Contacts of the helix formed by residues 45 - 72 (chain D) in PDB entry 2WLM
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D THR 3.8 1.0 + - - -
44D VAL* 1.3 76.2 - - - +
46D TRP* 1.3 66.3 + - - +
47D PRO* 3.6 13.3 - - - +
48D VAL* 2.9 29.7 + - - +
49D PHE* 2.8 19.4 + - - +
134D ARG* 3.9 0.7 - - - +
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Residues in contact with TRP 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C VAL* 6.2 0.9 - - + -
45D SER* 1.3 69.0 - - - +
47D PRO* 1.3 75.7 - - + +
49D PHE* 3.1 40.2 + + - +
50D ILE* 2.8 43.3 + - + +
131D ILE* 4.2 24.7 - - + -
134D ARG* 3.4 49.2 + - + +
135D PHE* 4.2 25.3 - + - -
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Residues in contact with PRO 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER* 3.4 13.5 - - - +
46D TRP* 1.3 98.8 - - + +
48D VAL* 1.3 64.9 + - + +
50D ILE* 3.2 10.0 + - + +
51D THR* 2.9 25.1 + - - -
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Residues in contact with VAL 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D VAL* 3.0 32.1 - - + -
45D SER* 2.9 19.2 + - - +
47D PRO* 1.3 78.9 - - + +
49D PHE* 1.3 54.8 + - - +
51D THR* 3.0 11.8 + - + -
52D LEU* 2.8 41.9 + - + +
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Residues in contact with PHE 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 3.8 21.3 - - + -
44D VAL* 3.2 7.1 - - + +
45D SER 2.8 12.2 + - - +
46D TRP* 3.4 31.2 - + - +
48D VAL* 1.3 72.9 - - - +
50D ILE* 1.3 68.6 + - + +
52D LEU* 3.3 7.4 + - - +
53D ILE* 3.0 50.0 + - + +
130D LEU* 3.9 32.3 - - + -
131D ILE* 3.3 32.5 - - + -
134D ARG* 3.5 39.9 - - - +
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Residues in contact with ILE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 5.6 2.7 - - + -
122C LEU* 4.5 22.0 - - + -
46D TRP* 2.8 39.9 + - + +
47D PRO* 3.5 8.7 - - + +
49D PHE* 1.3 82.4 - - + +
51D THR* 1.3 51.2 + - - +
53D ILE* 3.3 7.5 + - + +
54D THR* 2.6 46.8 + - - +
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Residues in contact with THR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D PRO 2.9 16.5 + - - -
48D VAL* 3.1 13.6 - - + -
50D ILE* 1.3 76.2 - - - +
52D LEU* 1.3 55.9 + - + +
54D THR* 3.0 9.1 + - - -
55D GLY* 2.6 34.9 + - - +
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D LEU* 3.9 28.0 - - + -
44D VAL* 4.8 10.3 - - + -
48D VAL* 2.8 32.4 + - + +
49D PHE* 3.4 12.8 - - - +
51D THR* 1.3 75.8 - - + +
53D ILE* 1.3 60.3 + - + +
55D GLY* 3.3 1.4 + - - -
56D LEU* 2.8 31.1 + - - +
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Residues in contact with ILE 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 4.2 21.3 - - + -
122C LEU* 4.7 14.4 - - + -
41D LEU* 6.4 0.7 - - + -
49D PHE* 3.0 52.9 + - + +
50D ILE* 3.5 11.0 - - + +
52D LEU* 1.3 79.7 - - + +
54D THR* 1.3 53.5 + - - +
56D LEU* 3.2 10.8 + - + +
57D TYR* 2.7 36.2 + - + +
127D ALA* 4.5 19.7 - - + -
130D LEU* 5.7 2.9 - - + -
131D ILE* 4.5 7.6 - - + -
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Residues in contact with THR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C LEU* 6.0 5.8 - - + -
118C LEU* 4.2 19.8 - - + +
50D ILE* 2.6 33.1 + - - +
51D THR* 3.2 10.7 - - - -
53D ILE* 1.3 74.5 - - - +
55D GLY* 1.3 65.2 + - - +
57D TYR* 2.8 11.4 + - + +
