Contacts of the strand formed by residues 31 - 40 (chain A) in PDB entry 2OA8
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 VAL 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.0 23.6 - - + -
20A GLU 3.6 5.8 - - - +
21A ALA* 4.2 0.9 - - - -
30A GLU* 1.3 74.1 - - - +
32A THR* 1.3 64.6 + - - +
33A GLU 3.6 23.3 - - - +
34A LEU* 4.6 0.4 - - + -
71A ILE* 3.7 35.2 - - + +
73A PRO* 4.3 7.3 - - - +
100A PHE* 4.4 9.5 - - + +
133A LEU* 3.8 25.1 - - + -
134A LEU* 5.4 0.2 - - - -
137A GLU* 2.7 38.4 + - + +
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Residues in contact with THR 32 (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 GLU* 2.7 28.5 + - - +
21A ALA* 3.3 6.6 + - - -
22A THR* 3.8 26.5 - - + -
30A GLU 3.5 1.3 + - - +
31A VAL* 1.3 76.2 - - - +
33A GLU* 1.3 58.7 + - - +
70A CYS* 3.6 3.8 - - - +
71A ILE* 2.8 33.0 + - - +
73A PRO* 3.9 16.4 - - + -
77A CYS* 4.0 13.0 - - - -
85A THR* 5.2 1.2 + - - -
87A LEU* 3.7 24.4 - - - +
92A LEU* 4.2 5.6 - - + +
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Residues in contact with GLU 33 (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* 3.3 3.3 - - - -
20A GLU* 2.7 38.3 + - + +
31A VAL* 3.6 7.4 - - - +
32A THR* 1.3 79.0 - - - +
34A LEU* 1.3 62.9 + - - +
68A SER* 4.4 10.1 + - - +
69A LEU 3.2 17.7 - - - +
70A CYS* 3.7 15.9 - - - -
71A ILE* 4.4 0.9 - - - +
87A LEU* 3.7 8.3 - - + -
196A THR* 4.3 2.1 + - - -
197A ALA* 3.0 30.2 + - + -
198A GLU* 5.1 1.0 + - - +
62B ARG* 2.6 47.5 + - - -
64B VAL* 5.2 1.9 - - - +
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Residues in contact with LEU 34 (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 LEU* 4.9 0.7 - - + -
18A ASP 3.6 6.1 - - - -
19A LEU* 4.0 20.4 - - + -
33A GLU* 1.3 75.2 - - - +
35A CYS* 1.3 64.9 + - - +
36A LEU* 3.8 28.0 - - + +
67A LEU* 4.5 9.9 - - + +
68A SER* 3.4 2.6 + - - -
69A LEU* 2.9 42.3 + - + +
71A ILE* 4.0 17.0 - - + -
100A PHE* 4.5 13.0 - - + -
104A LEU* 5.4 1.8 - - + -
108A LEU* 4.1 30.1 - - + -
134A LEU* 4.3 17.9 - - + -
197A ALA* 4.2 2.5 - - - -
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Residues in contact with CYS 35 (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 LEU* 3.4 7.3 - - - +
18A ASP 3.1 28.2 + - - -
34A LEU* 1.3 76.6 - - - +
36A LEU* 1.3 74.0 + - - +
66A LYS* 4.6 6.3 - - - -
67A LEU 3.1 11.2 - - - +
68A SER* 4.1 7.9 - - - +
197A ALA* 3.7 25.1 - - + +
198A GLU* 3.6 30.7 - - - +
201A VAL* 3.6 17.0 - - + +
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Residues in contact with LEU 36 (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 ILE* 3.7 20.9 - - + -
16A PHE 3.2 4.0 - - - -
17A LEU* 3.3 36.3 - - + -
34A LEU* 3.8 13.9 - - + -
35A CYS* 1.3 76.7 - - - +
37A LEU* 1.3 60.7 + - - +
38A ALA 4.2 0.4 - - - -
65A ASP 4.4 0.2 - - - -
66A LYS* 3.4 6.8 - - - +
67A LEU* 2.8 51.0 + - + +
108A LEU* 4.0 15.7 - - + -
111A PHE* 3.8 30.9 - - + -
112A LEU* 5.1 7.9 - - + -
121A LEU* 5.6 3.4 - - + -
134A LEU* 6.3 0.9 - - + -
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Residues in contact with LEU 37 (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 ILE* 3.4 2.9 - - - -
16A PHE* 2.7 52.0 + - + -
36A LEU* 1.3 75.4 - - - +
38A ALA* 1.3 56.8 + - - +
39A VAL* 3.3 27.4 - - + -
64A VAL* 4.0 26.9 - - + -
65A ASP 3.3 13.7 - - - +
66A LYS* 3.6 35.9 - - + -
201A VAL* 3.5 23.3 - - + +
202A LEU* 5.6 6.3 - - + -
205A LEU* 4.4 15.5 - - + -
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Residues in contact with ALA 38 (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 THR* 5.1 2.0 - - - +
14A LEU 3.4 4.7 - - - -
15A ILE* 4.2 10.8 - - + +
36A LEU 4.2 0.4 - - - -
37A LEU* 1.3 70.3 - - - +
39A VAL* 1.3 61.7 + - - +
40A HIS 4.5 0.2 + - - -
64A VAL* 3.5 7.4 - - - +
65A ASP* 2.9 38.3 + - + +
111A PHE* 4.1 11.0 - - + -
115A GLN* 3.7 40.7 - - + +
97B ARG* 5.0 3.3 + - - -
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Residues in contact with VAL 39 (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 THR* 3.4 4.9 - - - -
14A LEU* 2.9 33.0 + - - +
16A PHE* 3.6 24.7 - - + -
37A LEU* 3.3 31.2 - - + -
38A ALA* 1.3 73.2 - - - +
40A HIS* 1.3 63.7 + - - +
43A ALA* 3.3 31.4 - - + -
44A LEU* 4.5 13.9 - - + +
61A PRO* 3.8 14.6 - - + -
63A VAL 4.8 5.4 - - - +
64A VAL* 4.4 4.0 - - + -
205A LEU* 4.5 6.3 - - + -
97B ARG* 5.4 0.4 - - - -
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Residues in contact with HIS 40 (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 GLN* 3.6 28.7 + - - -
13A THR* 4.3 2.9 - - - -
39A VAL* 1.3 77.3 - - - +
41A ARG* 1.3 86.8 + - + +
42A ARG* 3.1 33.0 + - + +
43A ALA* 3.0 20.3 + - - +
44A LEU* 3.9 2.0 + - - +
63A VAL* 5.1 1.6 + - + -
116A PRO* 3.7 25.9 - - + +
94B VAL 3.8 7.7 + - - -
95B GLN* 3.2 50.2 + - + +
96B GLY* 4.1 3.4 + - - -
97B ARG* 4.2 7.4 - - - +
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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