Contacts of the helix formed by residues 27 - 51 (chain D) in PDB entry 1BL8
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 ARG 27 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D ALA* 4.4 11.4 - - - +
24D LEU* 2.6 23.3 + - - +
26D TRP* 1.3 75.1 - - - +
28D ALA* 1.3 58.4 + - - +
29D ALA 3.0 6.0 + - - -
30D GLY* 4.1 2.2 - - - +
31D ALA* 3.4 25.0 + - - +
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Residues in contact with ALA 28 (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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113C TRP* 4.9 4.9 - - + -
114C PHE* 3.6 23.1 - - + -
24D LEU* 2.4 43.1 + - + +
27D ARG* 1.3 68.8 - - - +
29D ALA* 1.3 55.3 + - - +
31D ALA* 4.6 2.4 - - - +
32D ALA* 3.3 24.8 + - - +
105D LEU* 3.4 11.3 - - + +
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Residues in contact with ALA 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C PHE* 5.0 0.2 - - + -
24D LEU 4.1 0.4 + - - -
25D HIS 4.1 4.4 + - - +
26D TRP* 4.8 3.6 - - + +
27D ARG* 3.0 0.8 - - - +
28D ALA* 1.3 76.7 - - - +
30D GLY* 1.3 57.2 + - - +
31D ALA 2.5 16.9 + - - -
32D ALA* 2.7 14.8 + - - +
33D THR* 3.3 15.7 + - - +
105D LEU* 4.2 10.3 - - + +
106D VAL* 4.3 24.2 - - + +
109D ALA* 4.1 25.8 - - + -
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Residues in contact with GLY 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D TRP 4.1 9.9 + - - -
27D ARG* 3.9 4.4 + - - -
29D ALA* 1.3 77.0 - - - +
31D ALA* 1.3 57.1 + - - +
33D THR* 3.5 18.6 + - - -
34D VAL* 3.7 8.5 - - - +
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ARG 3.4 18.5 + - - +
28D ALA* 4.6 2.9 - - - +
29D ALA 2.5 5.1 + - - -
30D GLY* 1.3 74.9 - - - +
32D ALA* 1.3 66.5 + - - +
33D THR 3.2 1.8 - - - -
34D VAL* 2.9 27.5 + - + +
35D LEU* 3.6 6.9 + - + +
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Residues in contact with ALA 32 (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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28D ALA 3.3 19.4 + - - +
29D ALA* 2.7 12.6 + - - +
31D ALA* 1.3 73.3 - - - +
33D THR* 1.3 54.1 + - + +
35D LEU* 2.4 56.5 + - + +
36D LEU* 3.1 3.7 + - - +
102D SER* 5.1 11.7 - - - +
105D LEU* 4.5 18.6 - - + -
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Residues in contact with THR 33 (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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29D ALA 3.4 17.5 - - - +
30D GLY* 3.5 14.8 + - - +
32D ALA* 1.3 74.4 - - - +
34D VAL* 1.3 60.7 + - - +
35D LEU 2.6 9.7 + - - -
36D LEU* 2.8 23.7 + - - +
37D VAL* 3.0 15.2 + - - +
102D SER* 4.5 11.8 + - - +
106D VAL* 4.5 17.9 - - + -
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Residues in contact with VAL 34 (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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30D GLY 3.7 16.2 - - - +
31D ALA* 2.9 17.6 + - - +
33D THR* 1.3 82.5 + - - +
35D LEU* 1.3 60.0 + - + +
37D VAL* 4.3 8.3 - - + -
38D ILE* 2.9 36.5 - - + +
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Residues in contact with LEU 35 (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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31D ALA* 3.8 4.9 - - + +
32D ALA* 2.4 58.3 + - + +
34D VAL* 1.3 70.6 - - + +
36D LEU* 1.3 63.5 + - - +
37D VAL 3.2 0.9 - - - -
38D ILE* 3.0 18.2 + - + +
39D VAL* 3.0 16.7 + - + +
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Residues in contact with LEU 36 (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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32D ALA 3.1 1.4 + - - -
