Contacts of the helix formed by residues 22 - 37 (chain B) in PDB entry 2AAO
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 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A SER 2.6 29.8 + - - -
21A LEU 4.5 0.4 - - - -
22A SER* 4.1 17.0 - - - -
20B SER 3.4 1.6 + - - -
21B LEU* 1.3 76.4 - - - +
23B GLU* 1.3 64.4 + - - +
24B GLU* 3.4 11.2 + - - -
25B GLU* 3.0 29.3 + - - +
26B ILE* 3.0 24.1 + - - +
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Residues in contact with GLU 23 (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 LEU 4.1 0.2 + - - -
22B SER* 1.3 73.4 - - - +
24B GLU* 1.3 70.6 + - - +
26B ILE* 3.3 11.7 + - + +
27B ALA* 2.9 29.3 + - - +
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Residues in contact with GLU 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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19A GLU 4.9 4.3 - - - +
20A SER* 3.4 38.8 - - - +
22B SER* 3.4 17.5 + - - -
23B GLU* 1.3 88.1 + - - +
25B GLU* 1.3 62.1 + - - +
27B ALA* 3.3 7.8 + - - +
28B GLY 3.1 16.5 + - - -
103B ALA* 3.5 14.8 - - + +
106B THR* 5.6 0.2 - - - -
107B TYR* 6.2 3.4 - - + -
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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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20A SER* 3.4 11.9 - - - +
21A LEU* 4.0 2.1 - - - -
25A GLU* 2.6 28.5 - - - +
100A HIS* 3.2 20.3 - - - +
21B LEU* 3.6 9.7 - - + -
22B SER* 3.0 35.5 + - - +
24B GLU* 1.3 75.2 - - - +
26B ILE* 1.3 64.0 + - - +
28B GLY* 3.1 4.0 + - - -
29B LEU* 3.0 26.9 + - + +
99B ASP* 5.3 7.3 - - + +
100B HIS* 3.2 29.5 + - + -
103B ALA* 3.9 14.5 - - + +
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Residues in contact with ILE 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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18B ALA 5.5 0.9 - - - +
21B LEU* 3.9 37.9 - - + +
22B SER 3.0 21.9 + - - +
23B GLU* 3.3 8.7 + - + +
25B GLU* 1.3 72.1 - - - +
27B ALA* 1.3 66.9 + - - +
29B LEU* 3.0 11.3 + - + +
30B LYS* 2.9 50.2 + - - +
82B TYR* 3.8 5.6 - - - +
86B ILE* 5.4 7.0 - - + -
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Residues in contact with ALA 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 GLU 2.9 17.4 + - - +
24B GLU* 3.6 8.1 - - - +
25B GLU 3.3 0.2 - - - -
26B ILE* 1.3 76.8 - - - +
28B GLY* 1.3 62.5 + - - +
30B LYS* 3.3 13.9 + - - +
31B GLU* 3.1 17.5 + - - +
106B THR* 3.8 19.6 - - + +
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Residues in contact with GLY 28 (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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24B GLU 3.1 7.3 + - - -
25B GLU 3.1 8.6 + - - -
27B ALA* 1.3 75.9 - - - +
29B LEU* 1.3 57.6 + - - +
31B GLU 3.3 1.0 + - - -
32B MSE 2.9 24.1 + - - +
99B ASP 5.5 0.9 - - - -
102B PHE* 3.3 16.5 - - - -
103B ALA* 4.0 18.4 - - - -
106B THR* 3.5 17.6 - - - +
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Residues in contact with LEU 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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21B LEU* 4.1 19.7 - - + -
25B GLU* 3.0 20.0 + - + +
26B ILE* 3.0 11.4 + - - +
28B GLY* 1.3 76.4 - - - +
30B LYS* 1.3 58.1 + - - +
32B MSE 3.6 8.2 - - + +
33B PHE* 2.8 32.1 + - - +
82B TYR* 4.3 2.2 - - - +
85B PHE* 3.7 9.2 - - + -
86B ILE* 4.1 32.3 - - + -
89B THR* 3.5 32.3 - - + +
99B ASP* 3.6 35.7 - - + +
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Residues in contact with LYS 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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26B ILE* 2.9 31.3 + - - +
