Contacts of the helix formed by residues 8 - 25 (chain A) in PDB entry 5OQN
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 ASP 8 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ILE* 1.3 82.7 - - + +
9A ILE* 1.3 81.2 + - - +
10A ASN* 3.2 26.6 + - - +
11A THR* 2.7 33.9 + - + +
12A LYS* 3.1 13.4 + - - +
50A TYR* 4.8 5.2 + - - -
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Residues in contact with ILE 9 (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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7A ILE 5.2 2.0 - - - +
8A ASP* 1.3 83.1 + - - +
10A ASN* 1.3 65.1 + - - +
12A LYS* 3.2 12.9 + - + +
13A ILE* 3.0 28.4 + - + +
48A GLN* 4.0 26.5 - - + +
50A TYR* 3.7 50.9 - - + +
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Residues in contact with ASN 10 (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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8A ASP* 3.2 17.4 + - - +
9A ILE* 1.3 79.1 - - - +
11A THR* 1.3 64.3 + - + +
13A ILE* 3.2 14.1 + - - +
14A PHE* 3.1 16.5 + - - +
50A TYR* 4.5 13.1 - - + -
53A ALA* 4.7 11.9 - - - +
57A TRP* 2.4 45.5 + - - +
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Residues in contact with THR 11 (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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7A ILE* 3.2 25.2 - - + +
8A ASP* 2.7 38.3 + - + +
10A ASN* 1.3 77.7 - - + +
12A LYS* 1.3 57.3 + - - +
14A PHE* 3.1 9.0 + - - +
15A ASN* 2.3 40.0 + - - -
57A TRP* 5.8 1.8 - - + -
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Residues in contact with LYS 12 (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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7A ILE* 3.6 30.7 - - + +
8A ASP 3.1 12.6 + - - +
9A ILE* 3.2 15.9 + - + +
11A THR* 1.3 81.6 + - - +
13A ILE* 1.3 64.2 + - + +
15A ASN* 3.1 10.0 + - - +
16A SER* 3.0 28.0 + - - +
44A LYS* 6.0 4.8 - - - +
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Residues in contact with ILE 13 (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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9A ILE* 3.0 20.4 + - + +
10A ASN* 3.2 8.7 + - - +
12A LYS* 1.3 75.4 - - + +
14A PHE* 1.3 62.6 + - - +
16A SER* 3.2 6.2 + - - -
17A VAL* 3.1 33.4 + - + +
41A ILE* 4.8 8.1 - - + -
45A ALA* 4.2 16.6 - - + -
48A GLN* 5.5 2.2 - - - +
50A TYR* 3.7 34.1 - - + -
53A ALA* 3.9 12.1 - - + -
54A PHE* 4.3 21.3 - - + -
57A TRP* 4.2 15.5 - - + -
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Residues in contact with PHE 14 (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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10A ASN 3.1 10.2 + - - +
11A THR* 3.1 14.1 + - - +
13A ILE* 1.3 76.7 - - - +
15A ASN* 1.3 66.4 + - - +
17A VAL* 4.1 1.4 - - - +
18A ALA* 2.9 35.1 + - + +
57A TRP* 3.3 57.2 - + + -
60A LYS* 6.2 0.7 - - + -
61A LEU* 4.5 14.6 - - + -
463B PHE 3.4 25.1 - - - -
464B PHE* 3.7 32.8 - + + -
465B LYS 5.2 1.1 - - - -
466B THR* 6.5 0.2 - - - -
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Residues in contact with ASN 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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7A ILE* 5.6 4.2 - - - +
11A THR* 2.3 47.5 + - - +
12A LYS* 3.6 7.9 - - - +
14A PHE* 1.3 84.4 - - - +
16A SER* 1.3 59.1 + - - +
18A ALA* 3.8 0.7 - - - +
19A GLU* 2.9 30.5 + - - +
464B PHE* 3.9 19.7 - - + -
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Residues in contact with SER 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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12A LYS* 3.0 16.7 + - - +
13A ILE* 3.2 7.6 + - - -
15A ASN* 1.3 76.7 - - - +
17A VAL* 1.3 62.1 + - - +
19A GLU* 3.2 15.1 + - - +
20A VAL* 3.2 16.8 + - - +
41A ILE* 3.5 31.8 - - - +
44A LYS* 5.8 2.6 + - - -