33D THR* 2.8 11.1 + - - +
35D LEU* 1.3 80.2 - - - +
37D VAL* 1.3 58.2 + - + +
39D VAL* 2.8 13.0 + - - +
40D LEU* 2.8 42.0 + - + +
73D ALA* 4.4 14.1 - - + -
98D ALA* 3.4 42.4 - - + +
99D GLY* 3.5 6.7 - - - +
102D SER* 3.4 28.0 - - - +
103D PHE* 4.6 17.7 - - + -
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Residues in contact with VAL 37 (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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33D THR 3.0 14.4 + - - +
34D VAL* 4.4 7.4 - - + +
36D LEU* 1.3 78.8 - - + +
38D ILE* 1.3 81.1 + - + +
40D LEU* 3.4 19.9 - - + +
41D LEU* 3.2 33.1 + - + +
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Residues in contact with ILE 38 (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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34D VAL* 2.9 31.4 - - + +
35D LEU* 3.0 12.8 + - + +
37D VAL* 1.3 88.8 - - + +
39D VAL* 1.3 60.2 + - + +
40D LEU 3.2 0.2 + - - -
41D LEU* 3.3 4.6 + - - +
42D ALA* 2.5 45.4 + - + +
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Residues in contact with VAL 39 (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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35D LEU* 3.0 15.4 + - + +
36D LEU* 2.8 14.5 + - + +
38D ILE* 1.3 79.1 - - + +
40D LEU* 1.3 51.4 + - - +
42D ALA* 3.2 6.9 - - - +
43D GLY* 2.5 34.9 + - - +
94D VAL* 4.1 14.8 - - + -
95D VAL* 3.8 23.7 - - + +
98D ALA* 3.6 32.1 - - + -
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Residues in contact with LEU 40 (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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36D LEU* 2.8 33.8 + - + +
37D VAL* 3.4 22.9 - - + +
39D VAL* 1.3 79.1 - - - +
41D LEU* 1.3 72.0 + - + +
43D GLY* 3.4 0.3 - - - -
44D SER* 2.7 26.5 + - - +
66D LEU* 5.9 0.4 - - + -
69D SER* 3.5 22.9 + - - +
70D VAL* 4.0 24.5 - - + -
73D ALA* 3.6 30.5 - - + -
95D VAL* 3.9 6.5 - - + -
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Residues in contact with LEU 41 (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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37D VAL* 3.2 23.4 + - + +
38D ILE* 3.8 4.0 - - - +
40D LEU* 1.3 87.0 - - + +
42D ALA* 1.3 60.2 + - - +
44D SER* 3.9 5.6 - - - -
45D TYR* 3.3 34.3 + - + +
66D LEU* 3.8 25.4 - - + -
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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
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38D ILE* 2.5 31.8 + - + +
39D VAL* 3.2 10.3 - - - +
40D LEU 2.7 3.0 + - - -
41D LEU* 1.3 73.2 - - - +
43D GLY* 1.3 63.3 + - - +
45D TYR* 3.8 1.7 + - - +
46D LEU* 3.2 28.0 + - + +
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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
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39D VAL* 2.5 21.0 + - - -
40D LEU 3.4 0.4 - - - -
42D ALA* 1.3 70.7 - - - +
44D SER* 1.3 59.0 + - - +
46D LEU* 4.3 1.6 - - - -
47D ALA* 2.8 36.4 + - - +
68D TRP* 4.7 1.6 - - - -
69D SER* 4.0 5.8 - - - -
91D VAL* 3.5 23.1 - - - +
94D VAL* 6.4 1.6 - - - -
95D VAL* 5.4 4.3 - - - -
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Residues in contact with SER 44 (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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40D LEU 2.7 18.2 + - - -
41D LEU 3.7 0.9 - - - -
43D GLY* 1.3 73.8 - - - +
45D TYR* 1.3 67.1 + - - +
46D LEU 2.9 6.6 + - - -
47D ALA* 5.2 0.2 - - - -
