Contacts of the helix formed by residues 22 - 37 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A SER 3.4 2.4 + - - -
21A LEU* 1.3 76.6 - - - +
23A GLU* 1.3 59.4 + - - +
24A GLU* 3.3 15.1 + - - -
25A GLU* 2.9 29.0 + - - +
26A ILE* 2.9 26.5 + - - +
20B SER 2.6 31.2 + - - -
21B LEU 4.5 0.7 - - - -
22B SER* 4.1 17.0 - - - -
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Residues in contact with GLU 23 (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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21A LEU 4.1 6.4 - - - +
22A SER* 1.3 77.4 - - - +
24A GLU* 1.3 63.2 + - - +
26A ILE* 3.6 16.7 - - + +
27A ALA* 3.0 26.3 + - - +
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Residues in contact with GLU 24 (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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22A SER* 3.1 16.9 + - - -
23A GLU* 1.3 80.0 + - - +
25A GLU* 1.3 65.7 + - - +
27A ALA* 3.4 7.4 + - - +
28A GLY 3.0 17.8 + - - -
103A ALA* 3.3 17.9 - - + +
106A THR* 5.4 0.2 + - - -
16B VAL* 6.0 2.7 - - + +
19B GLU* 3.5 24.8 - - + +
20B SER* 3.6 18.8 - - - +
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Residues in contact with GLU 25 (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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21A LEU* 3.4 12.8 - - + -
22A SER* 2.9 38.8 + - - +
24A GLU* 1.3 75.4 - - - +
26A ILE* 1.3 59.3 + - - +
28A GLY* 3.2 2.3 + - - -
29A LEU* 2.9 34.3 + - + +
99A ASP* 3.4 23.5 - - + +
100A HIS* 2.9 31.9 + - - +
103A ALA* 4.1 5.2 - - - -
20B SER* 3.9 3.1 - - - +
25B GLU* 2.6 21.5 - - - +
100B HIS* 2.8 32.1 + - - -
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Residues in contact with ILE 26 (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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18A ALA 5.0 2.7 - - - +
21A LEU* 3.8 33.4 - - + +
22A SER 2.9 21.4 + - - +
23A GLU* 3.6 21.3 - - + +
24A GLU 3.3 0.2 - - - -
25A GLU* 1.3 75.2 - - - +
27A ALA* 1.3 64.1 + - - +
29A LEU* 3.1 10.4 + - + +
30A LYS* 3.0 24.3 + - + +
82A TYR* 3.7 18.7 + - - +
86A ILE* 5.4 7.6 - - + -
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Residues in contact with ALA 27 (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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23A GLU 3.0 17.6 + - - +
24A GLU* 3.8 7.6 - - - +
25A GLU 3.3 0.4 - - - -
26A ILE* 1.3 77.3 - - - +
28A GLY* 1.3 62.5 + - - +
30A LYS* 3.4 9.8 + - - +
31A GLU* 3.0 22.5 + - - +
106A THR* 3.9 12.6 + - - +
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Residues in contact with GLY 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 GLU 3.0 14.5 + - - -
25A GLU 3.2 4.2 + - - -
27A ALA* 1.3 77.2 - - - +
29A LEU* 1.3 55.3 + - - +
31A GLU* 3.1 1.9 + - - +
32A MSE 2.9 24.1 + - - +
99A ASP 5.2 0.7 - - - -
102A PHE* 3.3 29.4 - - - -
103A ALA 4.2 0.4 - - - -
106A THR* 3.2 21.6 - - - +
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Residues in contact with LEU 29 (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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21A LEU* 4.0 22.7 - - + -
25A GLU 2.9 19.1 + - - +
26A ILE* 3.1 10.3 + - + +
28A GLY* 1.3 76.1 - - - +
30A LYS* 1.3 57.5 + - - +
32A MSE 3.3 31.1 - - + +
33A PHE* 2.8 30.0 + - - +
82A TYR* 4.6 3.1 - - - +
85A PHE* 3.7 7.1 - - + -
86A ILE* 4.6 21.8 - - + -
89A THR* 3.8 33.9 - - + +
90A LEU* 5.8 0.2 - - + -
99A ASP* 3.7 27.4 - - + +
