Contacts of the helix formed by residues 41 - 69 (chain D) in PDB entry 2VT4
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 GLU 41 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA* 1.3 63.6 + - - +
43D GLY* 3.3 6.0 - - - +
44D MET* 3.9 18.8 - - - +
45D SER* 2.7 39.8 + - - +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLU* 1.3 76.7 - - - +
43D GLY* 1.3 65.0 + - - +
45D SER* 3.2 7.1 + - - -
46D LEU* 2.9 24.7 + - - +
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Residues in contact with GLY 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLU 3.3 3.8 - - - +
42D ALA* 1.3 77.1 - - - +
44D MET* 1.3 70.6 + - - +
46D LEU* 3.1 7.7 + - - +
47D LEU* 3.0 22.2 + - - +
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Residues in contact with MET 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLU* 3.7 18.2 + - - +
42D ALA 3.4 0.4 - - - -
43D GLY* 1.3 78.4 - - - +
45D SER* 1.3 63.9 + - - +
47D LEU* 3.3 24.2 + - + +
48D MET* 3.0 33.0 + - + +
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D GLU* 2.7 28.9 + - - +
42D ALA* 3.5 6.5 - - - -
44D MET* 1.3 77.2 - - - +
46D LEU* 1.3 62.3 - - - +
48D MET* 3.4 6.2 + - - +
49D ALA* 3.1 22.7 + - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ALA 2.9 16.7 + - - +
43D GLY* 3.7 5.2 - - - +
45D SER* 1.3 73.2 - - - +
47D LEU* 1.3 67.9 + - - +
49D ALA* 3.0 19.8 + - + +
50D LEU* 3.0 39.9 + - + +
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Residues in contact with LEU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLY 3.0 12.0 + - - +
44D MET* 3.6 28.3 - - + +
46D LEU* 1.3 76.0 - - - +
48D MET* 1.3 75.6 + - + +
50D LEU* 2.9 8.3 + - - -
51D VAL* 2.9 33.1 + - + +
54D LEU* 3.7 26.5 - - + -
334D ALA* 4.4 14.8 - - + -
337D ALA* 5.6 3.8 - - + -
338D MET* 5.9 4.9 - - + -
341D ILE* 6.5 0.7 - - + -
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Residues in contact with MET 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D MET* 3.0 27.1 + - + +
45D SER* 3.8 6.7 - - - +
47D LEU* 1.3 103.6 - - + +
49D ALA* 1.3 60.3 + - - +
51D VAL* 3.1 35.0 + - + +
330D TRP* 4.3 34.1 - - + +
334D ALA* 4.5 9.6 - - + -
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER 3.1 12.0 + - - +
46D LEU* 3.0 16.5 + - + +
48D MET* 1.3 74.2 - - - +
50D LEU* 1.3 64.3 + - + +
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 3.0 44.4 + - + +
47D LEU* 2.9 6.5 + - - +
49D ALA* 1.3 85.8 - - + +
51D VAL* 1.3 52.4 + - - +
52D VAL 3.5 2.2 - - - -
53D LEU* 3.2 31.1 + - + +
54D LEU* 2.7 54.3 + - + +
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 2.9 18.0 + - + +
48D MET* 3.1 44.8 + - + +
50D LEU* 1.3 68.8 - - - +
52D VAL* 1.3 60.8 + - + +
54D LEU* 4.1 4.9 - - - -
55D ILE* 2.7 51.6 + - + +
95D VAL* 5.0 12.1 - - + -
330D TRP* 5.0 8.7 - - + -
333D TYR* 5.4 1.3 - - + -
334D ALA* 4.3 22.7 - - + +
337D ALA* 4.5 9.2 - - + -
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU 3.5 0.8 - - - -
51D VAL* 1.3 77.7 - - + +
53D LEU* 1.3 64.9 + - - +
55D ILE* 4.1 3.7 - - - +
56D VAL* 3.1 30.7 + - + +
91D GLY 3.8 19.7 - - - +
