5 + - - +
46A LEU* 3.0 28.5 + - - +
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Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU 5.0 0.9 - - - +
42A SER* 1.3 75.8 - - - +
44A GLU* 1.3 57.8 + - - +
46A LEU* 3.5 8.6 + - - +
47A LYS* 2.9 36.9 + - + +
306A LYS* 4.9 5.4 + - - -
308A LEU* 3.4 44.1 - - + +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER* 3.2 7.0 + - - +
43A ASP* 1.3 77.0 - - - +
45A GLN* 1.3 61.2 + - + +
47A LYS* 3.1 26.4 + - - +
48A GLU* 2.9 38.6 + - + +
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Residues in contact with GLN 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLU 4.2 2.8 + - - +
41A LEU* 3.4 22.7 - - + +
42A SER* 2.8 43.1 + - - +
44A GLU* 1.3 77.2 - - + +
46A LEU* 1.3 63.8 + - - +
48A GLU* 3.2 3.5 + - - -
49A LEU* 3.0 22.0 + - - +
90A PHE* 3.5 31.2 - - + -
242A TYR* 5.5 1.8 + - - -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.7 40.2 - - + +
42A SER 3.0 24.2 + - - +
43A ASP* 3.6 7.6 - - - +
45A GLN* 1.3 75.9 - - - +
47A LYS* 1.3 60.8 + - - +
49A LEU* 3.6 2.1 + - - +
50A MET 3.3 15.8 + - - -
239A LEU* 4.2 9.6 - - + -
299A PHE* 3.5 31.9 - - + -
302A PHE* 4.5 9.4 - - + -
303A LEU* 3.7 21.5 - - + +
306A LYS* 4.3 25.4 - - - -
308A LEU* 4.4 5.8 - - + -
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP* 2.9 31.0 + - + +
44A GLU* 3.1 29.4 + - - +
46A LEU* 1.3 77.5 - - + +
48A GLU* 1.3 58.9 + - - +
50A MET 3.4 1.2 + - - -
51A ARG* 2.9 26.5 + - - +
303A LEU* 4.6 3.1 - - + -
308A LEU* 2.9 46.8 + - + +
309A TRP* 3.6 13.9 - - + -
313A GLU* 2.5 36.6 + - - +
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Residues in contact with GLU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A GLU* 2.9 26.1 + - + +
45A GLN* 3.9 4.9 - - - +
47A LYS* 1.3 73.4 - - - +
49A LEU* 1.3 61.5 + - - +
51A ARG* 3.0 30.5 + - - +
52A ARG* 2.8 69.6 + - - +
90A PHE* 4.4 9.6 - - + -
110A TRP* 4.7 5.7 - - - -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.9 14.4 - - + -
45A GLN 3.0 16.3 + - - +
46A LEU* 3.8 6.5 - - + +
48A GLU* 1.3 75.1 - - - +
50A MET* 1.3 59.6 + - - +
52A ARG* 3.3 2.5 + - - +
53A MET* 3.0 44.2 + - + +
86A ILE* 4.1 8.7 - - + -
87A ALA* 3.7 34.1 - - + +
90A PHE* 3.8 35.3 - - + -
238A PRO* 4.2 19.1 - - + +
239A LEU* 5.0 1.3 - - + -
242A TYR* 5.2 2.7 - - + -
299A PHE* 4.0 17.7 - - + -
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Residues in contact with MET 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU 3.3 2.8 + - - +
47A LYS 3.6 8.5 - - - +
48A GLU 3.2 0.2 - - - -
49A LEU* 1.3 75.5 - - - +
51A ARG* 1.3 59.2 + - - +
53A MET* 3.3 13.0 + - - -
54A VAL* 3.0 53.3 + - + +
296A LEU* 3.8 14.6 - - + +
299A PHE* 3.6 32.7 - - + -
300A ARG* 3.7 36.1 - - + +
303A LEU* 3.6 12.3 - - + -
309A TRP* 3.7 36.3 - - + +
314A GLU* 4.1 4.7 - - - +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LYS 2.9 15.7 + - - +
48A GLU* 3.0 33.6 + - - +
50A MET* 1.3 77.4 - - - +
52A ARG* 1.3 57.2 + - - +
55A TYR* 2.9 30.7 + - + +
110A TRP* 5.3 1.6 - - + -
309A TRP* 4.1 10.2 - - + -
313A GLU* 4.7 17.4 + - - +
316A ASN* 4.9 8.1 + - - +
317A VAL* 3.4 50.8 - - + +
320A GLN* 2.9 32.5 + - - +
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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
