Contacts of the helix formed by residues 14 - 30 (chain A) in PDB entry 2DPD
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 LYS 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 6.0 6.5 - - - -
11A PHE* 6.0 5.9 - - - +
12A LEU 3.7 19.8 + - - +
13A VAL* 1.3 84.1 - - - +
15A GLN* 1.3 65.8 + - - +
16A ARG* 4.3 20.4 - - + +
17A ALA* 3.6 8.1 + - + +
18A PHE* 3.3 18.2 + - - +
106A GLU* 5.0 3.2 + - - +
11B PHE* 4.1 0.2 - - - -
12D A 3.6 43.3 + - - +
13D T 3.7 13.4 + - - +
13E T 5.6 8.7 + - - -
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Residues in contact with GLN 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 LYS* 1.3 69.9 - - - +
16A ARG* 1.3 65.3 + - - +
18A PHE* 2.9 6.4 + - - +
19A LEU* 2.9 31.2 + - + +
50A PHE* 3.8 24.3 - - + -
52A PRO* 4.2 7.8 - - - +
56A GLU* 3.6 21.6 - - - +
9B THR* 3.9 4.2 + - - -
11B PHE* 3.6 40.8 - - + +
13D T 2.7 39.6 + - - +
14D G 3.2 28.3 + - - -
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Residues in contact with ARG 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 LYS* 4.4 14.7 - - + +
15A GLN* 1.3 77.7 - - - +
17A ALA* 1.3 63.2 + - - +
19A LEU* 3.2 3.6 + - - +
20A LYS* 2.7 52.6 + - - +
56A GLU* 3.9 12.5 + - - +
59A ARG* 6.0 1.1 - - + -
60A SER* 3.8 21.5 + - - +
63A GLU* 3.3 39.0 + - - +
12D A 3.5 33.2 + - + -
13D T 3.1 19.0 + - - +
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Residues in contact with ALA 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 VAL* 3.8 11.2 - - + -
14A LYS* 3.6 15.9 + - + +
15A GLN 3.1 0.4 - - - -
16A ARG* 1.3 83.6 - - - +
18A PHE* 1.3 58.2 + - - +
20A LYS* 3.8 2.5 - - - +
21A LEU* 2.9 31.7 + - - +
99A TYR* 3.9 15.9 - - - +
103A LEU* 3.5 28.2 - - + +
106A GLU* 4.6 5.4 - - - +
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Residues in contact with PHE 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 VAL* 4.4 8.2 - - + +
14A LYS 3.3 11.6 + - - +
15A GLN 2.9 11.6 + - - +
17A ALA* 1.3 79.9 - - - +
19A LEU* 1.3 68.5 + - + +
21A LEU* 3.7 6.4 - - + +
22A TYR* 3.4 33.8 + + - -
45A PHE* 3.7 28.0 - + - -
50A PHE* 3.8 19.7 - + - -
107A LEU* 4.6 14.6 - - + -
11B PHE* 3.7 30.5 - + + -
113B LEU* 4.2 17.3 - - + -
114B ILE* 4.9 5.4 - - + -
117B ALA* 3.3 34.8 - - + -
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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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15A GLN* 2.9 26.1 + - - +
16A ARG* 3.7 1.1 - - - +
18A PHE* 1.3 79.0 - - + +
20A LYS* 1.3 59.0 + - - +
22A TYR* 2.6 29.8 + - + +
23A MET* 2.9 23.2 + - + +
41A LEU* 3.5 30.5 - - + -
50A PHE* 4.2 21.3 - - + -
52A PRO* 4.6 4.7 - - + -
56A GLU* 3.7 33.4 - - + -
57A VAL* 4.2 8.5 - - + +
60A SER* 3.5 24.5 - - - +
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Residues in contact with LYS 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 ARG* 2.7 44.6 + - - +
17A ALA 3.8 2.0 - - - +
19A LEU* 1.3 72.4 - - - +
21A LEU* 1.3 63.4 + - - +
23A MET* 3.2 9.4 + - - +
24A ILE* 3.0 28.7 + - - +
60A SER* 3.6 25.4 - - - +
63A GLU* 2.9 34.1 + - + +
64A LEU* 3.6 28.2 - - + +
67A ASP* 4.0 12.3 + - - -
99A TYR* 3.2 38.5 + - + +
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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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17A ALA 2.9 18.8 + - - +
18A PHE* 3.7 7.9 - - + +
19A LEU 2.9 0.4 + - - -
20A LYS* 1.3 76.5 - - - +
22A TYR* 1.3 63.2 + - + +
24A ILE* 3.1 4.4 + - + +
25A THR* 3.0 23.9 + - - -
100A LYS* 3.8 33.0 - - + -
103A LEU* 3.7 27.8 - - + +
107A LEU* 3.8 20.2 - - + -
117B ALA* 4.9 2.9 - - + +
121B ASN* 3.1 21.5 - - + +
122B PHE* 3.6 32.1 - - + -
