Contacts of the strand formed by residues 144 - 150 (chain M) in PDB entry 2OR9
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 ILE 144 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113M PRO* 4.0 26.2 - - + -
136M LEU* 3.3 26.5 - - + -
139M PHE* 3.7 31.4 - - + -
142M LYS 3.2 1.2 + - - +
143M ASP* 1.3 75.5 - - - +
145M ASN* 1.3 74.7 + - - +
163M TRP* 3.8 26.5 - - - +
175M MET* 3.9 15.6 - - - +
196M ALA* 4.5 1.6 - - + -
197M THR 3.9 13.7 - - - +
198M HIS* 4.0 13.0 - - + -
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Residues in contact with ASN 145 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136M LEU* 5.3 0.2 - - - -
144M ILE* 1.3 84.3 - - - +
146M VAL* 1.3 76.2 + - - +
147M LYS* 4.4 19.3 - - - +
175M MET* 5.8 0.7 - - - -
195M GLU 3.7 0.6 + - - +
196M ALA* 3.2 5.5 - - - +
197M THR* 2.8 56.2 + - - +
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Residues in contact with VAL 146 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136M LEU* 4.6 10.8 - - + -
145M ASN* 1.3 84.0 + - - +
147M LYS* 1.3 75.4 + - - +
148M TRP* 4.9 7.5 - - + +
159M VAL* 5.5 1.3 - - + -
161M ASN* 4.1 9.0 - - - +
175M MET* 3.5 30.2 - - + +
177M SER* 4.0 15.9 - - - +
194M CYS* 3.9 27.1 - - - -
195M GLU 3.2 11.4 - - - +
196M ALA* 4.5 1.8 - - - +
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Residues in contact with LYS 147 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145M ASN* 4.4 17.0 - - - +
146M VAL* 1.3 80.3 - - - +
148M TRP* 1.3 66.6 + - - +
149M LYS* 5.2 6.1 - - - -
154M GLU* 3.7 38.5 + - + +
193M THR 3.9 0.2 - - - +
194M CYS* 3.9 1.2 - - - -
195M GLU* 2.7 61.0 + - + +
197M THR* 6.5 0.4 - - + -
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Residues in contact with TRP 148 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117M ILE* 4.2 5.6 - - + -
132M VAL* 3.2 53.2 - - + -
134M CYS* 3.5 31.2 - - + -
146M VAL* 4.9 6.8 - - + +
147M LYS* 1.3 79.3 - - - +
149M LYS* 1.3 68.1 + - - +
154M GLU* 3.3 6.4 - - - +
155M ARG* 3.1 33.7 + - + +
159M VAL* 3.9 27.8 - - + +
177M SER* 2.9 30.5 + - - -
179M LEU* 4.0 31.8 - - + +
192M TYR* 5.3 3.8 - + + -
193M THR 3.4 21.5 - - - -
194M CYS* 4.1 16.4 - - + -
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Residues in contact with LYS 149 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M LYS* 5.2 7.4 - - - +
148M TRP* 1.3 81.7 - - - +
150M ILE* 1.3 63.6 + - - +
151M ASP 3.9 0.4 - - - -
152M GLY* 4.3 17.0 - - - +
153M SER 3.0 20.6 - - - +
154M GLU* 4.1 15.7 - - + +
191M SER 3.5 3.1 - - - +
192M TYR* 3.6 2.6 - - - +
193M THR* 3.0 49.2 + - + +
195M GLU* 3.7 32.9 + - + +
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Residues in contact with ILE 150 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149M LYS* 1.3 74.5 - - - +
151M ASP* 1.3 75.5 + - - +
153M SER* 2.7 24.4 + - - +
155M ARG* 3.4 47.3 - - + +
179M LEU* 4.2 6.5 - - + -
181M LEU* 3.9 22.9 - - + -
185M GLU 5.8 0.2 - - - +
189M HIS* 3.7 30.0 + - + -
191M SER 3.5 2.2 - - - +
192M TYR* 3.2 33.9 - - + +
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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