27B ALA* 3.5 12.7 - - - +
29B LEU* 1.3 77.6 - - - +
31B GLU* 1.3 56.9 + - - +
33B PHE* 3.4 2.3 + - - +
34B ASN* 2.9 40.9 + - - +
82B TYR* 2.4 58.6 - - + +
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Residues in contact with GLU 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 ALA 3.1 10.0 + - - +
28B GLY 3.7 2.0 - - - +
30B LYS* 1.3 76.4 - - - +
32B MSE 1.3 64.2 + - - +
34B ASN* 3.3 7.7 + - - +
35B MSE 2.9 27.0 + - + +
102B PHE* 3.6 17.0 - - + -
105B PHE* 3.6 17.4 - - - -
106B THR* 3.3 34.8 - - + +
109B ASP* 2.4 33.8 - - - +
112B GLY* 3.6 18.9 - - - -
114B GLY* 3.8 6.7 - - - -
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Residues in contact with MSE 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 GLY 2.9 14.5 + - - +
29B LEU* 3.3 12.1 + - + +
31B GLU* 1.3 75.0 - - - +
33B PHE* 1.3 63.0 + - - +
35B MSE 3.2 4.2 + - - +
36B ILE* 3.2 24.2 + - + +
56B VAL* 3.8 30.5 - - + +
85B PHE* 3.7 24.2 - - + -
95B ILE* 3.6 22.9 - - - +
98B GLU* 4.8 2.2 - - + +
99B ASP* 3.3 25.1 - - - +
102B PHE* 3.3 47.9 - - + -
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Residues in contact with PHE 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 LEU 2.8 21.0 + - - +
30B LYS 3.6 4.0 - - - +
32B MSE 1.3 72.3 - - - +
34B ASN* 1.3 70.2 + - - +
36B ILE* 3.2 5.0 + - - +
37B ASP* 2.9 44.8 + - + +
42B GLY* 3.5 29.8 - - - -
44B ILE* 3.5 31.6 - - + -
80B ILE 3.6 6.3 - - - -
81B ASP 3.5 8.3 - - - -
82B TYR* 3.5 44.2 - + + -
85B PHE* 3.6 30.2 - - + -
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Residues in contact with ASN 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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30B LYS* 2.9 28.5 + - - +
31B GLU* 3.8 7.0 - - - +
33B PHE* 1.3 89.6 - - - +
35B MSE 1.3 65.2 + - - +
37B ASP* 3.4 23.9 - - - +
40B LYS* 3.6 24.7 + - + +
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Residues in contact with MSE 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 GLU* 2.9 20.3 + - + +
32B MSE 3.2 10.3 + - - +
34B ASN* 1.3 76.2 - - - +
36B ILE* 1.3 54.8 + - - +
38B ALA* 4.5 3.5 + - - -
52B GLY 5.7 0.4 - - - -
55B ARG* 2.7 95.3 + - + +
56B VAL* 3.7 9.2 - - + -
102B PHE* 3.7 26.5 - - + -
105B PHE* 5.3 2.0 - - - -
114B GLY* 4.8 22.9 - - - +
151B ASP* 6.4 1.3 - - + -
152B TYR* 4.4 10.8 - - + +
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Residues in contact with ILE 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 MSE 3.2 15.5 + - + +
33B PHE 3.2 6.6 + - - +
35B MSE 1.3 77.5 - - - +
37B ASP* 1.3 58.2 + - - +
38B ALA* 3.0 11.3 + - - +
44B ILE* 3.6 28.0 - - + -
48B GLU* 3.6 33.7 - - - +
49B LEU* 3.9 14.1 - - + -
52B GLY* 4.1 20.2 - - - +
53B LEU* 4.9 5.4 - - + -
55B ARG* 4.3 5.5 + - - +
56B VAL* 4.1 22.4 - - + -
85B PHE* 4.0 27.4 - - + -
95B ILE* 5.8 0.4 - - + -
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Residues in contact with ASP 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 PHE* 2.9 29.2 + - + +
34B ASN* 3.4 11.3 + - - +
35B MSE 3.4 0.4 - - - -
36B ILE* 1.3 72.6 - - - +
38B ALA* 1.3 56.9 + - - +
39B ASP* 3.1 6.9 - - - +
40B LYS* 3.0 29.9 + - - +
41B SER 3.3 5.0 + - - -
42B GLY* 2.7 31.6 + - - -
43B GLN 3.1 8.5 - - - +
44B ILE* 4.2 8.0 - - + +
48B GLU* 4.3 2.7 - - - -
297B CA 2.3 32.1 - - - -
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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
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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