58D LEU* 2.8 48.0 + - + +
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Residues in contact with GLY 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 THR* 2.6 19.3 + - - -
52D LEU* 3.7 2.5 - - - -
54D THR* 1.3 71.3 - - - +
56D LEU* 1.3 54.3 + - - +
58D LEU* 3.7 6.4 - - - +
59D VAL* 2.8 46.4 + - - +
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Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU 2.8 15.8 + - - +
53D ILE* 3.3 13.0 - - + +
55D GLY* 1.3 70.4 - - - +
57D TYR* 1.3 58.1 + - - +
59D VAL* 3.5 8.9 - - + +
60D THR* 2.8 57.1 + - + +
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Residues in contact with TYR 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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114C THR* 3.3 31.1 + - - -
117C ALA* 4.1 13.0 - - - +
118C LEU* 3.8 36.6 - - + -
53D ILE* 2.7 17.8 + - + +
54D THR* 2.8 11.8 + - + +
56D LEU* 1.3 72.2 - - - +
58D LEU* 1.3 90.5 + - + +
60D THR* 3.2 11.5 + - - -
61D ASN* 3.1 25.5 + - - -
91D VAL* 4.2 16.2 - - + +
94D MET* 3.3 29.2 - - + -
95D ALA* 4.7 7.3 - - + +
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Residues in contact with LEU 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR* 5.0 7.2 - - - +
54D THR* 2.8 36.1 + - + +
55D GLY* 3.8 7.2 - - - +
57D TYR* 1.3 94.1 - - + +
59D VAL* 1.3 69.2 + - + +
61D ASN* 3.0 7.6 + - - +
62D ALA* 3.0 18.5 + - - +
87D PHE* 3.7 26.7 - - + -
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Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D GLY* 2.8 34.8 + - - +
56D LEU* 3.5 9.4 - - + +
58D LEU* 1.3 75.5 - - + +
60D THR* 1.3 69.6 + - + +
62D ALA* 2.9 16.5 + - - +
63D LEU* 2.9 26.6 + - + +
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Residues in contact with THR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D LEU* 2.8 47.2 + - + +
57D TYR* 3.2 10.2 + - - -
59D VAL* 1.3 74.8 - - + +
61D ASN* 1.3 59.7 + - - +
63D LEU* 3.2 17.9 + - + +
64D PHE* 2.8 39.7 + - - -
94D MET* 4.1 17.3 - - - -
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Residues in contact with ASN 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 TYR* 3.1 27.9 + - - -
58D LEU* 3.0 9.1 + - - +
60D THR* 1.3 78.0 + - - +
62D ALA* 1.3 55.4 + - - +
64D PHE* 3.2 1.5 + - - -
65D ALA* 2.7 34.7 + - - +
87D PHE* 3.6 18.1 - - + -
90D SER* 2.5 38.5 + - - +
91D VAL* 3.7 15.4 - - + +
94D MET* 2.7 40.1 - - - +
116D GLU* 3.6 1.6 - - - +
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Residues in contact with ALA 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 LEU 3.0 9.7 + - - +
59D VAL* 2.9 13.6 + - - +
61D ASN* 1.3 74.6 - - - +
63D LEU* 1.3 65.6 + - + +
65D ALA* 3.1 3.8 + - - +
66D LEU* 2.9 29.7 + - + +
83D PHE* 3.6 27.6 - - + -
87D PHE* 3.7 6.8 - - + -
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Residues in contact with LEU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D VAL* 2.9 24.2 + - + +
60D THR* 3.3 23.6 - - + +
62D ALA* 1.3 77.8 - - + +
64D PHE* 1.3 65.0 + - + +
66D LEU* 3.2 17.8 + - + +
67D ALA* 3.0 19.3 + - - +
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Residues in contact with PHE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D THR* 2.8 30.7 + - - +
61D ASN 3.6 5.8 - - - +
63D LEU* 1.3 72.4 - - + +