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Residues in contact with LYS 30 (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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26A ILE* 3.0 13.3 + - + +
27A ALA* 3.5 13.0 - - - +
29A LEU* 1.3 74.9 - - - +
31A GLU* 1.3 60.2 + - - +
33A PHE* 3.3 5.7 + - - +
34A ASN* 2.9 54.3 + - - +
82A TYR* 4.0 40.1 - - + +
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Residues in contact with GLU 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 ALA 3.0 9.3 + - - +
28A GLY 3.1 0.2 + - - -
30A LYS* 1.3 75.9 - - - +
32A MSE 1.3 51.4 + - - +
34A ASN* 3.3 8.5 + - - +
35A MSE 2.8 36.5 + - + +
102A PHE* 3.7 16.6 - - + -
105A PHE* 3.4 17.0 - - + -
106A THR* 3.5 34.8 - - + -
109A ASP* 2.4 34.7 - - - +
112A GLY* 3.6 16.8 - - - -
114A GLY* 4.0 5.8 - - - -
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Residues in contact with MSE 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 GLY 2.9 9.3 + - - +
29A LEU* 3.3 38.6 - - + +
31A GLU* 1.3 73.0 - - - +
33A PHE* 1.3 66.9 + - - +
35A MSE 3.2 5.7 + - - +
36A ILE* 3.1 27.6 + - - +
56A VAL* 3.6 19.1 - - + +
85A PHE* 4.1 17.0 - - + -
95A ILE* 3.7 29.6 - - + +
98A GLU* 4.9 2.0 - - + +
99A ASP* 3.8 14.1 - - - +
102A PHE* 3.0 66.7 - - + -
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Residues in contact with PHE 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 LEU 2.8 19.9 + - - +
30A LYS* 3.3 8.3 + - - +
32A MSE 1.3 73.5 - - - +
34A ASN* 1.3 71.2 + - - +
36A ILE* 3.2 4.3 + - - +
37A ASP* 2.8 47.8 + - + +
42A GLY* 3.4 30.7 - - - -
43A GLN 4.3 1.3 - - - -
44A ILE* 3.6 28.7 - - + +
80A ILE 3.8 4.9 - - - -
81A ASP 3.6 6.7 - - - -
82A TYR* 3.5 45.3 - + + -
85A PHE* 3.7 28.4 - + + -
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Residues in contact with ASN 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 LYS* 2.9 43.9 + - - +
31A GLU* 3.7 7.2 - - - +
33A PHE* 1.3 87.1 - - - +
35A MSE 1.3 66.1 + - - +
37A ASP* 3.3 25.4 - - - +
40A LYS* 3.7 23.9 + - - +
112A GLY 6.0 1.8 - - - +
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Residues in contact with MSE 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 GLU* 2.8 14.1 + - + +
32A MSE 3.2 11.0 + - - +
34A ASN* 1.3 79.9 - - - +
36A ILE* 1.3 61.3 + - - +
38A ALA* 4.2 8.0 + - - +
40A LYS* 5.7 0.2 + - - -
52A GLY* 5.5 0.8 - - - -
55A ARG* 2.8 93.2 + - + +
56A VAL* 3.8 8.1 - - + -
102A PHE* 3.8 21.1 - - - -
105A PHE* 5.0 3.4 - - - -
114A GLY* 4.6 23.1 - - - +
151A ASP* 6.2 1.6 - - + -
152A TYR* 4.1 15.0 - - + +
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Residues in contact with ILE 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 MSE 3.1 14.8 + - - +
33A PHE 3.7 5.2 - - - +
35A MSE 1.3 74.5 - - + +
37A ASP* 1.3 52.3 + - - +
38A ALA* 2.7 21.4 + - - +
44A ILE* 3.6 29.8 - - + -
48A GLU* 3.6 34.2 - - - +
49A LEU* 4.0 7.0 - - + -
52A GLY* 3.9 22.8 - - - +
53A LEU* 4.2 13.2 - - + -
56A VAL* 4.0 25.4 - - + -
85A PHE* 4.0 25.4 - - + -
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Residues in contact with ASP 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 PHE* 2.8 26.7 + - + +
34A ASN* 3.3 9.5 - - - +
35A MSE 3.4 0.2 - - - -
36A ILE* 1.3 72.8 - - - +
38A ALA* 1.3 56.9 + - - +
39A ASP* 3.1 8.1 - - - +
40A LYS* 2.9 29.3 + - - +
41A SER 3.2 6.2 + - - -
42A GLY* 2.7 32.1 + - - -
43A GLN 3.1 6.9 - - - +
44A ILE* 4.0 14.8 - - + +
48A GLU* 4.0 3.4 - - - -
293A CA 2.3 32.0 - - - -
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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