Contacts of the helix formed by residues 30 - 52 (chain B) in PDB entry 3BLR
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 ASP 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B ARG* 3.7 0.7 - - - +
28B GLY 3.2 11.8 - - - +
29B VAL* 1.3 78.5 - - - +
31B PRO* 1.3 70.5 - - + +
32B ASP* 3.3 7.0 - - + +
33B LYS* 3.3 13.2 + - + +
34B GLU* 3.0 26.7 + - - +
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Residues in contact with PRO 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLU* 3.9 19.3 - - - +
25B ARG* 3.6 38.0 + - - +
30B ASP* 1.3 91.5 - - + +
32B ASP* 1.3 63.5 + - - +
34B GLU* 3.7 1.6 + - - +
35B LEU* 3.3 33.7 + - - +
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Residues in contact with ASP 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ASP* 3.3 4.0 - - + +
31B PRO* 1.3 84.7 - - - +
33B LYS* 1.3 65.5 + - - +
35B LEU* 3.6 15.7 + - - +
36B SER* 3.3 20.1 + - - -
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 3.9 9.9 - - + -
30B ASP* 3.6 19.8 - - + +
32B ASP* 1.3 78.0 - - - +
34B GLU* 1.3 64.2 + - - +
36B SER* 3.0 11.0 + - - -
37B TYR* 2.9 60.7 + - + +
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU 4.4 1.3 - - - +
22B SER* 2.9 24.7 + - - -
24B SER* 3.8 12.1 + - - -
25B ARG* 2.7 33.3 + - - +
29B VAL* 3.7 8.9 - - + +
30B ASP 3.0 15.9 + - - +
31B PRO 3.9 4.0 - - - +
32B ASP 3.3 0.2 - - - -
33B LYS* 1.3 74.8 - - - +
35B LEU* 1.3 69.6 + - + +
37B TYR* 3.1 16.8 + - - +
38B ARG* 3.2 41.8 + - - +
70B TYR 4.1 2.8 - - - +
75B PHE* 4.0 20.6 - - + -
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ARG* 6.0 1.3 - - - +
31B PRO 3.3 19.8 + - - +
32B ASP* 3.9 15.3 - - - +
33B LYS 3.3 0.4 - - - -
34B GLU* 1.3 82.6 - - + +
36B SER* 1.3 62.6 + - - +
38B ARG* 3.4 13.0 + - - +
39B GLN* 3.1 34.5 + - - +
184B LEU 5.7 4.5 - - - +
185B THR* 6.6 0.2 - - - -
186B THR* 4.7 20.0 - - + +
244B ILE* 5.7 7.2 - - + -
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ASP 3.3 11.9 + - - -
33B LYS* 3.1 20.4 - - - -
34B GLU 3.0 0.2 - - - -
35B LEU* 1.3 77.8 - - - +
37B TYR* 1.3 59.9 + - - +
39B GLN* 3.1 14.5 + - - +
40B GLN* 2.9 49.9 + - - +
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Residues in contact with TYR 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 3.9 29.0 - - + +
33B LYS* 2.9 46.8 + - + +
34B GLU* 3.1 6.5 + - - +
36B SER* 1.3 77.1 - - - +
38B ARG* 1.3 57.4 + - - +
40B GLN* 3.6 24.6 + - - +
41B ALA* 3.1 26.7 + - - +
75B PHE* 3.7 48.9 - + + -
80B GLY* 5.6 0.9 - - - -
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B LEU* 5.3 2.1 - - - +
34B GLU* 3.2 45.9 + - - +
35B LEU* 3.6 14.5 - - - +
36B SER 3.2 0.4 - - - -
37B TYR* 1.3 73.6 - - - +
39B GLN* 1.3 67.5 + - + +
40B GLN 3.2 0.2 - - - -
41B ALA 3.3 0.3 + - - -
42B ALA* 3.0 25.1 + - - +
66B MET* 3.6 16.6 - - + +
67B HIS* 3.1 61.7 + - + +
70B TYR* 3.5 24.5 + - - +
71B MET* 3.8 17.4 - - - -
75B PHE* 3.9 12.6 - - + -
183B HIS 4.5 2.2 - - - +
186B THR* 3.9 16.1 - - - +
189B LEU* 3.8 9.5 - - - +
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Residues in contact with GLN 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.1 25.8 + - - +
36B SER* 3.1 13.9 + - - +
38B ARG* 1.3 76.6 - - + +
40B GLN* 1.3 58.1 + - + +
42B ALA* 3.4 2.5 + - - +
43B ASN* 3.0 35.9 + - - +
183B HIS* 3.2 23.9 - - - +
184B LEU* 3.0 41.0 + - + +
244B ILE* 3.7 16.6 - - - +
248B THR* 5.5 0.4 + - - -
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Residues in contact with GLN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B SER* 2.9 35.7 + - - +
37B TYR* 3.7 25.7 - - - +
39B GLN* 1.3 78.4 - - + +
41B ALA* 1.3 58.0 + - - +
43B ASN* 3.3 9.8 + - - +
44B LEU* 3.0 27.5 + - - +
81B ASN* 5.6 5.5 - - - +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B TYR 3.1 17.5 + - - +
38B ARG 3.3 4.0 + - - +
40B GLN* 1.3 77.1 - - - +
42B ALA* 1.3 55.7 + - - +
44B LEU* 3.3 8.1 + - - +
45B LEU* 2.9 34.3 + - - +
66B MET* 3.9 27.1 - - + -
75B PHE* 5.2 1.3 - - + -
80B GLY* 4.6 24.0 - - - +
81B ASN* 5.8 1.1 - - - -