48D VAL* 3.5 11.3 + - - +
62D TYR* 4.5 0.7 - - - -
65D ALA* 3.1 26.5 - - - +
66D LEU* 2.8 47.8 - - - +
68D TRP* 5.2 0.2 - - - -
69D SER* 2.9 21.7 + - - -
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Residues in contact with TYR 45 (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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41D LEU* 3.3 26.5 + - + +
42D ALA* 3.9 2.7 - - - +
43D GLY 3.5 0.2 - - - -
44D SER* 1.3 77.1 - - - +
46D LEU* 1.3 58.9 + - - +
49D LEU* 3.0 18.2 - - - +
62D TYR* 3.3 54.9 - + + +
63D PRO* 5.4 1.6 - - - +
66D LEU* 3.6 34.4 - - + +
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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
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42D ALA* 3.2 21.5 - - + +
43D GLY* 3.7 5.2 - - - +
44D SER 2.9 1.0 + - - -
45D TYR* 1.3 77.0 - - - +
47D ALA* 1.3 66.8 + - - +
48D VAL 3.2 1.5 - - - +
49D LEU* 3.2 36.5 - - + +
50D ALA* 3.4 9.0 - - + +
87D TRP* 6.3 3.4 - - + -
91D VAL* 3.4 26.2 - - + -
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Residues in contact with ALA 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 2.8 16.4 + - - +
44D SER 4.2 2.0 - - - +
46D LEU* 1.3 75.1 - - - +
48D VAL* 1.3 66.4 + - - +
50D ALA* 2.9 10.2 + - - +
51D GLU* 2.9 27.5 + - - +
59D LEU* 4.3 9.9 - - + -
65D ALA* 5.0 2.2 - - + -
68D TRP* 3.6 29.6 - - + -
88D GLY* 4.8 6.7 - - - +
91D VAL* 4.0 14.6 - - + +
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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
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44D SER 3.5 4.2 + - - +
46D LEU 3.2 0.2 - - - -
47D ALA* 1.3 72.9 - - - +
49D LEU* 1.3 54.1 + - - +
50D ALA 2.5 12.4 + - - -
51D GLU 2.6 1.2 + - - -
52D ARG* 2.5 44.5 + - - +
59D LEU 3.3 11.2 - - - +
60D ILE 3.8 21.1 - - - +
61D THR* 3.2 34.3 - - - +
62D TYR* 3.4 34.5 - - + +
65D ALA* 3.4 20.2 - - + -
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Residues in contact with LEU 49 (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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45D TYR 3.0 26.5 - - - +
46D LEU* 3.2 34.1 - - + +
48D VAL* 1.3 80.0 - - - +
50D ALA* 1.3 57.3 + - + +
52D ARG* 4.4 9.0 - - - +
62D TYR* 3.9 17.7 - - - +
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Residues in contact with ALA 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* 3.4 13.2 + - + +
47D ALA* 3.1 14.1 - - - +
48D VAL 2.5 6.7 + - - -
49D LEU* 1.3 77.8 - - + +
51D GLU* 1.3 55.7 + - - -
53D GLY 5.3 1.0 - - - +
54D ALA* 5.3 2.8 - - - +
85D THR* 2.8 26.3 + - - +
87D TRP* 4.4 12.8 - - + -
88D GLY* 4.0 23.1 - - - +
91D VAL* 5.5 1.6 - - + -
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Residues in contact with GLU 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 ALA 2.9 14.0 + - - +
48D VAL 2.6 2.4 + - - -
50D ALA* 1.3 80.0 - - + +
52D ARG* 1.3 51.7 + - - -
53D GLY 2.6 18.2 + - - -
54D ALA* 3.2 19.5 + - - +
56D GLY* 5.1 5.6 + - - -
57D ALA 4.6 4.9 + - - +
59D LEU* 3.1 39.6 - - + +
60D ILE* 3.9 8.5 - - + +
82D TYR 3.4 3.6 - - - +
83D PRO* 3.0 26.1 - - + +
84D VAL* 2.5 15.3 + - - +
85D THR* 2.3 49.2 + - - +
88D GLY* 4.6 1.1 - - - -
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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
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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) + - + + + + + -
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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