Contacts of the strand formed by residues 106 - 114 (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 GLY 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B ILE 3.9 1.0 - - - +
103B THR* 2.6 41.1 + - - +
104B ASN 3.4 0.4 - - - -
105B TYR* 1.3 82.1 - - - +
107B ASN* 1.3 67.4 + - - -
314B ILE* 3.7 8.2 - - - +
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Residues in contact with ASN 107 (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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101B ILE 3.4 5.4 - - - +
102B LYS* 3.6 36.8 - - + +
103B THR 4.3 1.6 + - - +
106B GLY* 1.3 82.4 - - - +
108B ILE* 1.3 68.4 + - - +
109B ASP* 4.1 3.8 + - + +
313B LEU 4.5 3.8 - - - +
314B ILE* 4.1 9.1 - - - +
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Residues in contact with ILE 108 (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* 4.9 5.4 - - + -
99B TYR 4.1 0.9 - - - +
100B LYS* 3.1 6.6 - - - +
101B ILE* 2.9 59.5 + - + +
103B THR* 4.7 7.9 - - + -
107B ASN* 1.3 77.8 - - - +
109B ASP* 1.3 63.2 + - - +
110B ARG* 3.9 25.1 - - + -
133B ILE* 4.8 7.9 - - + -
134B PRO* 4.3 16.4 - - + -
313B LEU* 4.1 34.8 - - + +
314B ILE* 3.9 26.2 - - + -
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Residues in contact with ASP 109 (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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98B GLN* 3.0 31.0 + - - +
99B TYR 3.5 3.1 - - - -
100B LYS* 2.7 33.3 + - - +
107B ASN* 4.1 5.3 + - + -
108B ILE* 1.3 77.4 - - - +
110B ARG* 1.3 63.5 + - - +
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Residues in contact with ARG 110 (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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209A ASP* 3.7 9.9 + - - +
98B GLN* 3.2 7.7 + - - +
99B TYR* 2.8 39.3 + - - +
108B ILE* 3.9 20.2 - - + -
109B ASP* 1.3 79.4 - - - +
111B ASN* 1.3 69.1 + - - +
112B VAL* 4.4 0.2 - - - -
134B PRO* 3.2 25.4 + - + -
135B GLY* 3.3 26.1 - - - +
311B HIS* 3.4 35.9 + - - +
312B THR 5.6 3.7 + - - -
313B LEU* 4.0 15.8 - - - +
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Residues in contact with ASN 111 (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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176A LYS* 4.6 20.8 + - - +
177A ASN* 5.3 7.7 + - - +
97B ALA 3.6 7.1 - - - +
98B GLN* 2.6 28.6 + - - +
110B ARG* 1.3 78.9 + - - +
112B VAL* 1.3 68.3 + - - +
134B PRO* 3.9 6.2 - - - +
135B GLY 5.2 2.1 + - - -
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Residues in contact with VAL 112 (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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176A LYS* 5.9 2.5 - - - +
80B ILE* 6.0 0.4 - - + -
95B VAL 3.9 0.2 - - - +
96B ASP* 3.6 6.1 - - - +
97B ALA* 3.0 35.7 + - + +
99B TYR* 3.1 37.5 - - + +
111B ASN* 1.3 84.7 - - - +
113B GLN* 1.3 64.8 + - - +
114B PHE* 3.7 32.7 - - + -
130B SER* 3.3 26.2 - - - +
134B PRO* 3.2 15.5 - - + -
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Residues in contact with GLN 113 (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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176A LYS* 6.1 2.5 - - - +
94B ARG* 2.8 50.0 + - - +
95B VAL 3.3 4.0 - - - +
96B ASP* 4.0 5.2 - - - +
112B VAL* 1.3 79.3 - - - +
114B PHE* 1.3 72.7 - - - +
115B ASN* 3.0 27.2 + - - +
128B ASP* 4.8 6.9 - - - +
130B SER* 4.1 7.2 + - - -
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Residues in contact with PHE 114 (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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34B ILE* 4.1 22.0 - - + -
37B ILE* 3.8 24.9 - - + -
80B ILE* 4.3 24.0 - - + -
94B ARG* 3.4 0.5 - - - -
95B VAL* 2.5 58.4 + - + +
97B ALA* 5.5 2.0 - - + -
99B TYR* 4.3 16.6 - + - -
112B VAL* 3.7 25.6 - - + -
113B GLN* 1.3 81.7 - - - +
115B ASN* 1.3 62.1 + - - +
116B PHE* 4.2 11.9 + + + -
125B LEU* 4.6 9.2 - - + -
128B ASP* 5.3 1.3 - - - -
130B SER* 4.3 1.3 - - - -
131B VAL* 3.3 36.3 - - + -
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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