Contacts of the strand formed by residues 48 - 55 (chain A) in PDB entry 2M0O
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 LEU 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASP* 4.8 14.6 - - + +
37A VAL 3.6 13.2 - - - +
38A LEU* 3.8 14.1 - - + -
47A TYR* 1.3 71.5 - - - +
49A GLY* 1.3 60.1 + - - +
65A PHE* 3.0 14.5 - - - +
66A GLU* 3.4 22.0 + - + -
81A ALA* 3.8 17.3 - - + -
336B M3L 4.0 8.7 - - + +
337B LYS* 3.4 50.3 - - + +
338B PRO* 3.6 20.1 - - + +
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Residues in contact with GLY 49 (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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36A ASP* 3.5 4.4 - - - -
37A VAL* 2.6 43.8 + - - +
47A TYR 4.0 0.2 + - - -
48A LEU* 1.3 78.6 - - - +
50A THR* 1.3 58.4 - - - -
63A VAL* 3.4 15.7 - - - -
64A GLN 3.1 13.2 - - - -
65A PHE* 3.8 2.8 - - - -
66A GLU 4.8 0.4 - - - -
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Residues in contact with THR 50 (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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34A GLY* 3.5 35.7 - - - +
35A GLN 3.3 9.4 - - - -
36A ASP* 3.7 20.3 + - - +
49A GLY* 1.3 74.4 - - - -
51A ILE* 1.3 61.7 + - - +
52A LYS 3.3 0.3 + - - -
63A VAL* 3.0 4.1 - - - -
64A GLN* 2.6 43.7 + - - +
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Residues in contact with ILE 51 (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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31A LEU* 3.5 18.6 - - + -
32A TRP 2.9 28.5 - - - +
33A GLU* 3.2 7.0 - - - +
34A GLY* 2.7 26.0 + - - -
35A GLN* 3.0 25.3 + - + +
37A VAL* 3.5 24.9 - - + -
50A THR* 1.3 71.7 - - - +
52A LYS* 1.3 57.9 + - - +
53A LYS 3.1 24.5 - - - +
54A VAL* 3.4 17.5 - - + -
61A CYS* 4.0 6.5 - - + -
62A LEU 3.5 0.9 - - - -
63A VAL* 3.6 24.5 - - + -
78A ILE* 5.0 1.3 - - + -
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Residues in contact with LYS 52 (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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33A GLU* 3.6 16.9 - - - +
50A THR 3.3 2.2 + - - +
51A ILE* 1.3 73.6 - - - +
53A LYS* 1.3 106.1 + - + +
62A LEU* 2.7 15.3 + - + +
63A VAL 4.7 0.7 - - - -
64A GLN* 3.4 41.5 - - + +
70A GLN* 3.7 16.6 - - + +
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Residues in contact with LYS 53 (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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33A GLU* 4.6 10.9 + - - -
51A ILE* 3.1 10.4 - - - +
52A LYS* 1.3 123.2 + - + +
54A VAL* 1.3 68.2 + - - +
55A ASP* 5.1 6.7 - - - +
61A CYS* 3.4 1.2 - - - +
62A LEU* 2.8 46.1 + - + +
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Residues in contact with VAL 54 (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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31A LEU 3.7 24.0 - - - +
32A TRP* 3.8 10.3 - - - -
33A GLU* 4.2 6.5 - - + +
51A ILE* 3.4 19.5 - - + -
53A LYS* 1.3 85.0 - - - +
55A ASP* 1.3 71.2 + - - +
56A SER* 3.4 23.8 + - - +
61A CYS* 3.3 17.9 - - - +
75A TRP* 3.9 4.0 - - + -
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Residues in contact with ASP 55 (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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53A LYS* 5.1 7.6 - - - +
54A VAL* 1.3 79.7 + - - +
56A SER* 1.3 56.3 + - - +
57A ALA* 3.1 8.4 + - - +
58A ARG* 4.8 17.3 + - + +
59A GLU* 3.1 8.5 + - - -
60A VAL* 2.6 61.1 + - + +
61A CYS* 4.1 2.1 - - - +
62A LEU* 5.5 0.9 + - - +
72A LEU* 6.1 2.1 - - - +
75A TRP* 4.1 1.5 + - - -
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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