Contacts of the helix formed by residues 22 - 33 (chain A) in PDB entry 2DO6
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 ALA 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 1.3 72.9 - - - +
23A PHE* 1.3 65.7 + - - +
24A GLU* 4.3 10.8 - - + +
25A GLU* 3.1 23.5 + - + +
26A VAL* 3.1 22.1 + - - +
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Residues in contact with PHE 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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10A ASP* 6.0 1.1 - - - -
13A ILE* 3.7 31.2 - - + -
17A MET* 3.8 31.7 - - + +
21A TYR 3.8 1.6 + - - -
22A ALA* 1.3 71.0 - - - +
24A GLU* 1.3 65.1 + - + +
26A VAL* 3.2 2.5 + - - +
27A LYS* 2.8 63.1 + - + +
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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 ALA* 3.2 8.2 - - + +
23A PHE* 1.3 88.5 - - + +
25A GLU* 1.3 69.5 + - + +
27A LYS* 3.3 6.4 + - - +
28A ARG* 3.1 21.5 + - - +
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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 TYR* 4.9 1.6 - - + -
22A ALA* 3.1 28.0 + - + +
24A GLU* 1.3 77.2 - - + +
26A VAL* 1.3 61.3 + - - +
28A ARG* 3.3 16.6 + - - +
29A ALA* 3.0 27.0 + - - +
44A LEU* 3.7 20.9 - - + +
47A PHE* 5.7 8.8 - - + +
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Residues in contact with VAL 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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13A ILE* 3.4 39.7 - - + +
16A LEU* 3.5 20.4 - - + -
17A MET* 3.8 23.1 - - + +
21A TYR* 3.7 22.7 - - + -
22A ALA 3.1 13.4 + - - +
23A PHE 3.5 7.2 - - - +
25A GLU* 1.3 74.1 - - - +
27A LYS* 1.3 65.0 + - - +
29A ALA* 3.1 4.7 + - - +
30A LEU* 2.9 27.2 + - + +
44A LEU* 4.1 6.1 - - + -
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Residues in contact with LYS 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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13A ILE* 3.9 24.4 - - + +
23A PHE* 2.8 49.9 + - + +
24A GLU* 3.6 6.3 - - - +
26A VAL* 1.3 72.1 - - - +
28A ARG* 1.3 62.1 + - - +
30A LEU* 3.5 2.1 + - - +
31A GLU* 2.8 64.0 + - - +
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Residues in contact with ARG 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 3.1 14.0 + - - +
25A GLU* 3.4 21.5 + - - +
27A LYS* 1.3 75.3 - - - +
29A ALA* 1.3 64.3 + - - +
31A GLU* 3.1 15.0 + - - +
32A ILE* 3.1 40.8 + - + +
47A PHE* 4.2 25.4 - - + -
46B GLU* 2.7 40.5 + - - +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLU 3.0 13.2 + - - +
26A VAL 3.1 7.6 + - - +
28A ARG* 1.3 76.0 - - - +
30A LEU* 1.3 56.0 + - - +
33A ALA* 2.9 32.6 + - - +
40A ALA* 3.9 19.5 - - + +
43A ILE* 3.4 23.4 - - + +
44A LEU* 3.8 27.1 - - + -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 5.0 4.0 - - + +
12A LYS* 3.6 38.6 - - + +
13A ILE* 4.3 13.9 - - + -
16A LEU* 4.1 4.9 - - + -
26A VAL* 2.9 43.8 + - + +
27A LYS 4.2 2.9 - - - +
29A ALA* 1.3 71.3 - - + +
31A GLU* 1.3 61.2 + - - +
33A ALA* 4.4 0.9 - - - -
34A GLN 3.7 1.2 + - - -
35A ASN* 2.8 45.3 + - - +
36A ASN 3.6 36.8 - - - +
37A VAL* 4.0 2.0 - - - +
40A ALA* 3.9 13.7 - - + -
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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 LYS* 2.8 50.2 + - - +
28A ARG* 3.1 18.6 + - - +
30A LEU* 1.3 78.5 - - - +
32A ILE* 1.3 65.9 + - + +
34A GLN* 3.3 10.9 + - - +
35A ASN* 4.4 5.7 + - - +
42B SER* 5.2 0.3 + - - -
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Residues in contact with ILE 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 ARG* 3.2 38.6 - - + +
31A GLU* 1.3 77.3 - - + +
33A ALA* 1.3 55.4 + - - +
34A GLN* 3.0 9.2 + - - +
43A ILE* 3.7 34.1 - - + -
47A PHE* 4.3 4.7 - - + -
39B VAL* 3.6 6.8 - - - +
42B SER* 3.3 53.0 + - - +
43B ILE* 3.8 13.2 - - + -
46B GLU* 3.8 28.5 - - + +
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Residues in contact with ALA 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 2.9 19.6 + - - +
30A LEU* 4.2 1.1 - - - +
31A GLU 3.4 0.4 - - - -
32A ILE* 1.3 72.5 - - - +
34A GLN* 1.3 68.8 + - - +
35A ASN 3.1 1.0 + - - -
36A ASN* 3.1 40.1 + - - +
39A VAL* 3.7 14.1 - - + +
40A ALA* 3.7 7.9 - - + +
43A ILE* 3.8 4.5 - - + +
39B VAL* 3.7 18.8 - - - +
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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