Contacts of the strand formed by residues 140 - 145 (chain C) in PDB entry 1MQ8
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 ALA 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C CYS 3.1 17.2 - - - +
109C GLN* 3.2 10.0 - - - -
110C VAL* 2.6 38.8 + - + +
116C ARG* 4.5 0.4 - - - +
121C VAL* 5.0 2.8 - - + +
135C ALA* 3.9 9.2 - - + -
136C VAL 3.1 31.9 - - - +
137C GLY 3.9 3.4 + - - +
139C PRO* 1.3 68.9 - - - +
141C GLU* 1.3 63.7 + - - +
142C VAL* 3.5 2.8 + - + +
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Residues in contact with GLU 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ARG* 3.2 37.9 + - - +
108C CYS 4.1 1.8 - - - -
109C GLN* 4.2 15.9 - - - +
133C GLU* 5.6 0.3 - - - +
136C VAL* 3.6 25.7 + - + +
139C PRO 3.1 6.9 + - - +
140C ALA* 1.3 73.0 - - - +
142C VAL* 1.3 66.8 + - - +
143C THR* 4.6 0.9 - - - +
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Residues in contact with VAL 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU 3.9 0.2 - - - +
107C ARG* 3.4 1.1 - - - +
108C CYS* 2.9 55.1 + - + +
121C VAL* 4.0 25.4 - - + +
123C LEU* 3.6 16.8 - - + +
131C LYS* 5.5 8.7 - - + +
133C GLU* 4.1 34.1 - - + +
134C PRO 6.0 0.4 - - - +
140C ALA* 4.4 2.9 - - + +
141C GLU* 1.3 78.3 - - - +
143C THR* 1.3 69.7 + - - +
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Residues in contact with THR 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C THR* 4.1 22.2 - - + -
106C LEU 3.1 23.6 - - - +
107C ARG* 3.0 44.9 + - - +
123C LEU* 3.9 2.5 - - - -
131C LYS* 3.3 23.4 + - - +
141C GLU* 4.6 0.7 - - - +
142C VAL* 1.3 84.6 + - - +
144C THR* 1.3 62.9 + - - +
145C THR* 5.3 1.3 - - + -
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Residues in contact with THR 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 3.1 32.8 + - + +
123C LEU* 3.7 30.1 - - + -
130C LEU* 4.3 23.9 + - + +
131C LYS* 3.9 21.5 + - + +
143C THR* 1.3 76.8 - - - +
145C THR* 1.3 66.8 + - - +
146C VAL* 3.2 6.0 + - + +
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Residues in contact with THR 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ASN* 3.5 24.6 + - - +
104C LEU 3.2 12.1 - - - -
105C THR* 3.4 27.1 - - + +
143C THR* 5.3 2.2 - - + -
144C THR* 1.3 72.7 + - - +
146C VAL* 1.3 62.6 + - - +
147C LEU* 4.0 3.5 + - - +
407C NAG 3.1 34.4 + - + +
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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