Contacts of the helix formed by residues 15 - 29 (chain A) in PDB entry 2DA2
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 THR 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ARG 4.2 0.6 + - - -
14A PHE* 1.3 75.1 - - - +
16A ASP* 1.3 62.7 + - - +
17A TYR* 2.9 17.3 + - + +
18A GLN* 2.5 52.6 + - + +
19A LEU* 2.8 11.3 + - - -
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Residues in contact with ASP 16 (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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14A PHE 4.4 0.2 + - - -
15A THR* 1.3 76.8 + - - +
17A TYR* 1.3 54.2 + - - +
19A LEU* 4.2 13.5 - - - +
20A ARG* 2.7 37.0 + - - +
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Residues in contact with TYR 17 (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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15A THR* 2.7 18.8 + - + +
16A ASP* 1.3 77.7 - - - +
18A GLN* 1.3 82.5 + - + +
20A ARG* 3.5 12.9 - - - +
21A VAL* 3.7 14.9 + - + +
43A LEU* 3.4 34.9 + - + +
44A LEU* 3.9 14.8 - - + +
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Residues in contact with GLN 18 (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 ARG 5.1 0.7 - - - +
14A PHE* 3.5 24.6 - - + +
15A THR* 2.5 28.4 + - + +
17A TYR* 1.3 83.2 - - + +
19A LEU* 1.3 65.5 + - - +
20A ARG 3.0 2.1 + - - -
21A VAL* 3.0 4.7 + - - +
22A LEU* 2.9 32.4 + - + +
44A LEU* 3.0 44.3 + - + +
46A LEU* 2.8 35.4 - - - +
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Residues in contact with LEU 19 (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 ARG* 5.2 9.4 - - - +
14A PHE* 3.9 39.0 - - + +
15A THR 2.8 17.8 + - - +
16A ASP* 4.0 10.5 - - - +
18A GLN* 1.3 73.2 - - - +
20A ARG* 1.3 54.6 + - - +
22A LEU* 4.3 5.2 - - + -
23A GLN* 2.8 40.6 + - + +
54A TRP* 3.8 31.0 - - + +
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Residues in contact with ARG 20 (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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16A ASP 2.7 19.8 + - - +
17A TYR* 3.5 8.5 - - - +
18A GLN 3.0 0.2 + - - -
19A LEU* 1.3 78.1 - - - +
21A VAL* 1.3 66.6 + - - +
23A GLN* 4.2 1.9 - - - +
24A ASP* 2.8 53.5 + - - +
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Residues in contact with VAL 21 (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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17A TYR* 3.7 20.9 - - + +
18A GLN 3.0 6.3 + - - +
20A ARG* 1.3 80.7 - - - +
22A LEU* 1.3 60.8 + - - +
24A ASP* 3.8 5.1 - - - +
25A PHE* 2.9 29.9 + - + +
40A LEU* 3.4 24.9 - - + -
43A LEU* 3.5 31.6 - - + -
44A LEU* 3.9 14.1 - - + -
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Residues in contact with LEU 22 (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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14A PHE* 3.6 39.0 - - + -
18A GLN* 2.9 23.9 + - + +
19A LEU* 4.0 9.6 - - + +
21A VAL* 1.3 76.8 - - - +
23A GLN* 1.3 61.2 + - - +
25A PHE* 4.7 0.7 - - - -
26A PHE* 3.2 18.9 + - - +
40A LEU* 4.8 4.5 - - + -
44A LEU* 3.3 24.7 - - + -
46A LEU* 4.8 0.7 - - + -
51A ILE* 3.6 38.1 - - + -
54A TRP* 3.9 17.9 - - + -
55A PHE* 3.5 21.1 - - + -
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Residues in contact with GLN 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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19A LEU* 2.8 26.5 + - + +
20A ARG* 4.2 2.0 - - - +
22A LEU* 1.3 72.1 - - - +
24A ASP* 1.3 59.4 + - - +
26A PHE* 3.2 20.1 + - - +
27A ASP* 3.0 30.6 + - + +
54A TRP* 3.0 34.9 - - + -
61A LYS* 4.0 16.2 + - - +
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Residues in contact with ASP 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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20A ARG* 2.8 44.8 + - - +
21A VAL* 3.8 6.3 - - - +
23A GLN* 1.3 78.6 - - - +
25A PHE* 1.3 61.4 + - - +
26A PHE 3.4 0.2 + - - -
27A ASP* 3.6 7.3 + - - +
28A ALA* 3.5 20.4 + - - +
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Residues in contact with PHE 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 VAL* 2.9 19.9 + - + +
22A LEU 3.8 3.8 - - - +
24A ASP* 1.3 76.8 + - - +
26A PHE* 1.3 52.3 + - - +
28A ALA* 4.0 3.0 - - - +
29A ASN* 2.4 59.2 + - + +
32A PRO* 3.6 33.4 - - + -
36A GLU* 4.0 28.3 - - + -
39A GLN* 5.3 4.9 - - + -
40A LEU* 3.6 32.5 - - + -
55A PHE* 3.8 11.9 - + + -
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Residues in contact with PHE 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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22A LEU 3.2 14.6 + - - +
23A GLN* 3.5 25.8 - - - +
24A ASP 3.2 0.2 - - - -
25A PHE* 1.3 74.7 - - - +
27A ASP* 1.3 70.3 + - - +
28A ALA 3.0 4.1 + - - -
29A ASN 3.1 20.6 + - - -
30A ALA* 3.5 28.0 + - + +
54A TRP* 4.0 8.1 - + + -
55A PHE* 3.7 14.8 - + + -
58A ALA* 3.3 44.2 - - + -
59A ARG* 3.6 18.8 - - + -
61A LYS* 5.3 2.7 - - - -
62A ALA* 4.5 10.8 - - + -
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Residues in contact with ASP 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 GLN* 3.0 17.7 + - + +
24A ASP* 3.9 8.5 - - - +
25A PHE 3.5 0.2 - - - -
26A PHE* 1.3 83.4 - - + +
28A ALA* 1.3 58.1 + - - +
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Residues in contact with ALA 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 ASP 3.5 13.9 + - - +
25A PHE* 4.1 3.6 - - - +
26A PHE 3.0 0.6 - - - -
27A ASP* 1.3 82.1 - - + +
29A ASN* 1.3 62.7 + - + +
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Residues in contact with ASN 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 PHE* 2.4 52.0 + - + +
26A PHE* 3.1 9.9 + - - -
28A ALA* 1.3 78.0 - - + +
30A ALA* 1.3 61.5 + - - +
31A TYR* 3.6 16.5 + - - +
32A PRO* 3.1 39.6 - - - +
36A GLU* 5.1 3.4 - - - +
55A PHE* 3.6 2.8 - - - -
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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