Contacts of the helix formed by residues 23 - 37 (chain B) in PDB entry 3UTR
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 LYS 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A C 5.8 2.0 - - - +
49A G 4.9 5.3 + - - -
50A C 4.5 26.7 + - - +
21B ILE 4.1 0.2 + - - -
22B LYS* 1.3 73.7 - - - +
24B ASP* 1.3 65.6 + - - +
26B LEU* 3.6 1.6 - - - +
27B LYS* 2.9 42.9 + - + +
45B VAL* 3.5 39.8 + - + -
46B SER* 4.6 5.7 + - - +
47B ARG* 3.7 29.1 - - + +
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Residues in contact with ASP 24 (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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22B LYS* 3.4 1.8 - - + +
23B LYS* 1.3 81.2 - - - +
25B GLU* 1.3 58.5 + - - +
27B LYS* 3.5 13.6 + - - +
28B LYS* 2.9 32.1 + - - +
96D LYS* 4.1 8.9 + - - +
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Residues in contact with GLU 25 (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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21B ILE* 3.6 17.8 - - + +
22B LYS* 3.4 20.1 + - + +
23B LYS 3.4 0.2 - - - -
24B ASP* 1.3 76.9 - - - +
26B LEU* 1.3 63.0 + - - +
28B LYS* 3.3 7.5 + - - +
29B SER* 3.0 29.7 + - - +
78B TYR* 3.3 33.5 + - - +
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Residues in contact with LEU 26 (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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17B LEU* 4.3 25.8 - - + -
18B ASN 5.4 3.4 - - - +
21B ILE* 3.6 29.7 - - + +
22B LYS 2.9 19.1 + - - +
23B LYS 3.6 3.6 - - - +
25B GLU* 1.3 76.1 - - - +
27B LYS* 1.3 57.0 + - - +
29B SER* 3.3 4.0 + - - -
30B LEU* 2.9 45.5 + - + +
45B VAL* 3.8 30.1 - - + -
53B GLY* 6.3 0.9 - - - +
54B GLN 4.8 2.7 - - - +
77B PHE* 3.8 28.5 - - + -
78B TYR* 4.6 2.0 - - + -
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Residues in contact with LYS 27 (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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23B LYS* 2.9 29.6 + - + +
24B ASP* 3.8 12.9 + - - +
26B LEU* 1.3 74.8 - - - +
28B LYS* 1.3 58.0 + - - +
30B LEU* 3.4 5.3 + - - -
31B TYR* 2.9 31.0 + - - +
42B ASP* 4.8 7.5 + - - -
43B ILE* 3.6 37.2 + - + +
45B VAL* 4.1 26.7 - - + +
96D LYS* 4.2 12.8 - - - +
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP 2.9 18.8 + - - +
25B GLU* 3.6 8.3 - - - +
27B LYS* 1.3 74.5 - - - +
29B SER* 1.3 59.3 + - - +
31B TYR* 3.4 5.5 + - - +
32B ALA* 3.0 29.1 + - + +
96D LYS* 3.8 25.6 - - - +
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Residues in contact with SER 29 (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 GLU* 3.0 16.0 + - - +
26B LEU 3.8 2.9 - - - -
28B LYS* 1.3 73.6 - - - +
30B LEU* 1.3 64.6 + - - +
32B ALA* 3.4 7.0 + - - +
33B ILE* 3.2 29.6 + - - +
77B PHE* 3.9 21.5 - - - -
78B TYR* 2.8 26.6 + - - -
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Residues in contact with LEU 30 (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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14B ILE* 4.1 10.1 - - + -
17B LEU* 4.8 3.6 - - + -
26B LEU* 2.9 36.5 + - + +
27B LYS 3.8 3.4 - - - +
29B SER* 1.3 76.4 - - - +
31B TYR* 1.3 56.5 + - - +
33B ILE* 3.4 2.5 + - + -
34B PHE* 2.9 62.6 + - + +
43B ILE* 3.9 24.5 - - + -
