Contacts of the helix formed by residues 15 - 30 (chain A) in PDB entry 1D1D
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 GLU 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 PRO 4.0 0.8 + - - -
14A LEU* 1.3 90.0 - - + +
16A PRO* 1.4 66.9 - - - +
17A LYS* 3.5 25.4 + - + -
18A LEU* 3.1 43.3 + - + +
19A ILE* 3.6 7.3 + - - +
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Residues in contact with PRO 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 LEU* 3.2 16.6 - - + +
15A GLU* 1.4 83.7 - - + +
17A LYS* 1.3 58.8 + - + +
18A LEU 3.2 0.9 - - - -
19A ILE* 3.6 8.4 - - + +
20A THR* 2.4 47.9 + - - +
55A ASN* 5.0 8.3 - - - +
58A ARG* 6.2 0.7 - - - +
59A VAL* 4.5 15.5 - - + -
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Residues in contact with LYS 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 GLU* 3.9 29.4 - - + -
16A PRO* 1.3 82.8 - - + +
18A LEU* 1.3 74.5 + - + +
20A THR* 3.3 9.2 + - - +
21A ARG* 3.0 27.5 + - - +
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Residues in contact with LEU 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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15A GLU* 3.1 45.0 + - + +
16A PRO 3.2 0.2 - - - -
17A LYS* 1.3 90.0 - - + +
19A ILE* 1.3 66.7 + - + +
21A ARG* 3.1 34.4 - - - +
22A LEU* 3.1 25.2 + - + +
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Residues in contact with ILE 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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14A LEU* 2.9 49.4 - - + -
15A GLU 3.6 3.2 + - - +
16A PRO* 3.1 6.4 + - + +
18A LEU* 1.3 80.2 - - + +
20A THR* 1.3 53.8 + - - +
22A LEU* 3.2 7.8 + - + +
23A ALA* 2.7 33.3 + - - +
43A LEU* 4.7 11.6 - - + +
55A ASN* 4.5 0.7 - - - +
56A LEU* 3.0 54.7 - - + +
59A VAL* 3.5 25.6 - - + -
60A ILE* 4.7 1.3 - - + +
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Residues in contact with THR 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 PRO* 2.4 29.8 + - - +
17A LYS* 3.3 10.8 - - - +
19A ILE* 1.3 74.2 - - - +
21A ARG* 1.3 52.8 + - - +
23A ALA* 3.3 1.6 + - - +
24A ASP* 2.7 40.3 + - + +
59A VAL* 3.5 21.7 - - + +
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Residues in contact with ARG 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 LYS 3.0 12.3 + - - +
18A LEU* 3.1 32.9 - - - +
20A THR* 1.3 76.9 - - - +
22A LEU* 1.3 77.2 + - + +
24A ASP* 3.1 20.4 - - - +
25A THR* 3.2 11.8 + - - -
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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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18A LEU* 3.1 12.4 + - + +
19A ILE* 3.7 7.6 - - + +
21A ARG* 1.3 87.9 - - + +
23A ALA* 1.3 64.6 + - - +
25A THR* 3.1 17.6 + - - -
26A VAL* 3.2 16.8 + - - +
39A GLU* 3.6 33.9 - - + +
42A ALA* 4.6 6.7 - - + -
43A LEU* 3.4 48.7 - - + +
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Residues in contact with ALA 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 ILE 2.7 21.5 + - - +
20A THR 3.7 3.8 - - - +
22A LEU* 1.3 69.9 - - - +
24A ASP* 1.3 65.1 + - - +
26A VAL* 3.1 12.8 + - - +
27A ARG* 2.9 23.6 + - - +
31A LEU* 5.1 1.2 - - - +
59A VAL* 4.1 12.1 - - + +
60A ILE* 3.7 40.8 - - + +
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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 THR* 2.7 20.3 + - + +
21A ARG* 3.1 15.3 - - - +
23A ALA* 1.3 78.3 - - - +
25A THR* 1.3 53.1 + - - +
27A ARG* 3.3 24.3 + - - +
28A THR* 2.6 46.9 + - - +
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Residues in contact with THR 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 ARG 3.2 8.5 + - - -
22A LEU* 3.1 11.8 + - - -
24A ASP* 1.3 73.8 - - - +
26A VAL* 1.3 54.4 + - - +
28A THR* 2.4 24.5 + - - +
29A LYS* 2.6 45.2 + - + +
39A GLU* 3.2 33.2 - - + +
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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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22A LEU 3.2 10.2 + - - +
23A ALA* 3.1 13.6 + - - +
25A THR* 1.3 77.6 - - - +
27A ARG* 1.3 52.2 + - - +
29A LYS* 3.0 6.2 + - - +
30A GLY 2.5 40.2 + - - +
31A LEU* 3.4 18.4 - - + -
35A ILE* 4.8 1.1 - - - -
36A THR* 3.0 46.2 - - + +
39A GLU* 3.4 31.2 - - + -
40A VAL* 4.3 8.1 - - + -
43A LEU* 6.0 0.4 - - + -
60A ILE* 4.4 7.2 - - + -
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Residues in contact with ARG 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 ALA 2.9 12.0 + - - +
24A ASP* 3.6 34.9 + - - +
26A VAL* 1.3 77.2 - - - +
28A THR* 1.3 69.1 + - - +
30A GLY* 2.9 18.2 + - - -
31A LEU* 3.8 17.4 + - + +
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Residues in contact with THR 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* 2.6 33.2 - - - +
25A THR* 2.4 29.2 + - - +
27A ARG* 1.3 91.1 - - - +
29A LYS* 1.3 63.2 + - - +
30A GLY 3.6 0.2 + - - -
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Residues in contact with LYS 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 THR* 2.6 44.4 + - - +
26A VAL 3.3 2.7 - - - +
28A THR* 1.3 82.4 - - - +
30A GLY* 1.3 58.4 + - - +
33A SER* 2.9 20.3 + - - +
35A ILE* 3.0 46.1 - - + +
39A GLU* 3.6 8.9 + - - -
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Residues in contact with GLY 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 VAL 2.5 12.9 + - - +
27A ARG 2.9 12.4 + - - -
28A THR 3.2 0.4 + - - -
29A LYS* 1.3 73.9 - - - +
31A LEU* 1.3 56.0 + - - -
32A ARG* 3.1 3.6 - - - -
33A SER* 2.9 18.7 + - - -
36A THR* 2.6 25.5 + - - -
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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