Contacts of the strand formed by residues 31 - 33 (chain A) in PDB entry 1MUI
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 THR 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP* 1.3 74.9 - - - +
32A VAL* 1.3 60.6 + - - +
33A LEU* 4.4 15.0 - - + -
64A ILE* 5.2 0.7 - - + -
74A THR 4.1 9.7 + - - +
75A VAL* 3.7 11.8 - - + -
76A LEU* 2.9 30.5 + - - +
84A ILE 3.1 17.0 - - - +
85A ILE* 3.6 11.1 - - + -
86A GLY 2.8 15.6 + - - -
88A ASN* 2.8 22.8 + - - -
89A LEU* 3.6 23.0 - - + +
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP 4.1 1.0 + - - -
31A THR* 1.3 73.7 - - - +
33A LEU* 1.3 67.8 + - - +
47A ILE* 4.5 12.8 - - + -
54A ILE* 4.8 1.1 - - + -
56A VAL* 4.3 11.0 - - + -
76A LEU* 3.1 22.4 - - + +
78A GLY 4.3 7.0 - - - +
80A THR* 3.8 25.6 - - + +
82A VAL 4.0 1.4 - - - +
83A ASN* 3.8 1.7 - - - -
84A ILE* 2.9 53.9 + - + -
50B ILE* 4.8 2.0 - - + -
100B AB1 3.9 14.6 - - + -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.1 15.5 - - + -
15A ILE* 4.1 32.1 - - + -
20A LYS* 5.7 0.7 - - + -
31A THR* 4.4 7.0 - - + -
32A VAL* 1.3 80.0 - - - +
34A GLU* 1.3 72.0 + - - +
36A MET* 4.3 15.7 - - - -
38A LEU* 6.0 0.9 - - + -
64A ILE* 5.8 1.3 - - + -
75A VAL* 3.7 28.0 - - + -
76A LEU 2.6 12.2 + - - +
77A VAL* 3.2 20.6 - - + -
78A GLY 3.3 5.5 + - - -
80A THR* 3.6 5.9 - - - +
83A ASN* 3.4 25.6 - - + +
84A ILE 4.2 10.1 - - - +
85A ILE* 4.7 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
------------------------------------------------------------
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