----------------------------------------------------------
48A GLU* 2.8 48.1 + - - +
49A LEU 3.7 2.0 - - - +
51A ARG* 1.3 74.3 - - - +
53A MET* 1.3 56.9 + - - +
55A TYR* 3.5 1.0 - - - +
56A THR* 2.7 37.7 + - - -
86A ILE* 3.6 20.4 - - + -
89A HIS* 3.6 31.7 + - - -
90A PHE* 3.9 31.0 - - - +
110A TRP* 3.7 46.6 + - + +
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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 LEU* 3.0 29.3 + - + +
50A MET* 3.3 9.6 + - - +
52A ARG* 1.3 74.6 - - - +
54A VAL* 1.3 59.4 + - - +
56A THR* 3.5 1.1 + - - -
57A ARG* 3.0 25.3 + - - +
82A GLU* 3.4 27.8 - - + +
83A ALA* 4.1 16.8 - - - -
86A ILE* 4.0 15.7 - - + -
238A PRO* 3.7 30.7 - - + -
295A PRO* 4.8 3.6 - - - +
296A LEU* 3.5 17.4 - - + +
299A PHE* 3.3 39.5 - - + -
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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
----------------------------------------------------------
50A MET* 3.0 49.5 + - + +
51A ARG 4.0 2.7 - - - +
53A MET* 1.3 73.4 - - - +
55A TYR* 1.3 65.7 + - - +
57A ARG* 3.2 6.5 + - + +
58A ILE* 3.1 23.4 + - + +
296A LEU* 4.0 12.6 - - + -
309A TRP* 4.4 3.4 - - + -
314A GLU* 3.9 27.4 - - + +
317A VAL* 4.1 12.3 - - + -
318A ILE* 3.9 28.5 - - + -
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 2.9 21.7 + - + +
52A ARG 3.5 5.6 - - - +
53A MET 3.3 0.2 - - - -
54A VAL* 1.3 77.3 - - - +
56A THR* 1.3 58.7 + - - +
58A ILE* 3.2 5.9 + - - +
59A LEU* 2.8 37.3 + - + -
109A ILE* 5.9 5.4 - - + -
110A TRP* 3.5 32.3 - + + -
115A LEU* 3.8 21.2 - - + +
317A VAL* 4.0 13.2 - - + +
320A GLN* 4.4 10.3 - - + -
321A ALA* 3.5 39.0 + - + +
324A GLU* 2.6 40.5 + - - +
325A ILE* 5.3 1.8 - - + -
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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
----------------------------------------------------------
52A ARG 2.7 25.2 + - - -
53A MET 3.8 4.0 - - - -
55A TYR* 1.3 73.3 - - - +
57A ARG* 1.3 65.9 + - - +
59A LEU* 3.2 12.7 + - + +
60A ASP* 3.1 21.5 + - - +
78A THR* 4.1 10.6 + - - +
82A GLU* 4.2 11.0 - - + -
85A GLN* 4.9 3.1 - - - +
86A ILE* 3.4 14.4 - - + +
106A PRO* 3.8 30.7 - - + -
110A TRP* 3.1 21.8 + - - -
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET 3.0 14.5 + - - +
54A VAL* 3.2 10.1 + - + +
56A THR* 1.3 74.9 - - - +
58A ILE* 1.3 63.6 + - + +
60A ASP* 3.3 7.1 + - - +
61A GLN* 3.3 41.9 + - - +
79A ALA* 4.0 14.1 - - - -
80A GLY* 3.7 13.9 - - - +
82A GLU* 2.6 44.3 + - - -
268A TYR* 4.1 8.3 - - - -
294A ASP* 2.8 43.2 + - - -
295A PRO* 4.1 0.6 - - - +
296A LEU* 3.6 26.8 - - + +
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.1 16.3 + - + +
55A TYR 3.5 6.7 - - - +
57A ARG* 1.3 75.2 - - + +
59A LEU* 1.3 66.1 + - - +
61A GLN* 3.3 28.8 + - - +
62A ARG* 3.1 36.6 + - + +
318A ILE* 3.6 45.8 - - + +
321A ALA* 3.8 20.9 - - + -
322A LYS* 4.2 17.9 - - + -
325A ILE* 4.3 2.2 - - + -
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Residues in contact with LEU 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 2.8 23.7 + - + +
56A THR* 3.2 18.4 + - + +
58A ILE* 1.3 77.9 - - - +
60A ASP* 1.3 53.3 + - - +
62A ARG* 3.9 1.1 - - + +
63A SER* 2.7 47.9 + - - +
75A TYR* 5.6 3.4 - - + +
78A THR* 6.1 0.4 - - - +
105A VAL* 6.0 0.7 - - + -
106A PRO* 4.8 18.8 - - + -
109A ILE* 3.9 26.5 - - + -