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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 PHE* 3.4 49.0 + + - +
19A LEU* 2.6 15.8 + - - +
21A LEU* 1.3 74.8 - - + +
23A MET* 1.3 61.9 + - - +
25A THR* 3.3 2.5 + - - -
26A MET* 2.9 41.1 + - + +
37A LEU* 4.4 7.6 - - + -
41A LEU* 3.8 30.1 - - + -
44A GLU* 3.8 11.9 - - - -
45A PHE* 3.3 16.3 - + - -
117B ALA* 3.2 21.7 + - + -
120B ASP* 2.5 32.3 + - + -
121B ASN* 3.2 28.7 - - - +
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Residues in contact with MET 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* 2.9 43.0 + - + +
20A LYS* 3.5 9.6 - - - +
22A TYR* 1.3 71.4 - - - +
24A ILE* 1.3 56.0 + - - +
26A MET* 3.1 3.6 + - - +
27A THR* 2.8 41.4 + - - +
32A LEU* 6.0 0.7 - - - -
37A LEU* 3.5 36.9 - - + +
57A VAL* 3.5 9.6 - - + +
60A SER* 3.3 26.7 - - - +
61A LEU* 2.8 38.1 - - + -
64A LEU* 4.0 12.6 - - + -
70A LEU* 5.0 4.0 - - + -
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Residues in contact with ILE 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 LYS 3.0 17.4 + - - +
21A LEU* 3.5 8.5 - - - +
23A MET* 1.3 79.3 - - - +
25A THR* 1.3 65.1 + - - +
27A THR* 3.5 4.0 + - - -
28A GLU* 3.2 24.0 + - - +
64A LEU* 3.7 22.7 - - + -
69A ILE* 4.6 13.5 - - + -
70A LEU* 5.5 2.5 - - + -
90A PHE* 3.7 10.5 - - + -
96A ALA* 4.4 19.3 - - + +
99A TYR* 3.5 35.4 - - + -
100A LYS* 3.7 30.5 - - + +
103A LEU* 4.9 1.3 - - + -
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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 LEU 3.0 4.8 + - - -
22A TYR* 3.9 2.9 - - - -
24A ILE* 1.3 77.7 - - - +
26A MET* 1.3 62.6 + - - +
28A GLU* 3.1 38.0 + - - +
29A GLN* 3.5 21.1 + - - +
100A LYS* 3.4 20.1 - - - +
120B ASP 4.8 3.8 - - - +
121B ASN* 2.5 47.9 + - - +
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Residues in contact with MET 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* 2.9 33.9 + - + +
23A MET* 3.9 3.1 - - - +
25A THR* 1.3 75.8 - - - +
27A THR* 1.3 60.1 + - - +
29A GLN* 3.1 16.7 + - - +
30A GLU* 2.9 35.3 + - + +
32A LEU* 3.5 28.7 - - + -
37A LEU* 4.1 19.1 - - - -
40A VAL* 4.5 17.0 - - + -
41A LEU* 5.1 1.6 - - - -
44A GLU* 3.7 25.4 - - - +
120B ASP* 6.2 1.6 - - + -
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Residues in contact with THR 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 MET* 2.8 25.9 + - - +
24A ILE 3.7 4.9 - - - -
26A MET* 1.3 69.3 - - - +
28A GLU* 1.3 67.4 + - - +
29A GLN 3.0 1.0 + - - -
30A GLU 3.2 16.1 + - - +
32A LEU* 5.3 7.7 + - - +
70A LEU* 4.2 17.3 - - + +
88A TYR* 4.2 24.0 - - - +
89A GLN* 4.2 11.0 - - - -
90A PHE* 3.6 29.9 - - + -
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Residues in contact with GLU 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 ILE* 3.2 17.4 + - - +
25A THR* 3.1 22.3 + - - +
27A THR* 1.3 79.8 - - - +
29A GLN* 1.3 61.8 + - + +
90A PHE* 3.9 18.8 - - + -
93A TYR* 3.1 29.3 + - + +
97A LYS* 5.4 3.3 - - - +
100A LYS* 3.5 34.2 + - - +
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Residues in contact with GLN 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* 3.5 23.6 + - - +
26A MET* 3.1 21.7 + - - +
27A THR 3.0 0.8 - - - -
28A GLU* 1.3 84.9 - - + +
30A GLU* 1.3 71.2 + - + +
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Residues in contact with GLU 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 MET* 2.9 19.2 + - + +
27A THR* 3.2 21.1 - - - +
29A GLN* 1.3 82.9 - - + +
31A ARG* 1.3 75.0 + - - +
32A LEU* 4.2 16.6 - - + -
36A LYS* 4.9 6.3 - - - +
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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