92D LEU* 6.0 1.6 - - + -
95D VAL* 3.8 27.1 - - + -
96D PRO* 4.6 14.8 - - + -
99D ALA* 6.1 2.0 - - + -
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D LEU* 3.2 32.0 + - + +
52D VAL* 1.3 80.0 - - - +
54D LEU* 1.3 64.1 + - + +
56D VAL* 5.0 1.1 - - - -
57D ALA* 2.9 49.8 + - + +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D LEU* 3.7 29.6 - - + -
50D LEU* 2.7 44.4 + - + +
51D VAL* 3.6 4.5 - - - +
53D LEU* 1.3 79.8 - - + +
55D ILE* 1.3 59.4 + - - +
57D ALA* 5.4 0.7 - - - -
58D GLY* 3.5 18.5 + - - +
59D ASN* 4.7 0.7 + - - -
337D ALA* 3.8 23.9 - - + +
340D PRO* 4.8 1.0 - - - +
341D ILE* 5.5 15.0 - - + -
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Residues in contact with ILE 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D VAL* 2.7 37.6 + - + +
52D VAL* 4.1 2.9 - - - +
54D LEU* 1.3 71.6 - - - +
56D VAL* 1.3 60.0 + - - +
59D ASN* 2.6 41.4 + - - +
87D ASP 3.2 27.1 - - - +
90D VAL* 4.8 0.9 - - + -
91D GLY* 3.7 19.3 - - - -
95D VAL* 4.7 14.4 - - + -
333D TYR* 3.8 11.7 - - + +
336D SER* 3.4 42.4 - - - +
337D ALA* 3.4 7.6 - - + +
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 3.1 24.4 + - + +
53D LEU* 4.2 1.6 - - - +
55D ILE* 1.3 75.1 - - - +
57D ALA* 1.3 62.6 + - + +
60D VAL* 2.9 48.2 + - + +
88D LEU* 3.9 12.5 - - + +
91D GLY* 3.7 26.9 - - - +
92D LEU* 3.8 30.3 - - + -
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LEU* 2.9 37.0 + - + +
54D LEU* 5.4 0.4 - - - -
56D VAL* 1.3 76.9 - - - +
58D GLY* 1.3 58.8 + - - +
60D VAL* 3.8 6.0 - - - +
61D LEU* 2.9 35.2 + - + +
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Residues in contact with GLY 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D LEU* 3.5 19.0 + - - +
56D VAL 3.3 0.4 - - - -
57D ALA* 1.3 80.9 - - - +
59D ASN* 1.3 56.7 + - - +
61D LEU* 3.5 9.2 + - - +
62D VAL* 3.1 29.5 + - - +
340D PRO* 3.4 19.9 - - - +
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Residues in contact with ASN 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ILE* 2.6 30.7 + - - +
56D VAL 4.3 0.7 - - - +
58D GLY* 1.3 73.7 - - - +
60D VAL* 1.3 67.5 + - - +
61D LEU 3.0 1.3 - - - -
62D VAL* 3.7 6.4 - - - +
63D ILE* 3.0 30.1 + - - +
84D ALA* 3.5 35.6 - - + +
87D ASP* 3.6 20.9 - - + +
88D LEU* 4.6 7.4 - - + -
336D SER 2.9 26.1 + - - -
339D ASN* 5.2 2.1 - - - +
340D PRO* 3.9 15.9 - - - +
343D TYR* 6.0 0.5 - - - -
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Residues in contact with VAL 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D VAL* 2.9 34.8 + - + +
57D ALA* 3.8 7.0 - - - +
59D ASN* 1.3 76.6 - - - +
61D LEU* 1.3 62.7 + - + +
63D ILE* 3.6 11.3 + - + +
64D ALA* 3.1 28.3 + - + +
88D LEU* 4.0 23.1 - - + +
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Residues in contact with LEU 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ALA* 2.9 21.4 + - + +
58D GLY* 3.5 10.3 - - - +
59D ASN 3.0 0.4 - - - -
60D VAL* 1.3 79.9 - - + +
62D VAL* 1.3 59.9 + - - +
64D ALA* 3.3 5.4 + - + +
65D ALA* 2.9 30.3 + - - +
353D PHE* 3.9 28.4 - - + -
356D LEU* 4.1 24.2 - - + +
357D LEU* 4.2 32.3 - - + -