110A TRP* 6.0 1.6 - - - +
115A LEU* 3.7 24.9 - - + -
119A PHE* 4.2 9.2 - - + -
325A ILE* 3.9 21.3 - - + +
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR 3.1 7.9 + - - +
57A ARG 3.5 9.4 - - - +
58A ILE 3.2 0.4 - - - -
59A LEU* 1.3 75.6 - - - +
61A GLN* 1.3 66.6 + - - +
63A SER* 3.3 0.9 + - - -
64A ILE* 2.9 44.0 + - - +
75A TYR* 2.4 40.5 + - - +
77A PRO* 3.4 4.5 - - - +
78A THR* 3.2 19.9 + - - +
79A ALA* 2.8 41.0 + - + +
269A GLY* 5.8 0.7 - - - -
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 3.3 31.3 + - + +
58A ILE* 3.3 32.3 + - - +
60A ASP* 1.3 79.1 - - + +
62A ARG* 1.3 63.1 + - + +
64A ILE* 3.3 9.0 + - - +
65A SER* 3.0 27.8 + - - -
322A LYS* 5.7 2.3 - - - -
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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
----------------------------------------------------------
58A ILE* 3.1 25.4 + - + +
59A LEU 4.0 0.4 - - - +
61A GLN* 1.3 79.5 - - + +
63A SER* 1.3 61.2 + - - +
65A SER* 3.2 25.4 + - - -
66A LEU* 2.8 59.9 + - + +
69A GLN* 4.5 5.5 - - - +
71A ARG* 5.6 2.2 - - - +
119A PHE* 6.2 0.2 - - + -
322A LYS* 4.9 19.3 - - + +
325A ILE* 3.7 39.7 - - + +
326A LYS* 4.7 18.6 - - - +
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 2.7 36.5 + - - +
60A ASP 3.7 0.4 - - - -
62A ARG* 1.3 76.2 - - - +
64A ILE* 1.3 63.2 + - - +
66A LEU* 4.9 0.7 - - - -
67A ASN* 3.0 26.7 + - - +
72A LEU* 3.7 17.1 - - - +
75A TYR* 3.6 38.7 - - - -
119A PHE* 4.1 11.0 - - - -
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASP* 2.9 41.6 + - - +
61A GLN* 3.5 7.2 - - - +
63A SER* 1.3 76.2 - - - +
65A SER* 1.3 59.0 + - - +
67A ASN* 3.5 2.9 + - - +
68A ARG* 3.0 58.0 + - - +
75A TYR* 3.8 14.6 - - + -
77A PRO* 4.5 11.2 - - + -
269A GLY* 5.4 3.1 - - - -
270A PRO* 4.9 9.6 - - + -
273A MET* 3.9 20.4 - - + -
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN 3.0 16.2 + - - -
62A ARG* 3.2 21.7 + - - -
64A ILE* 1.3 75.3 - - - +
66A LEU* 1.3 60.2 + - - +
68A ARG* 3.1 11.6 + - - +
69A GLN* 2.9 50.0 + - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 2.8 43.9 + - - +
65A SER* 1.3 68.8 + - - +
67A ASN* 1.3 66.2 + - - +
69A GLN* 2.9 16.5 + - - +
71A ARG* 2.8 65.9 + - + +
72A LEU* 3.7 25.4 - - + -
119A PHE* 4.6 4.5 - - + -
325A ILE* 4.3 19.7 - - + -
329A ILE* 3.8 27.8 - - + -
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 3.0 19.9 + - - +
64A ILE 3.7 3.5 - - - +
66A LEU* 1.3 75.1 - - - +
68A ARG* 1.3 64.7 + - - +
70A GLY* 3.0 19.2 + - - -
72A LEU* 3.8 20.8 + - + +
73A GLY* 2.7 28.4 + - - +
74A PHE* 4.9 0.2 - - - +
75A TYR* 4.5 2.9 - - + +
273A MET* 3.1 47.9 + - + +
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Residues in contact with ARG 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 3.0 44.0 + - + +
65A SER* 3.1 14.3 + - - +
67A ASN* 1.3 82.4 + - - +
69A GLN* 1.3 58.1 + - + +
70A GLY 3.1 0.8 + - - -
270A PRO* 5.6 2.6 - - - +
273A MET* 4.6 8.6 - - - +
278A PRO* 4.0 28.9 + - - +
279A THR* 4.7 7.1 - - - +
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Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.5 8.5 - - - +
65A SER* 2.9 40.1 + - - +
66A LEU* 2.9 21.1 + - - +
68A ARG* 1.3 77.6 - - + +
70A GLY* 1.3 59.4 + - - +
71A ARG* 3.1 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