84B ALA* 4.1 4.9 - - + +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ARG 3.0 17.5 + - - +
39B GLN 3.6 4.7 - - - +
41B ALA* 1.3 74.5 - - - +
43B ASN* 1.3 61.3 + - - +
45B LEU* 3.2 3.7 + - - +
46B GLN* 2.8 29.6 + - - +
63B ILE* 4.0 25.9 - - + +
66B MET* 4.4 2.5 - - + +
67B HIS* 5.9 0.2 - - - +
183B HIS* 3.9 39.7 + - + +
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Residues in contact with ASN 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLN* 3.0 21.6 + - - +
40B GLN* 3.3 12.0 + - - +
42B ALA* 1.3 75.0 - - - +
44B LEU* 1.3 57.9 + - - +
46B GLN* 3.3 6.8 + - - +
47B ASP* 2.9 31.3 + - - +
183B HIS* 3.9 16.1 - - - +
251B ARG* 4.0 13.7 + - - +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLN 3.0 13.6 + - - +
41B ALA* 3.6 9.9 - - - +
42B ALA 3.2 0.2 - - - -
43B ASN* 1.3 77.1 - - - +
45B LEU* 1.3 63.5 + - - +
47B ASP* 3.4 4.7 + - + +
48B MET* 3.0 41.2 + - + +
80B GLY 4.4 0.4 - - - +
81B ASN* 3.6 40.4 - - - +
84B ALA* 4.1 13.2 - - + -
85B PRO* 4.4 4.7 - - + -
111B CYS* 4.0 24.0 - - + +
112B LEU* 3.8 27.6 - - + -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA 2.9 22.5 + - - +
42B ALA* 3.2 7.2 + - - +
44B LEU* 1.3 77.0 - - - +
46B GLN* 1.3 57.5 + - - +
48B MET* 3.8 4.5 - - + +
49B GLY* 2.8 28.6 + - - -
59B ILE* 4.0 10.8 - - + +
62B ALA* 3.7 15.7 - - + +
63B ILE* 3.7 42.2 - - + +
66B MET* 4.4 11.2 - - + -
84B ALA* 3.2 37.2 - - + +
87B ALA* 4.7 0.9 - - + -
88B LEU* 3.6 24.1 - - + +
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Residues in contact with GLN 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA 2.8 20.0 + - - +
43B ASN* 3.3 6.3 + - - +
45B LEU* 1.3 72.7 - - - +
47B ASP* 1.3 62.9 + - - +
50B GLN* 2.9 56.6 + - - +
56B GLN* 2.8 42.9 + - - -
59B ILE* 3.7 14.0 - - - +
179B THR* 5.5 1.1 - - - +
183B HIS* 3.1 24.7 + - + +
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Residues in contact with ASP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ASN 2.9 17.4 + - - +
44B LEU* 3.8 7.3 - - + +
46B GLN* 1.3 76.4 - - - +
48B MET* 1.3 65.8 + - - +
49B GLY 3.1 0.3 + - - -
50B GLN* 3.2 16.8 + - - +
51B ARG* 3.1 47.8 + - - +
111B CYS* 3.3 20.4 - - - +
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Residues in contact with MET 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.0 39.6 + - + +
45B LEU* 3.8 22.9 - - + -
47B ASP* 1.3 75.4 - - - +
49B GLY* 1.3 57.1 + - - +
51B ARG* 3.4 1.2 + - - +
52B LEU* 2.9 35.9 + - + +
84B ALA* 4.0 0.7 - - + -
85B PRO* 3.8 44.6 - - + -
88B LEU* 3.7 14.1 - - + -
104B VAL* 5.2 3.6 - - - +
107B VAL* 3.9 18.8 - - + -
108B ALA* 4.0 16.8 - - - -
111B CYS* 3.9 18.8 - - - -
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Residues in contact with GLY 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B LEU 2.8 20.2 + - - -
47B ASP 3.1 0.2 - - - -
48B MET* 1.3 77.5 - - - +
50B GLN* 1.3 59.9 + - - +
52B LEU* 3.6 0.8 + - - -
53B ASN 3.2 3.3 + - - -
54B VAL* 3.1 36.2 + - - +
59B ILE* 3.5 22.7 - - - -
88B LEU* 3.9 7.4 - - - +
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Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B GLN* 2.9 55.4 + - - +
47B ASP* 3.9 11.4 + - - +
49B GLY* 1.3 76.2 - - - +
51B ARG* 1.3 63.5 + - + +
53B ASN* 3.2 14.8 + - - +
54B VAL 5.1 2.5 - - - +
59B ILE* 4.8 2.9 - - + -
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Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ASP* 3.1 45.5 + - - +
48B MET 3.9 3.1 - - - +
50B GLN* 1.3 74.1 - - + +
52B LEU* 1.3 60.0 + - - +
53B ASN* 3.1 7.7 + - - +
103B HIS* 5.2 2.9 + - - -
107B VAL* 4.2 15.7 - - + +
110B THR* 3.5 32.9 + - - +
111B CYS* 3.5 24.6 + - - +
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B MET* 2.9 22.5 + - + +
49B GLY* 4.2 1.3 - - - +
51B ARG* 1.3 74.6 - - - +
53B ASN* 1.3 70.8 + - - +
54B VAL* 4.1 13.0 - - + -
88B LEU* 3.8 23.6 - - + -
99B LYS* 3.1 31.2 + - + +
103B HIS* 3.7 40.0 - - + +
104B VAL* 3.8 27.6 - - + -
107B VAL* 3.6 31.2 - - + -
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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