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D GLY 3.1 18.6 + - - +
59D ASN* 3.7 10.1 - - - +
61D LEU* 1.3 75.0 - - - +
63D ILE* 1.3 66.7 + - + +
65D ALA* 3.4 2.8 + - - +
66D ILE* 3.1 42.8 + - + +
80D ILE* 4.0 15.9 - - + +
81D THR* 5.7 0.2 - - - -
84D ALA* 4.4 11.9 - - + -
340D PRO* 3.9 15.9 - - + -
343D TYR* 3.5 30.5 - - + -
349D PHE* 4.4 4.9 - - + -
353D PHE* 4.2 14.6 - - + -
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D ASN 3.0 19.5 + - - +
60D VAL* 3.7 7.6 - - + +
62D VAL* 1.3 79.4 - - - +
64D ALA* 1.3 65.0 + - + +
66D ILE* 3.4 6.3 + - - +
67D GLY* 3.2 18.2 + - - -
81D THR* 4.0 23.9 - - + +
84D ALA* 4.2 15.3 - - + +
85D CYS* 4.0 24.7 - - - -
88D LEU* 4.3 20.4 - - + -
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Residues in contact with ALA 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D VAL* 3.1 20.3 + - + +
61D LEU* 3.3 7.4 + - + +
63D ILE* 1.3 76.1 - - + +
65D ALA* 1.3 67.2 + - - +
67D GLY* 3.0 4.1 + - - +
68D SER* 3.0 27.6 + - - +
356D LEU* 4.5 18.8 - - + -
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Residues in contact with ALA 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D LEU 2.9 18.3 + - - +
62D VAL 3.8 3.8 - - - +
64D ALA* 1.3 76.5 - - - +
66D ILE* 1.3 62.5 - - - +
67D GLY 3.1 0.9 + - - -
68D SER* 3.1 12.4 + - - -
69D THR* 3.3 19.9 + - - -
72D LEU* 4.0 10.7 - - + +
349D PHE* 4.3 4.3 - - + -
352D ALA* 4.1 23.1 - - + -
353D PHE* 4.2 13.9 - - + -
356D LEU* 4.0 12.5 - - + +
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Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D VAL* 3.1 25.0 + - + +
63D ILE* 3.9 4.7 - - - +
65D ALA* 1.3 75.6 - - - +
67D GLY* 1.3 57.2 + - - +
68D SER 3.4 0.4 + - - -
69D THR 3.9 3.9 - - - +
72D LEU* 3.8 22.9 - - + +
73D GLN* 3.1 27.6 + - + +
77D ASN* 3.5 34.5 - - + +
78D LEU* 5.7 2.9 - - + -
80D ILE* 3.7 22.9 - - + -
81D THR* 3.5 19.1 - - - +
349D PHE* 4.0 18.8 - - + -
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Residues in contact with GLY 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE 3.2 10.7 + - - -
64D ALA* 3.0 9.0 + - - -
65D ALA 3.0 1.0 - - - -
66D ILE* 1.3 78.8 - - - +
68D SER* 1.3 60.0 + - - +
73D GLN* 4.4 14.2 + - - -
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Residues in contact with SER 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ALA* 3.0 16.7 + - - +
65D ALA* 3.1 5.1 + - - -
67D GLY* 1.3 80.0 - - - +
69D THR* 1.3 59.9 + - - +
70D GLN* 2.8 31.9 + - - +
352D ALA* 6.1 1.1 - - - -
355D ARG* 6.2 1.6 - - - -
356D LEU* 4.3 14.9 - - - +
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Residues in contact with THR 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D ALA 3.3 7.2 + - - -
66D ILE 3.9 5.1 - - - +
68D SER* 1.3 73.9 - - - +
70D GLN* 1.3 53.8 + - - +
71D ARG* 2.9 43.3 - - + +
72D LEU* 2.6 48.0 + - + +
73D GLN 3.4 2.8 + - - -
348D ASP* 5.7 1.6 - - + +
352D ALA* 3.8 22.3 - - - +
355D ARG* 4.8 17.0 + - - +
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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