Contacts of the helix formed by residues 27 - 51 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ALA* 4.4 12.3 - - + +
24A LEU* 2.6 24.1 + - - +
26A TRP* 1.3 74.2 - - - +
28A ALA* 1.3 58.6 + - - +
29A ALA 3.0 6.5 + - - -
30A GLY* 4.1 3.1 - - - +
31A ALA* 3.4 24.8 + - - +
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Residues in contact with ALA 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 2.4 44.1 + - + +
27A ARG* 1.3 67.5 - - - +
29A ALA* 1.3 56.8 + - - +
31A ALA* 4.6 2.5 - - - +
32A ALA* 3.3 25.2 + - - +
105A LEU* 3.4 11.0 - - + +
113D TRP* 5.2 4.0 - - + -
114D PHE* 3.5 24.2 - - + -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU 4.1 0.4 + - - -
25A HIS 4.1 15.2 + - - +
26A TRP* 4.8 3.4 - - + +
27A ARG 3.0 0.6 - - - +
28A ALA* 1.3 78.1 - - - +
30A GLY* 1.3 56.1 + - - +
31A ALA 2.5 17.3 + - - -
32A ALA* 2.7 14.4 + - - +
33A THR* 3.3 16.9 + - - +
105A LEU* 4.3 10.1 - - + -
106A VAL* 4.3 23.8 - - + +
109A ALA* 4.1 15.0 - - + -
114D PHE* 5.2 0.4 - - + -
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Residues in contact with GLY 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP 4.1 10.8 + - - -
27A ARG* 3.9 4.0 + - - -
29A ALA* 1.3 77.5 - - - +
31A ALA* 1.3 57.8 + - - +
33A THR* 3.5 18.8 + - - -
34A VAL* 3.7 8.1 - - - +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ARG 3.4 18.3 + - - +
28A ALA* 4.6 2.7 - - - +
29A ALA 2.5 6.1 + - - -
30A GLY* 1.3 74.4 - - - +
32A ALA* 1.3 65.4 + - - +
33A THR 3.2 2.0 - - - -
34A VAL* 2.9 26.5 + - - +
35A LEU* 3.6 6.4 + - - +
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA 3.3 19.4 + - - +
29A ALA* 2.7 12.8 + - - +
31A ALA* 1.3 73.7 - - - +
33A THR* 1.3 53.1 + - + +
35A LEU* 2.4 55.9 + - + +
36A LEU* 3.1 3.2 + - - +
102A SER* 5.1 12.3 - - - +
105A LEU* 4.5 17.9 - - + -
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Residues in contact with THR 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA 3.4 17.0 - - - +
30A GLY* 3.5 14.2 + - - +
32A ALA* 1.3 73.4 - - - +
34A VAL* 1.3 61.3 + - - +
35A LEU 2.6 10.6 + - - -
36A LEU* 2.8 23.5 + - - +
37A VAL* 3.0 14.9 + - - +
102A SER* 4.5 11.2 + - - +
106A VAL* 4.5 18.4 - - + -
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 3.7 15.5 - - - +
31A ALA* 2.9 17.8 + - - +
33A THR* 1.3 83.1 + - - +
35A LEU* 1.3 58.5 + - + +
37A VAL* 4.3 7.9 - - + -
38A ILE* 2.9 37.1 - - + +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.8 4.9 - - + +
32A ALA* 2.4 57.2 + - + +
34A VAL* 1.3 69.9 - - + +
36A LEU* 1.3 63.4 + - - +
37A VAL 3.2 1.3 - - - -
38A ILE* 3.0 18.3 + - + +
39A VAL* 3.1 16.7 + - + +
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Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA 3.1 1.6 + - - -
33A THR* 2.8 10.4 + - - +
35A LEU* 1.3 79.7 - - - +
37A VAL* 1.3 59.2 + - + +
39A VAL* 2.8 12.9 + - - +
40A LEU* 2.8 40.9 + - + +
73A ALA* 4.4 15.5 - - + -
98A ALA* 3.4 42.0 - - + +
99A GLY* 3.5 6.7 - - - +
102A SER* 3.4 28.4 - - - +
103A PHE* 4.6 18.2 - - + -
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Residues in contact with VAL 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A THR 3.0 13.3 + - - +
34A VAL* 4.4 7.4 - - + +
36A LEU* 1.3 80.2 - - + +
38A ILE* 1.3 82.0 + - + +
40A LEU* 3.4 19.6 - - + +
41A LEU* 3.2 33.1 + - + +
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Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A VAL* 2.9 31.6 - - + +
35A LEU* 3.0 12.9 + - + +
37A VAL* 1.3 90.3 - - + +
39A VAL* 1.3 59.4 + - + +
40A LEU 3.2 0.3 + - - -
41A LEU* 3.3 4.3 + - - +
42A ALA* 2.5 45.4 + - + +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.1 15.7 + - + +
36A LEU* 2.8 18.7 + - + +
38A ILE* 1.3 78.5 - - + +
40A LEU* 1.3 50.5 + - - +
42A ALA* 3.8 6.7 - - - -
43A GLY* 2.5 34.8 + - - -
94A VAL* 4.1 14.8 - - + -
95A VAL* 3.8 24.1 - - + +
98A ALA* 3.6 28.5 - - + -
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Residues in contact with LEU 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 2.8 34.3 + - + +
37A VAL* 3.4 22.4 - - + +
39A VAL* 1.3 78.7 - - - +
41A LEU* 1.3 71.6 + - + +
43A GLY* 3.5 0.3 - - - -
44A SER* 2.7 25.8 + - - +
66A LEU* 5.9 0.4 - - + -
