Contacts of the strand formed by residues 10 - 24 (chain A) in PDB entry 3OAN
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 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLU* 3.3 27.0 - - + +
9A ASN* 1.3 82.1 - - - +
11A GLU* 1.3 60.0 + - - +
12A VAL* 4.2 4.2 + - - +
41A LEU* 3.8 27.8 - - + +
42A ARG 3.3 19.7 - - - +
43A LYS* 3.9 26.6 + - + +
44A LYS* 3.8 12.4 - - - +
49A LYS 5.5 0.5 - - - +
51A ARG* 3.0 49.6 + - - +
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Residues in contact with GLU 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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10A GLU* 1.3 74.7 - - - +
12A VAL* 1.3 64.1 + - - +
13A LEU* 3.7 21.1 + - + +
41A LEU* 3.3 7.6 - - - +
42A ARG* 2.8 73.5 + - + +
43A LYS 5.0 0.2 - - - +
44A LYS* 3.9 26.4 - - + +
47A LYS* 5.6 1.4 - - - +
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Residues in contact with VAL 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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10A GLU 5.0 2.7 - - - +
11A GLU* 1.3 75.3 - - - +
13A LEU* 1.3 62.7 + - - +
14A PHE 3.4 24.7 - - - +
15A CYS* 3.9 17.9 - - + -
39A LYS* 4.6 20.6 - - + +
40A LEU 3.6 4.9 - - - +
41A LEU* 4.0 13.7 - - + -
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Residues in contact with LEU 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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11A GLU* 3.7 22.4 - - - +
12A VAL* 1.3 73.3 - - - +
14A PHE* 1.3 61.8 + - - +
40A LEU* 2.7 34.0 + - + +
42A ARG* 3.7 52.3 - - + +
50A VAL* 4.9 1.1 - - + -
114A ALA* 4.1 12.9 - - + +
118A ALA* 3.9 28.7 - - + -
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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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12A VAL* 3.4 7.9 - - - +
13A LEU* 1.3 81.8 - - - +
15A CYS* 1.3 64.9 + - - +
16A GLU* 3.4 39.7 - - + -
38A LEU* 3.9 22.9 - - + -
39A LYS* 3.2 4.7 - - - -
40A LEU* 2.9 38.1 + - + -
102A VAL* 4.6 7.4 - - + -
107A ASP* 3.8 11.0 - - - -
110A ARG* 4.1 21.5 - - + -
111A LEU* 3.7 55.0 - - + -
114A ALA* 4.4 8.7 - - + -
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Residues in contact with CYS 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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12A VAL* 3.9 14.4 - - + -
14A PHE* 1.3 80.8 - - - +
16A GLU* 1.3 74.5 + - - +
37A GLU* 3.6 37.5 - - - -
38A LEU 3.2 5.4 - - - +
39A LYS* 4.0 16.8 - - + -
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Residues in contact with GLU 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 PHE* 3.4 29.6 - - + -
15A CYS* 1.3 84.5 - - - +
17A LYS* 1.3 75.7 + - + +
18A ALA* 3.5 0.3 + - - +
37A GLU* 4.5 5.4 - - - -
38A LEU* 2.8 40.6 + - - +
102A VAL* 4.7 3.1 - - + -
103A LYS 6.1 0.2 - - - +
107A ASP* 4.3 30.4 - - + +
110A ARG* 5.4 3.6 + - - -
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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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16A GLU* 1.3 84.3 + - + +
18A ALA* 1.3 61.4 + - - +
35A VAL* 4.4 15.0 - - + -
36A GLY 3.5 11.2 - - - +
37A GLU* 4.5 3.0 - - - +
57A GLU* 3.1 36.8 + - - +
102A VAL* 3.6 19.2 - - - +
103A LYS* 4.6 28.2 + - + +
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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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16A GLU 4.2 0.4 - - - +
17A LYS* 1.3 77.3 - - - +
19A LYS* 1.3 60.5 + - - +
34A GLY 4.1 0.2 - - - +
35A VAL* 3.3 6.8 - - - +
36A GLY 2.8 33.5 + - - +
38A LEU* 3.9 15.3 - - + -
54A MSE 3.6 23.5 - - + +
100A ILE* 3.8 14.4 - - + -
101A LYS 3.2 12.6 - - - +
102A VAL* 4.2 5.6 - - + -
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Residues in contact with LYS 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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18A ALA* 1.3 74.5 - - - +
20A LEU* 1.3 66.6 + - - +
21A LEU* 4.3 15.0 - - + -
32A SER* 3.2 34.0 - - - +
34A GLY 3.3 8.3 - - - +
35A VAL* 3.6 23.1 - - + +
54A MSE 4.1 4.0 - - - +
99A ILE 3.7 0.5 - - - +
100A ILE* 3.6 4.7 - - - -
101A LYS* 2.8 59.8 + - + +
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Residues in contact with LEU 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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19A LYS* 1.3 72.1 - - - +
21A LEU* 1.3 60.2 + - - +
22A ILE* 4.2 22.2 - - + -
32A SER* 3.4 4.9 + - - -
33A ARG* 2.7 43.4 + - + -
34A GLY 2.9 13.0 + - - +
54A MSE 3.9 14.9 - - + +
63A LEU* 3.6 36.1 - - + +
64A LEU* 4.5 16.2 - - + -
98A PHE* 4.0 27.8 - - + -
99A ILE 3.7 8.1 - - - +
100A ILE* 4.4 12.8 - - + -
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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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19A LYS* 4.2 13.5 - - + +
20A LEU* 1.3 77.9 - - - +
22A ILE* 1.3 68.2 + - - +
30A TYR* 3.8 23.7 - - + +
31A THR* 3.4 7.9 - - - +
32A SER* 3.7 28.0 - - - +
84A LEU* 4.4 5.8 - - + -
98A PHE* 3.7 1.9 - - - +
99A ILE* 2.8 53.8 + - + +
101A LYS* 3.7 31.4 - - + -
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Residues in contact with ILE 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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20A LEU* 4.2 14.6 - - + -
21A LEU* 1.3 81.1 - - - +
23A PHE* 1.3 67.1 + - - +
30A TYR* 3.5 6.7 - - - -
31A THR 3.0 21.4 + - - -
33A ARG* 2.8 58.8 + - + +
96A GLU* 4.0 9.6 - - - +
98A PHE* 3.7 48.9 - - + -
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Residues in contact with PHE 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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22A ILE* 1.3 81.6 - - - +
24A ASP* 1.3 58.2 + - - +
25A SER* 3.8 25.7 + - - -
28A LYS* 3.3 41.3 - - + -
29A GLY* 3.4 16.6 - - - -
30A TYR* 3.4 33.8 - + + +
33A ARG* 3.5 5.9 + - - -
96A GLU* 4.2 15.5 + - - +
97A THR 5.1 0.2 + - - -
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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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22A ILE 3.4 0.2 + - - -
23A PHE* 1.3 73.7 - - - +
25A SER* 1.3 53.9 + - - +
26A ASP* 2.8 25.4 + - - +
27A THR* 2.9 25.3 + - - -
28A LYS* 2.6 37.1 + - - -
29A GLY 2.8 17.5 + - - +
31A THR* 3.8 18.2 + - + +
33A ARG* 3.8 11.2 + - - +
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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