Contacts of the helix formed by residues 14 - 26 (chain A) in PDB entry 2DA6
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 GLY 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TRP* 1.3 76.4 - - - +
15A PRO* 1.3 75.6 - - - +
16A ALA 3.3 2.5 - - - -
17A SER* 3.9 8.3 - - - -
18A GLN* 3.2 28.8 + - - +
47A GLU* 3.8 19.2 + - - -
50A GLN* 4.8 0.4 - - - -
51A ARG* 5.6 6.1 - - - -
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Residues in contact with PRO 15 (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 GLY* 1.3 86.6 - - - +
16A ALA* 1.3 55.4 + - + +
18A GLN* 4.6 1.5 - - + +
19A GLN* 3.2 25.1 + - - +
50A GLN* 2.8 31.0 - - + +
51A ARG* 5.7 4.5 - - - +
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Residues in contact with ALA 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 GLY 3.3 0.2 - - - -
15A PRO* 1.3 81.4 - - + +
17A SER* 1.3 67.0 + - - +
19A GLN* 3.2 10.2 + - - +
20A ILE* 3.1 21.9 + - + +
46A ALA* 3.8 17.9 - - + -
50A GLN* 2.8 28.3 - - + +
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Residues in contact with SER 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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13A TRP* 3.8 16.6 - - - -
14A GLY 3.9 13.3 + - - -
16A ALA* 1.3 76.2 - - - +
18A GLN* 1.3 68.0 + - - +
20A ILE* 2.7 33.5 + - - +
21A LEU* 3.1 6.1 + - - +
43A CYS* 3.2 25.4 - - - +
46A ALA* 5.0 0.4 - - - +
47A GLU* 3.0 32.7 - - - +
50A GLN* 4.4 1.4 - - - +
66A VAL* 4.3 0.2 - - - +
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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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12A LYS* 5.9 3.6 - - - +
13A TRP* 3.2 39.8 + - + +
14A GLY 3.2 15.6 + - - +
15A PRO 4.6 2.7 - - - +
17A SER* 1.3 76.4 - - - +
19A GLN* 1.3 66.7 + - + +
21A LEU* 2.7 27.9 + - + +
22A TYR* 3.0 39.6 + - + -
74A TRP* 5.0 3.8 - - - +
78A ARG* 4.7 3.1 + - - -
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Residues in contact with GLN 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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15A PRO 3.2 20.6 - - - +
16A ALA* 3.2 10.2 + - - +
18A GLN* 1.3 79.5 - - + +
20A ILE* 1.3 63.2 + - + +
22A TYR* 3.0 20.7 + - - +
23A GLN* 3.0 26.7 + - + +
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Residues in contact with ILE 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 ALA* 3.3 18.4 - - + +
17A SER* 2.7 27.3 + - - +
19A GLN* 1.3 73.0 - - + +
21A LEU* 1.3 59.9 + - - +
23A GLN* 3.3 9.3 + - + +
24A ALA* 3.1 21.0 + - - +
39A LEU* 4.1 14.4 - - + -
42A GLU* 3.7 38.4 - - + +
43A CYS* 3.7 28.9 - - - -
46A ALA* 3.9 11.0 - - + -
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Residues in contact with LEU 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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13A TRP* 3.5 36.8 - - + -
17A SER 3.1 6.5 + - - +
18A GLN* 2.7 22.9 + - - +
20A ILE* 1.3 72.0 - - - +
22A TYR* 1.3 49.2 + - - +
24A ALA* 3.2 2.8 + - - +
25A TYR* 2.7 36.2 + - - +
39A LEU* 4.1 24.9 - - + -
43A CYS* 3.5 25.1 - - - -
71A VAL* 4.3 6.3 - - + -
74A TRP* 3.5 51.6 - - + +
75A PHE* 3.8 3.0 - - + -
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Residues in contact with TYR 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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18A GLN* 3.0 52.5 + - + -
19A GLN* 3.0 21.0 + - - +
21A LEU* 1.3 75.3 - - - +
23A GLN* 1.3 57.9 + - + +
25A TYR* 3.8 2.2 - - + +
26A ASP* 2.7 38.3 + - - +
74A TRP* 3.6 23.8 - + - -
78A ARG* 3.0 41.9 + - - -
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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 GLN* 3.0 14.6 + - + +
20A ILE* 3.3 11.6 + - - +
22A TYR* 1.3 76.9 - - + +
24A ALA* 1.3 57.5 + - - +
26A ASP* 4.0 9.4 + - - +
27A ARG* 3.2 43.3 + - - +
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Residues in contact with ALA 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 ILE 3.1 6.4 + - - +
21A LEU 3.6 3.4 - - - +
22A TYR 3.0 0.6 - - - -
23A GLN* 1.3 76.6 - - - +
25A TYR* 1.3 59.0 + - - +
26A ASP 3.2 0.2 - - - -
27A ARG* 3.2 9.2 + - - +
28A GLN* 2.9 30.7 + - - +
31A PRO* 6.0 2.0 - - + +
35A GLU* 5.1 7.2 - - + +
39A LEU* 3.2 46.9 - - + -
75A PHE* 4.2 1.8 - - + -
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Residues in contact with TYR 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 2.7 21.1 + - - +
22A TYR* 3.8 4.0 - - + +
24A ALA* 1.3 70.8 - - - +
26A ASP* 1.3 67.5 + - - +
27A ARG 3.2 0.2 + - - -
28A GLN 3.1 20.8 - - - +
29A LYS* 3.3 39.4 + - + +
74A TRP* 3.6 21.3 - + + -
75A PHE* 3.1 40.3 - + + -
78A ARG* 3.6 23.7 + - + -
79A ARG* 2.8 26.2 - - + +
82A GLU* 3.1 22.0 + - - -
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Residues in contact with ASP 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 TYR 2.7 22.3 + - - +
23A GLN* 4.1 13.2 + - - +
25A TYR* 1.3 76.8 - - - +
27A ARG* 1.3 63.4 + - + +
29A LYS* 4.5 10.0 - - - +
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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