Contacts of the helix formed by residues 23 - 39 (chain A) in PDB entry 2DO5
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 ASN 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLY* 1.3 76.0 - - - -
24A ARG* 1.3 69.5 + - - +
25A GLU* 3.2 8.5 - - + +
26A GLU* 3.0 24.8 + - + +
27A LEU* 3.0 14.5 + - - +
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Residues in contact with ARG 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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2A GLY 5.5 3.8 - - - -
4A TRP 5.4 8.7 + - - -
5A ALA* 6.2 0.8 - - - +
6A ALA* 5.0 17.2 - - + +
9A LEU* 4.3 12.6 - - + -
23A ASN* 1.3 73.4 + - - +
25A GLU* 1.3 71.2 + - + +
27A LEU* 3.0 15.8 + - - +
28A VAL* 2.9 38.0 + - + +
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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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23A ASN* 3.2 6.0 - - + -
24A ARG* 1.3 81.0 + - + +
26A GLU* 1.3 67.9 + - + +
28A VAL* 3.0 11.8 + - - +
29A GLU* 2.9 26.5 + - - +
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Residues in contact with GLU 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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21A GLN 4.8 3.6 - - - +
22A GLY* 4.3 10.0 - - - -
23A ASN* 3.0 29.6 + - + +
25A GLU* 1.3 79.5 - - + +
27A LEU* 1.3 62.5 + - - +
29A GLU* 3.6 6.8 + - - +
30A ARG* 3.1 34.7 + - - +
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Residues in contact with LEU 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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6A ALA* 4.5 9.6 - - + +
9A LEU* 4.3 16.6 - - + -
10A GLN* 3.6 28.5 - - + +
13A LEU* 3.3 30.9 - - + +
19A PRO 4.7 0.9 - - - +
20A ILE* 4.1 24.0 - - - +
21A GLN 4.1 11.9 - - - +
22A GLY 4.5 4.9 - - - +
23A ASN 3.0 15.7 + - - +
24A ARG* 3.0 15.8 + - - +
26A GLU* 1.3 73.2 - - - +
28A VAL* 1.3 68.6 + - - +
30A ARG* 3.1 15.8 + - - +
31A LEU* 3.1 17.8 + - - +
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Residues in contact with VAL 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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1A TYR* 3.7 34.5 - - + +
2A GLY* 4.9 5.6 - - - +
9A LEU* 3.8 20.4 - - + -
24A ARG* 2.9 31.6 + - + +
25A GLU* 3.0 13.0 + - - +
27A LEU* 1.3 74.4 - - - +
29A GLU* 1.3 64.4 + - - +
31A LEU* 3.2 4.6 + - - +
32A GLN* 2.9 42.9 + - - +
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Residues in contact with GLU 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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25A GLU 2.9 18.9 + - - +
26A GLU* 3.8 6.7 - - - +
28A VAL* 1.3 73.8 - - - +
30A ARG* 1.3 63.8 + - - +
32A GLN* 3.2 20.7 + - - +
33A SER* 2.8 33.1 + - - -
36A ARG* 6.0 1.2 - - - -
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Residues in contact with ARG 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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13A LEU* 3.8 28.2 - - + +
18A ALA* 4.6 11.2 - - - +
19A PRO* 3.9 33.1 + - - +
21A GLN 4.2 15.4 + - - -
26A GLU* 3.1 26.1 + - - +
27A LEU* 3.1 13.3 + - - +
29A GLU* 1.3 75.8 - - - +
31A LEU* 1.3 65.0 + - - +
33A SER* 2.8 18.8 + - - -
34A TYR* 2.8 15.6 + - + +
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Residues in contact with LEU 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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1A TYR* 4.0 18.6 - - + -
4A TRP* 4.3 9.2 - - + -
9A LEU* 3.3 46.7 - - + +
12A LYS* 4.2 11.2 - - + -
13A LEU* 3.5 26.0 - - + +
16A ILE* 5.3 5.8 - - + -
27A LEU 3.1 8.6 + - - +
28A VAL 3.6 5.4 - - - +
30A ARG* 1.3 78.4 - - - +
32A GLN* 1.3 64.1 + - - +
34A TYR* 3.6 6.4 - - + +
35A THR* 3.0 30.1 + - - -
42A LEU* 3.3 30.5 - - + -
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Residues in contact with GLN 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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0A GLY* 5.8 3.5 - - - -
1A TYR* 4.1 26.4 + - + +
28A VAL* 2.9 39.5 + - - +
29A GLU* 3.3 24.3 + - - +
31A LEU* 1.3 76.1 - - - +
33A SER* 1.3 62.8 + - - +
35A THR* 4.1 2.3 - - - -
36A ARG* 3.1 38.1 + - - +
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Residues in contact with SER 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 GLU* 2.8 21.2 + - - -
30A ARG* 2.8 11.9 + - - -
32A GLN* 1.3 74.5 - - - +
34A TYR* 1.3 60.1 + - - +
36A ARG* 3.2 9.3 + - - +
37A GLN* 2.8 40.5 + - - +
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Residues in contact with TYR 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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13A LEU* 6.5 0.2 - - + -
16A ILE* 4.4 36.5 - - + +
30A ARG* 2.8 15.4 + - + +
31A LEU* 3.6 10.5 - - + +
33A SER* 1.3 75.4 - - - +
35A THR* 1.3 75.3 + - - +
37A GLN* 2.9 6.0 + - - +
38A THR* 2.7 69.1 + - + +
40A ILE* 4.1 32.0 - - + +
42A LEU* 4.4 20.7 - - + +
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Residues in contact with THR 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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1A TYR* 3.7 20.5 + - + +
31A LEU 3.0 14.3 + - - -
32A GLN* 4.1 2.7 - - - -
34A TYR* 1.3 85.7 - - - +
36A ARG* 1.3 58.3 + - + +
38A THR* 3.7 6.3 - - - -
39A GLY* 2.6 34.2 + - - +
40A ILE 3.6 10.1 + - - +
41A VAL* 3.5 40.8 - - + +
42A LEU* 4.2 4.3 - - - +
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Residues in contact with ARG 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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29A GLU* 6.0 1.1 - - - -
32A GLN* 3.1 33.6 + - - +
33A SER* 3.4 7.9 - - - +
34A TYR 3.1 0.2 - - - -
35A THR* 1.3 81.6 - - + +
37A GLN* 1.3 68.8 + - + +
39A GLY* 4.2 2.9 + - - -
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Residues in contact with GLN 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 SER* 2.8 30.9 + - - +
34A TYR* 2.9 4.8 + - - +
36A ARG* 1.3 80.2 + - + +
38A THR* 1.3 69.1 + - + +
39A GLY* 4.4 0.2 - - - -
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Residues in contact with THR 38 (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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34A TYR* 2.7 71.2 + - + +
37A GLN* 1.3 79.4 - - + +
39A GLY* 1.3 62.7 + - - -
40A ILE* 3.5 19.8 + - + +
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Residues in contact with GLY 39 (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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35A THR* 2.6 26.0 + - - -
36A ARG 4.5 3.1 - - - -
37A GLN 3.4 1.3 - - - -
38A THR* 1.3 75.8 + - - +
40A ILE* 1.3 62.8 + - - +
41A VAL* 3.9 5.3 + - - +
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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