Contacts of the strand formed by residues 95 - 103 (chain B) 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 VAL 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B ILE* 3.9 18.2 - - + -
34B ILE* 3.9 20.4 - - + -
83B ARG* 4.8 6.7 - - + -
84B LYS 3.3 3.1 - - - +
85B ILE* 3.6 33.9 - - + -
94B ARG* 1.3 76.7 - - - +
96B ASP* 1.3 75.5 + - - +
97B ALA* 4.5 5.4 - - + -
112B VAL 3.9 0.3 - - - +
113B GLN* 3.3 6.1 - - - +
114B PHE* 2.5 64.6 + - + +
116B PHE* 4.3 7.6 - - + -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ASP 3.4 2.0 - - - +
83B ARG* 3.4 0.3 - - - -
84B LYS* 2.7 57.7 + - + +
86B LYS* 5.0 9.2 - - - +
94B ARG* 3.5 39.0 + - - +
95B VAL* 1.3 77.3 - - - +
97B ALA* 1.3 64.4 + - - +
112B VAL 3.6 4.6 - - - +
113B GLN* 4.0 8.1 - - - +
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ILE* 3.7 22.4 - - + -
81B GLN 3.6 9.6 - - - +
82B ASP 3.5 8.3 - - - -
83B ARG* 4.0 13.5 - - + -
95B VAL* 4.2 7.2 - - + -
96B ASP* 1.3 76.2 - - - +
98B GLN* 1.3 62.6 + - - +
99B TYR 4.0 0.7 - - - -
111B ASN* 3.6 5.5 - - - +
112B VAL* 3.0 34.7 + - + +
114B PHE* 5.5 3.4 - - + -
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASN 3.3 3.8 - - - +
80B ILE* 3.2 5.9 - - - -
81B GLN* 3.0 34.3 + - + +
82B ASP* 4.3 12.5 + - + +
97B ALA* 1.3 75.0 - - - +
99B TYR* 1.3 58.4 + - - +
100B LYS* 3.6 12.2 + - + +
109B ASP* 3.0 33.9 + - - +
110B ARG* 3.2 27.6 - - - +
111B ASN* 2.6 26.0 + - - +
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ILE* 3.8 7.7 - - + +
70B TYR* 3.1 24.6 + - - -
78B ILE* 3.4 19.9 - - + +
79B ASN 3.9 1.6 - - - -
80B ILE* 3.9 28.3 - - + -
97B ALA 4.0 1.4 - - - -
98B GLN* 1.3 70.4 - - - +
100B LYS* 1.3 63.4 + - - +
101B ILE* 3.4 30.9 + - + -
108B ILE* 3.6 2.4 - - - +
109B ASP* 3.5 2.3 - - - -
110B ARG 2.8 33.0 + - - +
112B VAL* 3.1 36.1 - - + -
114B PHE* 4.3 6.3 - + - -
130B SER 3.9 8.5 - - - -
131B VAL 3.2 21.0 + - - -
132B ILE 3.2 5.1 + - - -
134B PRO* 3.7 19.3 - - + +
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ASP 3.9 0.3 - - - +
78B ILE* 3.3 3.8 - - - +
79B ASN* 2.7 60.9 + - + +
81B GLN* 5.4 8.5 - - + -
98B GLN* 3.9 15.3 - - + +
99B TYR* 1.3 77.7 - - - +
101B ILE* 1.3 65.0 + - - +
102B LYS* 5.4 10.3 - - + +
108B ILE 3.1 6.1 - - - +
109B ASP* 2.7 47.1 + - - +
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Residues in contact with ILE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B TYR* 5.1 2.7 - - + +
73B LEU* 6.5 0.2 - - + -
75B VAL* 3.8 30.7 - - + -
77B ASP 3.5 3.6 - - - +
78B ILE* 4.0 5.6 - - + -
99B TYR* 3.4 40.4 - - + +
100B LYS* 1.3 74.8 - - - +
102B LYS* 1.3 65.8 + - - +
103B THR* 3.9 13.6 + - + -
106B GLY 3.9 0.7 - - - +
107B ASN* 3.4 4.7 - - - +
108B ILE* 2.9 53.3 + - + +
132B ILE 4.3 1.3 - - - +
133B ILE* 4.0 21.3 - - + -
134B PRO* 4.0 16.6 - - + -
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.4 2.1 - - - -
76B LYS* 2.6 45.1 + - + -
77B ASP* 2.8 42.2 + - + +
79B ASN* 4.5 13.6 - - - +
100B LYS* 5.4 9.4 - - + +
101B ILE* 1.3 79.1 - - - +
103B THR* 1.3 59.2 + - - +
107B ASN* 3.6 30.7 - - + +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU* 3.1 24.9 - - + +
74B GLY 3.4 6.7 - - - -
75B VAL* 4.2 11.7 - - + -
76B LYS* 4.2 11.7 - - - +
101B ILE* 3.9 20.0 - - + +
102B LYS* 1.3 79.8 - - - +
104B ASN* 1.3 65.5 + - - +
105B TYR* 3.1 11.1 + - - +
106B GLY* 2.6 38.3 + - - +
107B ASN* 4.3 1.4 + - - +
108B ILE* 4.7 11.4 - - + -
314B ILE* 3.4 10.7 - - + +
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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
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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