69A SER* 3.5 24.0 + - - +
70A VAL* 4.0 24.5 - - + -
73A ALA* 3.6 30.1 - - + -
95A VAL* 3.9 6.7 - - + -
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 3.2 25.2 + - + +
38A ILE* 3.8 3.8 - - - +
40A LEU* 1.3 86.6 - - + +
42A ALA* 1.3 60.4 + - - +
44A SER* 3.9 5.8 - - - -
45A TYR* 3.3 34.1 + - + +
66A LEU* 3.8 25.1 - - + -
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 2.5 31.2 + - + +
39A VAL* 3.2 10.3 - - - +
40A LEU 2.7 3.2 + - - -
41A LEU* 1.3 70.0 - - - +
43A GLY* 1.3 65.7 + - - +
45A TYR* 3.8 2.1 + - - +
46A LEU* 3.2 27.8 + - + +
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Residues in contact with GLY 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 2.5 19.7 + - - -
40A LEU 3.5 2.2 - - - -
42A ALA* 1.3 70.7 - - - +
44A SER* 1.3 56.8 + - - +
46A LEU* 4.3 1.8 - - - -
47A ALA* 2.8 38.1 + - - +
68A TRP* 4.7 0.7 - - - -
69A SER* 4.0 6.1 - - - -
91A VAL* 3.5 23.5 - - - +
94A VAL* 6.4 1.3 - - - -
95A VAL* 5.4 4.0 - - - -
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU 2.7 18.5 + - - -
41A LEU 3.7 1.3 - - - -
43A GLY* 1.3 73.1 - - - +
45A TYR* 1.3 67.2 + - - +
46A LEU 2.9 6.1 + - - -
47A ALA* 5.2 0.2 - - - -
48A VAL* 3.5 11.4 + - - +
62A TYR* 4.5 0.7 - - - -
65A ALA* 3.1 26.8 - - - +
66A LEU* 2.8 48.0 - - - +
69A SER* 2.9 21.9 + - - -
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Residues in contact with TYR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 3.3 26.2 + - + +
42A ALA 3.9 2.2 - - - +
44A SER* 1.3 76.8 - - - +
46A LEU* 1.3 58.4 + - - +
49A LEU* 3.0 18.1 - - - +
62A TYR* 3.3 55.8 - + + +
63A PRO* 5.4 1.9 - - - +
66A LEU* 3.6 34.5 - - + +
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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
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42A ALA* 3.2 21.8 - - + +
43A GLY* 3.7 5.6 - - - +
44A SER 2.9 1.4 + - - -
45A TYR* 1.3 77.8 - - - +
47A ALA* 1.3 67.5 + - - +
48A VAL 3.2 0.9 - - - +
49A LEU* 3.2 36.5 - - + +
50A ALA* 3.4 9.0 - - + +
87A TRP* 6.3 3.4 - - + -
91A VAL* 3.4 26.0 - - + -
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Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A GLY 2.8 16.8 + - - +
44A SER 4.2 1.8 - - - +
46A LEU* 1.3 74.4 - - - +
48A VAL* 1.3 67.1 + - - +
50A ALA* 2.9 10.5 + - - +
51A GLU* 2.9 26.9 + - - +
59A LEU* 4.3 9.9 - - + -
65A ALA* 4.9 2.7 - - + -
68A TRP* 3.6 29.2 - - + -
88A GLY* 4.8 6.3 - - - +
91A VAL* 4.0 14.3 - - + +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER 3.5 3.7 + - - +
47A ALA* 1.3 72.6 - - - +
49A LEU* 1.3 54.2 + - - +
50A ALA 2.5 12.2 + - - -
51A GLU 2.6 1.2 + - - -
52A ARG* 2.5 44.5 + - - +
59A LEU 3.3 11.7 - - - +
60A ILE 3.8 20.6 - - - +
61A THR* 3.2 34.1 - - - +
62A TYR* 3.4 34.5 - - + +
65A ALA* 3.4 20.4 - - + -
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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
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45A TYR 3.0 26.5 - - - +
46A LEU* 3.2 33.4 - - + +
48A VAL* 1.3 79.8 - - - +
50A ALA* 1.3 57.6 + - + +
51A GLU 3.6 0.2 - - - -
52A ARG* 4.4 8.5 - - - -
62A TYR* 3.9 18.6 - - - +
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Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.4 13.9 + - + +
47A ALA* 3.1 13.9 - - - +
48A VAL 2.5 6.9 + - - -
49A LEU* 1.3 77.7 - - + +
51A GLU* 1.3 55.9 + - - -
53A GLY 5.3 1.0 - - - +
54A ALA* 5.3 2.6 - - - +
85A THR* 2.8 26.7 + - - +
87A TRP* 4.4 11.9 - - + -
88A GLY* 4.0 22.9 - - - +
91A VAL* 5.5 2.0 - - + -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA 2.9 13.5 + - - +
48A VAL 2.6 2.4 + - - -
50A ALA* 1.3 80.2 - - + +
52A ARG* 1.3 52.6 + - - -
53A GLY 2.6 17.9 + - - -
54A ALA* 3.2 19.3 + - - +
56A GLY* 5.1 5.5 + - - -
57A ALA 4.6 4.7 + - - +
59A LEU* 3.0 40.2 - - + +
60A ILE* 3.9 8.3 - - + +
82A TYR 3.4 3.5 - - - +
83A PRO* 3.0 25.3 - - + +
84A VAL* 2.5 16.3 + - - +
85A THR* 2.3 48.9 + - - +
88A GLY* 4.6 1.6 - - - -
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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
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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