Contacts of the strand formed by residues 78 - 85 (chain A) in PDB entry 1MWR
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 ILE 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A ILE 4.2 4.7 - - - +
38A GLU* 3.7 44.3 + - + +
40A LYS* 3.7 30.2 - - + +
70A TYR* 3.8 25.8 - - + +
75A VAL* 4.2 9.2 - - + -
76A LYS 3.8 7.1 + - - +
77A ASP* 1.3 79.3 - - - +
79A ASN* 1.3 75.8 + - - +
80A ILE* 4.5 3.6 - - + -
99A TYR* 3.7 28.7 - - + +
100A LYS 3.4 5.2 - - - +
101A ILE* 4.4 7.9 - - + -
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Residues in contact with ASN 79 (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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38A GLU* 3.9 7.5 - - - +
77A ASP* 4.3 17.4 + - - +
78A ILE* 1.3 89.7 - - - +
80A ILE* 1.3 61.5 + - - +
81A GLN* 3.0 24.1 + - + +
98A GLN 3.2 3.1 - - - +
100A LYS* 2.9 43.3 + - + +
102A LYS* 4.4 18.8 - - - +
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Residues in contact with ILE 80 (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 ILE* 3.5 35.2 - - + +
37A ILE* 4.1 21.3 - - + -
38A GLU* 2.8 24.6 + - + +
78A ILE* 4.5 2.0 - - + -
79A ASN* 1.3 73.6 - - - +
81A GLN* 1.3 62.2 + - - +
83A ARG* 3.1 23.9 + - + +
97A ALA* 3.4 29.2 - - + -
98A GLN 3.1 8.3 - - - +
99A TYR* 4.3 22.0 - - + -
114A PHE* 3.9 24.9 - - + -
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Residues in contact with GLN 81 (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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38A GLU* 4.3 2.6 + - - -
79A ASN* 3.0 34.9 + - - +
80A ILE* 1.3 79.1 + - - +
82A ASP* 1.3 73.7 + - + +
83A ARG* 3.0 4.9 + - - -
97A ALA* 3.2 17.2 - - - +
98A GLN* 3.1 17.7 + - + +
100A LYS* 3.7 28.7 - - + +
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Residues in contact with ASP 82 (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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81A GLN* 1.3 76.8 - - + +
83A ARG* 1.3 58.2 + - - +
84A LYS* 2.9 41.7 + - - +
96A ASP 3.0 11.1 - - - +
97A ALA* 3.8 1.4 - - - -
98A GLN* 5.2 10.8 - - + +
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Residues in contact with ARG 83 (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 ASN* 3.0 54.3 + - - +
34A ILE* 3.5 31.6 - - + +
35A ASP* 2.9 20.0 + - - -
38A GLU* 2.7 30.5 + - - -
80A ILE* 3.1 21.8 + - + +
81A GLN* 3.8 4.9 - - - +
82A ASP* 1.3 69.1 - - - +
84A LYS* 1.3 59.1 + - - +
85A ILE* 3.0 17.4 + - + +
95A VAL* 4.2 11.7 - - + -
96A ASP 3.8 4.3 - - - -
97A ALA* 3.9 10.1 - - + -
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Residues in contact with LYS 84 (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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82A ASP* 2.9 44.3 + - - +
83A ARG* 1.3 68.4 - - - +
85A ILE* 1.3 65.5 + - - +
86A LYS* 3.6 3.6 + - - +
94A ARG 3.8 2.1 - - - +
96A ASP* 3.0 40.5 + - + +
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Residues in contact with ILE 85 (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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27A ASP 3.5 24.7 - - - +
30A ILE* 3.4 45.1 - - + -
31A ASN* 4.6 11.2 - - - +
83A ARG* 3.0 14.5 + - + +
84A LYS* 1.3 73.9 - - - +
86A LYS* 1.3 70.8 + - - +
94A ARG 3.9 3.4 - - - -
95A VAL* 4.1 20.4 - - + +
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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