Contacts of the helix formed by residues 17 - 28 (chain A) in PDB entry 1O4W
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 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A VAL 4.1 0.8 + - - -
16A VAL* 1.3 74.1 - - - +
18A THR* 1.3 76.3 + - - +
19A ASN* 3.0 32.6 + - - +
20A VAL* 3.0 19.9 + - + +
21A LEU* 3.2 8.7 + - - +
49A VAL* 5.6 0.5 - - - +
88A ASP* 5.0 5.0 - - - +
91A LEU* 3.9 25.8 - - + +
102A LEU* 5.1 0.4 - - - +
103A ILE 2.9 21.9 + - - +
104A THR* 2.8 29.5 + - - -
105A ASN 4.6 1.4 + - - -
106A ASP* 4.4 5.7 - - - +
109A LEU* 4.1 6.1 - - - +
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Residues in contact with THR 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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16A VAL 3.5 0.4 + - - -
17A ASP* 1.3 76.1 + - - +
19A ASN* 1.3 69.0 + - - +
21A LEU* 3.2 13.3 + - + +
22A MSE 3.0 28.0 + - - +
45A ILE* 4.0 12.6 - - + -
49A VAL* 3.7 31.8 + - + +
53A LEU* 3.8 41.0 - - + +
71A ALA* 4.8 1.0 - - - +
75A LEU* 4.4 9.2 - - + -
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Residues in contact with ASN 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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17A ASP* 3.0 26.0 + - - +
18A THR* 1.3 81.2 + - - +
20A VAL* 1.3 61.5 + - + +
22A MSE 3.5 31.1 + - - +
23A TYR* 3.6 11.1 + - - +
56A LEU* 5.4 4.3 - - - +
88A ASP* 5.2 6.1 + - - -
106A ASP* 6.3 0.6 - - - +
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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 VAL* 3.8 16.8 - - + -
17A ASP* 3.0 13.2 + - + +
19A ASN* 1.3 78.7 - - + +
21A LEU* 1.3 62.6 + - - +
23A TYR* 3.1 20.3 + - - +
24A VAL* 3.7 4.3 + - - +
31A VAL* 4.0 19.4 - - + +
103A ILE* 4.0 14.1 - - + +
104A THR* 3.9 29.2 - - - +
105A ASN* 3.9 21.1 - - + +
123A LEU* 4.0 23.8 - - + +
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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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16A VAL* 3.7 24.5 - - + +
17A ASP 3.2 8.9 + - - +
18A THR* 3.2 19.6 + - + +
20A VAL* 1.3 77.8 - - - +
22A MSE 1.3 56.5 + - - +
24A VAL* 2.9 33.8 + - + +
25A TYR* 4.0 2.1 + - - +
31A VAL* 4.8 7.4 - - + -
32A VAL* 4.8 4.7 - - + -
67A ALA 4.9 0.9 - - - +
70A PHE* 5.4 0.3 - - - -
71A ALA* 3.9 26.7 + - + +
74A LEU* 4.2 18.9 - - + +
75A LEU* 3.8 33.7 - - + -
78A PHE* 4.2 17.7 - - + -
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Residues in contact with MSE 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 THR* 3.0 17.3 + - - +
19A ASN* 3.5 22.4 - - - +
20A VAL 3.3 0.4 - - - -
21A LEU* 1.3 75.2 - - - +
23A TYR* 1.3 62.7 + - + +
24A VAL 3.4 0.2 + - - -
25A TYR 3.6 2.4 + - - -
26A LEU* 3.2 34.8 + - + +
53A LEU* 4.0 14.8 - - + -
56A LEU* 3.9 28.0 - - + -
60A LEU* 4.3 6.7 - - + -
64A GLU* 4.7 2.0 - - + +
67A ALA* 3.8 17.4 - - + +
68A ALA* 3.7 34.8 - - + -
71A ALA* 4.4 2.2 - - - +
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ASN 3.6 8.2 + - - +
20A VAL 3.1 14.8 + - - +
22A MSE 1.3 79.0 - - + +
24A VAL* 1.3 63.4 + - - +
26A LEU* 3.8 14.4 - - + +
27A ASN* 2.9 59.1 + - + +
28A LYS 3.8 0.9 + - - -
29A ALA* 4.0 7.3 + - + +
123A LEU* 3.6 29.8 - - + -
125A GLU* 6.1 2.2 - - - -
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Residues in contact with VAL 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 3.7 0.2 + - - -
21A LEU* 2.9 23.7 + - + +
23A TYR* 1.3 76.3 - - - +
25A TYR* 1.3 57.9 + - - +
28A LYS* 3.0 29.7 + - - -
29A ALA 3.3 26.0 - - - +
30A ASP* 4.8 5.2 - - - +
31A VAL* 3.8 25.4 - - + +
32A VAL* 5.4 1.3 - - + +
70A PHE* 3.6 25.1 - - + -
74A LEU* 3.9 21.8 - - + -
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Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LEU 4.0 1.6 + - - +
22A MSE 3.6 2.2 + - - +
24A VAL* 1.3 82.3 - - - +
26A LEU* 1.3 68.3 + - + +
27A ASN 3.4 0.7 + - - -
28A LYS* 3.8 10.2 + - - +
63A LYS* 4.1 17.4 - - + +
66A VAL* 3.4 35.6 - - + +
67A ALA* 3.8 37.5 - - + +
70A PHE* 4.1 31.1 - + + -
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Residues in contact with LEU 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 MSE 3.2 29.2 + - + +
23A TYR* 4.4 11.4 - - + -
24A VAL 3.4 0.2 - - - -
25A TYR* 1.3 87.0 - - + +
27A ASN* 1.3 73.4 + - - +
28A LYS* 5.5 0.9 - - - +
63A LYS* 3.8 52.3 - - + +
64A GLU* 4.6 12.6 - - + +
67A ALA* 3.8 11.7 - - + -
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Residues in contact with ASN 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 TYR* 2.9 61.1 + - + +
26A LEU* 1.3 88.5 + - - +
28A LYS* 1.3 71.0 + - - +
29A ALA* 3.2 8.9 + - + +
125A GLU* 5.0 7.4 - - - +
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Residues in contact with LYS 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 VAL* 3.0 13.8 + - - -
25A TYR 3.8 8.4 + - - +
26A LEU 5.5 1.1 - - - +
27A ASN* 1.3 78.9 - - - +
29A ALA* 1.3 59.1 + - - +
30A ASP* 3.9 1.7 + - - +
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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