Contacts of the helix formed by residues 105 - 114 (chain B) in PDB entry 3MDR
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 ASP 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B ASN 3.7 0.6 + - - -
104B LYS* 1.3 70.9 - - - +
106B SER* 1.3 66.7 + - - +
107B LYS* 2.9 39.2 + - - +
108B MET* 2.8 27.8 + - + -
109B TYR* 3.3 13.1 - - - -
129B CYS* 3.9 2.7 - - - -
371B PHE* 3.8 14.1 + - + -
373B LEU* 3.4 31.8 - - + +
390B PRO* 3.1 35.4 - - + +
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Residues in contact with SER 106 (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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104B LYS 3.4 5.9 + - - -
105B ASP* 1.3 71.6 + - - +
107B LYS* 1.3 63.3 + - - +
109B TYR* 3.1 10.2 + - - +
110B ARG* 3.0 44.8 + - - +
113B GLN* 4.4 5.4 + - - +
129B CYS* 3.6 27.2 - - - +
130B ASN 5.3 0.3 + - - -
373B LEU* 5.4 4.1 - - - +
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Residues in contact with LYS 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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82B LYS* 2.9 37.9 + - + +
83B THR* 5.2 3.0 + - - +
105B ASP* 2.8 30.1 + - - +
106B SER* 1.3 77.0 - - - +
108B MET* 1.3 62.7 + - + +
109B TYR 3.6 0.3 + - - -
110B ARG* 3.8 25.1 + - - +
111B ALA 5.2 0.3 + - - -
373B LEU* 4.7 2.2 - - - -
388B ASN* 3.6 31.3 + - - +
390B PRO* 3.4 28.6 - - - +
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Residues in contact with MET 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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79B VAL* 3.4 28.5 - - + +
80B PHE* 3.6 27.3 - - + +
82B LYS* 3.9 25.6 - - + -
83B THR 4.9 2.0 - - - +
105B ASP* 2.8 18.0 + - + +
107B LYS* 1.3 74.1 - - - +
109B TYR* 1.3 62.1 + - + +
110B ARG 3.5 1.1 + - - -
111B ALA* 4.5 5.9 + - - +
226B ARG* 4.0 16.1 + - - -
371B PHE* 3.6 58.3 - - + -
390B PRO* 3.9 26.2 - - + -
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Residues in contact with TYR 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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104B LYS* 3.5 35.3 - - + +
105B ASP 3.3 26.5 - - - -
106B SER 3.1 7.4 + - - +
108B MET* 1.3 80.5 - - + +
110B ARG* 1.3 62.2 + - - +
111B ALA 3.1 5.8 - - - -
112B LEU* 3.1 33.5 + - + +
113B GLN* 3.1 22.0 + - - +
126B VAL* 4.5 11.4 - - + -
127B SER* 4.2 6.1 - - - +
129B CYS* 4.0 13.9 - - - -
226B ARG* 5.1 5.2 - - - +
370B THR* 3.0 22.9 + - - -
371B PHE* 3.5 27.1 + + + -
505B HEM 2.8 29.7 + - - -
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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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82B LYS* 4.6 10.3 - - - +
106B SER* 3.0 41.5 - - - +
107B LYS* 3.8 28.0 - - - +
108B MET 3.5 1.2 - - - -
109B TYR* 1.3 77.6 - - - +
111B ALA* 1.3 60.4 + - - +
112B LEU 3.2 1.1 + - - -
113B GLN* 3.6 24.5 + - - +
114B THR* 3.3 24.9 + - - +
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Residues in contact with ALA 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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80B PHE* 5.7 0.9 - - + -
107B LYS 5.2 0.4 + - - -
108B MET 4.5 7.3 + - - +
109B TYR 3.1 0.2 - - - -
110B ARG* 1.3 79.4 - - - +
112B LEU* 1.3 57.8 + - - +
114B THR 4.1 3.8 - - - -
115B VAL* 3.3 22.0 - - - +
222B ILE* 4.4 9.5 - - - +
225B SER* 4.5 14.9 + - - +
226B ARG* 3.5 40.6 - - + +
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Residues in contact with LEU 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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109B TYR* 3.1 23.5 + - + +
111B ALA* 1.3 78.1 - - - +
113B GLN* 1.3 64.3 + - - +
114B THR 3.3 2.7 + - - -
115B VAL* 4.8 1.3 - - - -
120B LEU* 3.5 6.2 - - - +
121B PHE* 3.0 45.6 + - + -
126B VAL* 4.1 21.1 - - + -
127B SER* 4.5 4.5 - - - -
222B ILE* 3.8 38.8 - - + -
226B ARG* 3.6 26.2 - - - +
474B ALA* 5.5 0.4 - - + -
506B GJZ 4.0 24.7 - - + -
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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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106B SER* 4.4 9.1 + - - +
109B TYR* 3.1 23.4 + - - +
110B ARG* 3.5 33.7 + - - +
112B LEU* 1.3 76.7 - - - +
114B THR* 1.3 66.7 + - - +
119B ARG* 3.9 1.7 - - - +
120B LEU 3.0 10.8 + - - -
121B PHE* 4.4 0.4 - - - +
122B GLY* 3.0 47.9 + - - +
123B GLN* 3.1 19.5 + - - +
127B SER* 2.9 29.4 + - - -
129B CYS* 4.4 4.8 - - - -
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Residues in contact with THR 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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110B ARG 3.3 15.2 + - - +
111B ALA* 3.9 4.0 - - - +
112B LEU 3.3 0.2 - - - -
113B GLN* 1.3 85.4 + - - +
115B VAL* 1.3 70.6 + - - +
116B PHE 4.4 0.2 + - - -
117B GLY* 4.1 11.0 - - - +
118B GLU 3.4 30.3 - - - +
119B ARG* 3.9 8.4 - - - +
120B LEU 4.1 0.7 - - - +
225B SER* 5.0 2.1 + - - -
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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