45B VAL* 4.4 0.9 - - + -
55B ALA* 3.6 29.8 - - + -
57B VAL* 4.7 2.9 - - + -
77B PHE* 3.7 26.9 - - + -
82B MET* 4.5 3.1 - - - -
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Residues in contact with TYR 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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27B LYS 2.9 18.8 + - - +
28B LYS* 3.6 7.6 - - - +
30B LEU* 1.3 74.7 - - - +
32B ALA* 1.3 58.9 + - - +
35B SER* 2.9 53.8 + - - -
39B GLN* 6.0 0.7 - - - +
40B ILE* 4.1 34.4 + - + -
41B LEU 6.3 0.2 - - - -
42B ASP* 6.3 0.4 - - - -
43B ILE* 3.5 19.4 - - + +
93D ILE 5.8 1.3 - - - -
96D LYS* 4.3 20.6 - - + +
97D MET* 3.4 51.3 - - + +
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Residues in contact with ALA 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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28B LYS* 3.0 17.7 + - + +
29B SER* 3.6 9.2 - - - +
31B TYR* 1.3 77.8 - - - +
33B ILE* 1.3 62.5 + - + +
35B SER* 3.4 12.3 + - - -
36B GLN* 4.7 2.9 + - - +
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Residues in contact with ILE 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 SER* 3.2 12.9 + - - +
30B LEU* 3.8 2.9 - - - +
32B ALA* 1.3 79.2 - - + +
34B PHE* 1.3 83.5 + - + +
35B SER 3.5 0.2 - - - -
36B GLN* 3.7 15.1 - - - +
37B PHE* 3.6 13.3 - - - -
72B MET* 3.8 28.3 - - + -
75B PHE* 5.6 6.5 - - + -
77B PHE* 3.3 42.2 - - + -
82B MET* 4.5 4.7 - - + -
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Residues in contact with PHE 34 (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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12B ILE* 3.7 12.6 - - + -
14B ILE* 3.5 29.8 - - + -
30B LEU* 2.9 42.5 + - + +
33B ILE* 1.3 82.9 - - + +
35B SER* 1.3 64.4 + - - +
36B GLN 3.2 2.7 - - - -
37B PHE* 3.1 23.4 + + - -
40B ILE* 3.7 14.1 - - + -
57B VAL* 4.3 13.7 - - + -
59B PHE* 3.5 21.8 - + + -
68B ALA* 3.7 24.2 - - + -
72B MET* 3.6 23.1 - - + -
82B MET* 3.8 22.4 - - + -
84B ILE* 4.0 4.9 - - + -
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Residues in contact with SER 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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31B TYR* 2.9 42.0 + - - -
32B ALA* 3.4 11.4 + - - -
34B PHE* 1.3 76.5 - - - +
36B GLN* 1.3 62.5 + - - +
37B PHE 3.1 0.2 - - - -
38B GLY* 3.2 20.9 + - - +
40B ILE* 3.5 9.6 - - - +
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Residues in contact with GLN 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 ALA 4.7 2.6 + - - +
33B ILE 3.7 12.6 + - - +
34B PHE 3.2 1.2 - - - -
35B SER* 1.3 80.9 + - - +
37B PHE* 1.3 98.1 + - + +
38B GLY* 3.6 0.5 + - - -
72B MET* 4.7 5.2 - - - +
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Residues in contact with PHE 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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33B ILE 3.6 15.7 - - - -
34B PHE* 3.1 20.9 + + - +
36B GLN* 1.3 100.7 - - + +
38B GLY* 1.3 56.4 + - - +
59B PHE* 4.2 1.6 - - + -
64B SER* 3.2 36.2 + - - +
67B ASN* 3.8 15.7 + - + -
68B ALA* 3.6 26.0 - - + +
71B SER* 3.3 38.1 - - - -
72B MET* 3.5 27.6 - - + -
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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