Contacts of the strand formed by residues 131 - 136 (chain D) 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 ASP 131 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D VAL* 1.3 68.7 - - - +
132D LEU* 1.3 63.1 + - - +
167D GLN* 2.9 40.9 + - - +
183D PHE* 3.9 20.1 - - + -
220D PHE* 3.7 10.6 - - + -
226D ALA* 4.2 6.5 - - + +
227D ARG 2.7 43.4 + - - +
230D ALA* 3.2 10.1 - - - +
231D THR 2.7 10.7 + - - +
232D LYS* 3.2 11.0 - - + -
233D VAL 3.0 17.3 + - - -
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D VAL* 3.3 5.2 + - + -
131D ASP* 1.3 74.8 - - - +
133D VAL* 1.3 84.4 + - - +
134D PHE* 3.4 38.1 - - + +
157D VAL* 5.8 2.2 - - + -
166D TYR* 4.9 6.3 - - + +
167D GLN 2.9 6.5 + - - -
168D PHE* 3.0 57.9 - - + -
169D ALA 3.3 0.2 + - - -
183D PHE* 4.0 1.2 - - - -
233D VAL* 3.6 37.0 - - + -
235D ILE* 3.7 6.7 - - + -
302D LEU* 3.9 26.2 - - + -
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU* 1.3 84.5 - - - +
134D PHE* 1.3 71.4 + - - +
135D LEU 4.5 0.2 - - - +
169D ALA* 3.5 25.4 - - + -
171D VAL* 4.1 9.9 - - + -
183D PHE* 4.6 1.3 - - + -
215D VAL* 3.4 26.0 - - + -
219D VAL* 4.2 3.8 - - + -
220D PHE* 3.2 34.8 - - + -
233D VAL 2.9 14.2 + - - +
234D LEU* 4.7 4.0 - - + -
235D ILE* 2.5 38.3 + - - +
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Residues in contact with PHE 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU* 3.4 24.0 - - + -
133D VAL* 1.3 73.4 - - - +
135D LEU* 1.3 59.5 + - - +
136D PHE 3.8 1.3 - - - -
153D PHE* 5.2 3.4 - + - -
154D MET* 3.8 52.9 - - + -
157D VAL* 4.4 11.7 - - + -
158D MET* 3.3 54.3 - - + -
168D PHE* 4.6 6.3 - + + -
169D ALA 3.1 15.3 + - - +
170D ALA* 3.2 4.2 - - + -
171D VAL* 3.0 28.2 + - - +
181D PHE* 5.2 0.7 - + - -
235D ILE* 3.3 35.2 - - + +
237D ILE* 4.7 2.0 - - + -
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D VAL* 4.9 2.5 - - + -
134D PHE* 1.3 73.6 - - - +
136D PHE* 1.3 53.7 + - - +
171D VAL* 3.3 35.9 - - + +
173D PHE* 3.8 18.3 - - + -
177D TYR* 6.0 0.4 - - + -
208D THR 5.1 0.2 - - - +
211D ALA* 3.9 16.2 - - + +
212D ILE* 3.9 22.4 - - + +
215D VAL* 3.9 19.1 - - + -
234D LEU* 4.7 3.8 - - + -
235D ILE 2.4 15.3 + - - +
236D ILE* 3.2 33.1 - - + +
237D ILE* 2.5 34.0 + - - +
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Residues in contact with PHE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D PHE 4.3 2.0 - - - -
135D LEU* 1.3 72.3 - - - +
137D ASP* 1.3 54.7 + - - +
147D PHE* 4.1 22.9 - + - -
150D ILE* 4.0 9.9 - - + -
151D LEU* 4.4 12.6 - - + -
154D MET* 4.2 20.9 - - + -
170D ALA* 3.8 9.6 - - + -
171D VAL 3.2 18.1 + - - -
172D GLN* 3.1 40.5 - - + -
173D PHE* 2.9 34.1 + - - -
180D GLU* 3.1 35.9 - - + -
196D LEU* 5.5 3.4 - - + -
199D VAL* 5.0 2.5 - - + -
237D ILE* 3.3 28.7 - - + -
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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