65D ALA* 1.3 66.8 + - - +
67D ALA* 2.9 18.5 + - + +
68D TYR* 2.9 23.1 + + + -
90D SER* 3.7 2.2 - - - +
94D MET* 5.9 2.2 - - - -
112D LEU* 3.5 30.3 - - + -
115D LEU* 4.3 12.1 - - + -
116D GLU* 3.2 70.0 - - + +
119D CYS* 4.2 23.1 - - + -
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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
----------------------------------------------------------
61D ASN 2.7 16.9 + - - +
62D ALA 3.3 9.4 - - - +
64D PHE* 1.3 70.9 - - - +
66D LEU* 1.3 58.8 + - - +
68D TYR* 2.8 26.7 + - - +
69D LEU* 2.9 16.6 + - - +
83D PHE* 3.6 16.6 - - + -
86D ALA* 3.7 12.5 - - + +
87D PHE* 3.5 29.8 - - - +
90D SER* 4.2 1.4 - - - -
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Residues in contact with LEU 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 ALA* 2.9 14.7 + - + +
63D LEU* 3.3 21.5 - - + +
65D ALA* 1.3 75.9 - - - +
67D ALA* 1.3 52.9 + - - +
69D LEU* 3.6 9.4 - - + +
70D ALA* 2.6 39.3 + - - +
83D PHE* 3.2 34.8 - - + -
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Residues in contact with ALA 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D LEU 3.0 11.4 + - - +
64D PHE* 2.9 18.3 + - + +
66D LEU* 1.3 74.2 - - - +
68D TYR* 1.3 62.0 + - - +
70D ALA* 3.2 19.4 - - - +
71D CYS* 3.3 13.5 + - - -
112D LEU* 3.5 29.2 - - + +
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Residues in contact with TYR 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D PHE* 2.9 30.9 + + - -
65D ALA* 2.8 12.5 + - - +
67D ALA* 1.3 73.1 - - - +
69D LEU* 1.3 67.4 - - + +
71D CYS* 2.9 17.2 + - - +
72D GLY 3.1 7.8 + - - -
73D ASP 5.6 0.2 - - - -
74D VAL* 3.4 11.7 - - + +
75D ILE* 4.0 23.1 - - + -
86D ALA* 4.7 4.5 - - + -
89D PHE* 3.6 29.3 - + - -
90D SER* 4.6 6.1 - - - -
93D THR* 4.3 1.0 - - - +
109D ALA* 3.4 31.6 - - + -
112D LEU* 3.5 18.2 - - + -
113D VAL* 3.3 29.6 + - + +
116D GLU* 3.2 27.9 + - - -
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Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ALA 2.9 16.7 + - - +
66D LEU* 3.6 11.9 - - + +
68D TYR* 1.3 71.9 - - + +
70D ALA* 1.3 57.0 + - - +
72D GLY* 2.5 30.8 + - - +
73D ASP 5.1 5.8 - - - +
81D GLY* 4.3 22.7 - - - +
82D SER 4.2 8.5 - - - +
83D PHE* 3.9 37.9 - - + +
86D ALA* 3.9 17.5 - - + -
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Residues in contact with ALA 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LEU 2.6 22.8 + - - +
67D ALA* 3.2 11.9 - - - +
69D LEU* 1.3 73.0 - - - +
71D CYS* 1.3 62.2 + - - +
72D GLY* 4.5 0.3 - - - -
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Residues in contact with CYS 71 (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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67D ALA 3.6 12.8 - - - -
68D TYR 2.9 9.4 + - - +
70D ALA* 1.3 80.6 - - - +
72D GLY* 1.3 64.0 + - - +
74D VAL* 3.6 20.9 - - + +
108D LEU* 3.8 39.3 - - + -
112D LEU* 4.3 14.4 - - - -
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Residues in contact with GLY 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D TYR 3.1 5.7 + - - -
69D LEU* 2.5 22.7 + - - -
70D ALA 4.5 0.4 - - - -
71D CYS* 1.3 76.2 - - - +
73D ASP* 1.3 76.2 + - - +
74D VAL* 3.2 8.0 + - - +
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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