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Residues in contact with VAL 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 ILE* 3.1 19.3 + - + +
14A PHE* 4.3 2.9 - - - +
16A SER* 1.3 74.6 - - - +
18A ALA* 1.3 63.1 + - - +
20A VAL* 3.1 18.9 + - - +
21A PHE* 3.1 28.9 + - + -
38A LEU* 4.5 6.7 - - + -
41A ILE* 4.1 13.2 - - + -
54A PHE* 3.7 31.9 - - + -
57A TRP* 5.4 4.7 - - + -
58A PHE* 4.3 13.7 - - + +
61A LEU* 3.7 25.8 - - + -
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Residues in contact with ALA 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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14A PHE* 2.9 24.5 + - + +
17A VAL* 1.3 76.8 - - - +
19A GLU* 1.3 62.8 + - - +
21A PHE* 3.4 2.0 + - - +
22A GLN* 2.9 26.3 + - - +
61A LEU* 4.1 24.4 - - + +
463B PHE* 4.3 10.9 - - + +
464B PHE* 3.4 29.6 - - + -
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Residues in contact with GLU 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 ASN 2.9 18.6 + - - +
16A SER* 3.4 7.9 - - - +
18A ALA* 1.3 77.4 - - - +
20A VAL* 1.3 65.0 + - + +
22A GLN* 3.3 8.1 + - - +
23A LYS* 3.2 45.1 + - - +
464B PHE* 3.7 18.0 - - + -
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Residues in contact with VAL 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 SER 3.3 14.8 - - - +
17A VAL 3.1 6.9 + - - +
19A GLU* 1.3 75.7 - - + +
21A PHE* 1.3 59.6 + - + +
23A LYS* 3.1 12.5 - - + +
24A ALA* 2.8 29.6 + - - +
34A HIS* 3.5 34.5 - - + -
37A VAL* 3.9 28.3 - - + -
38A LEU* 4.0 28.5 - - + -
41A ILE* 4.3 1.3 - - + -
81A LEU* 4.4 10.1 - - + -
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Residues in contact with PHE 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 VAL* 3.1 28.1 + - + +
18A ALA* 4.0 4.3 - - - +
20A VAL* 1.3 83.2 - - + +
22A GLN* 1.3 63.6 + - - +
24A ALA* 4.3 6.1 - - - -
25A GLN* 3.1 24.3 + - - +
38A LEU* 4.9 5.8 - - + -
58A PHE* 3.3 44.2 - + - -
61A LEU* 4.2 13.5 - - + -
62A VAL* 4.3 16.4 - - + -
78A ILE* 3.4 39.2 - - + +
81A LEU* 4.8 13.2 - - + -
82A VAL* 4.3 4.9 - - + -
463B PHE* 4.0 30.9 - + + -
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Residues in contact with GLN 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 ALA 2.9 17.7 + - - +
19A GLU* 3.6 10.3 - - - +
20A VAL 3.2 0.4 - - - -
21A PHE* 1.3 77.4 - - - +
23A LYS* 1.3 56.4 + - - +
25A GLN* 3.0 47.2 + - - +
26A GLY* 4.3 0.9 + - - -
460B GLU* 3.2 20.6 + - - +
461B ILE 2.8 23.4 + - - +
462B ASP* 4.1 6.8 + - - +
463B PHE* 3.0 23.9 + - - +
464B PHE* 4.1 22.1 - - + -
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Residues in contact with LYS 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 GLU* 3.2 34.6 + - - +
20A VAL* 3.1 17.3 - - + +
22A GLN* 1.3 77.0 - - - +
24A ALA* 1.3 63.9 + - - +
25A GLN 3.1 1.6 - - - -
26A GLY* 3.0 15.2 + - - +
27A SER* 3.9 4.0 + - - +
34A HIS* 3.1 31.1 - - + +
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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 VAL 2.8 22.1 + - - +
21A PHE* 4.0 3.4 - - - +
23A LYS* 1.3 73.8 - - - +
25A GLN* 1.3 61.8 + - - +
27A SER 2.9 21.3 + - - +
31A HIS* 3.8 7.3 - - + -
34A HIS* 3.3 25.6 - - - +
77A ARG* 3.7 11.0 - - - +
78A ILE* 4.3 5.4 - - + -
81A LEU* 3.5 26.2 - - + -
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Residues in contact with GLN 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 PHE 3.1 12.2 + - - +
22A GLN* 3.0 48.3 + - - +
23A LYS 3.1 1.0 - - - -
24A ALA* 1.3 77.1 - - - +
26A GLY* 1.3 62.3 + - - +
74A ILE* 3.5 32.5 - - + +
77A ARG* 2.8 27.1 + - - +
78A ILE* 3.6 20.8 - - + +
460B GLU* 3.8 20.9 - - + +
461B ILE* 3.0 33.9 + - - +
463B PHE* 3.8 4.7 - - + -
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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