Contacts of the strand formed by residues 148 - 153 (chain B) in PDB entry 4OMC
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 VAL 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B GLY 4.7 0.7 - - - +
147B ILE* 1.3 76.5 - - - +
149B VAL* 1.3 66.3 + - - +
168B ASP* 4.0 12.8 - - - +
171B ALA* 3.5 31.2 - - + -
220B ARG* 3.6 33.0 - - + +
246B HIS* 3.5 28.0 - - + +
247B ILE* 3.9 13.0 - - + -
248B HIS* 2.8 41.3 + - + +
249B ILE 3.1 8.1 + - - +
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Residues in contact with VAL 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 4.5 2.2 - - + -
148B VAL* 1.3 83.3 - - - +
150B SER* 1.3 68.6 + - - +
151B ILE* 4.6 5.4 - - + -
171B ALA* 4.3 1.4 - - - +
202B VAL* 4.0 30.5 - - + -
219B ALA* 4.7 5.8 - - + -
220B ARG 3.1 11.2 + - - +
221B ILE* 3.5 10.5 - - + +
222B GLY* 2.8 25.1 + - - -
249B ILE* 3.3 30.1 - - + +
251B SER* 4.9 1.3 - - - -
375B ALA* 4.4 10.5 - - + +
379B ALA* 4.2 22.2 - - + -
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Residues in contact with SER 150 (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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149B VAL* 1.3 75.1 - - - +
151B ILE* 1.3 65.2 + - - +
152B LEU* 3.7 18.2 + - - +
171B ALA 2.9 24.7 + - - -
222B GLY 3.5 4.8 + - - -
223B GLY 4.1 0.2 + - - -
224B VAL* 3.8 9.9 + - - +
247B ILE* 3.8 26.3 - - - +
249B ILE 2.9 8.0 + - - -
250B TYR* 3.5 4.9 - - - -
251B SER* 2.9 25.8 + - - -
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Residues in contact with ILE 151 (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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149B VAL* 4.6 2.5 - - + -
150B SER* 1.3 73.1 + - - +
152B LEU* 1.3 61.2 + - - +
153B ASP* 3.2 26.6 + - + +
155B GLY 5.6 2.2 - - - +
156B ILE* 5.6 1.8 - - + -
195B GLY* 3.9 15.7 - - - +
198B CYS* 4.1 15.3 - - + +
199B ALA* 3.8 17.9 - - + -
202B VAL* 3.9 18.4 - - + -
221B ILE* 3.6 27.8 - - + -
222B GLY 3.0 10.7 + - - +
223B GLY* 3.4 3.4 - - - -
224B VAL 2.9 22.9 + - - +
251B SER* 3.8 27.1 - - - +
253B SER 6.3 0.2 - - - +
372B PRO* 5.3 0.2 - - + -
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Residues in contact with LEU 152 (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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150B SER* 3.8 22.7 - - - +
151B ILE* 1.3 68.3 - - - +
153B ASP* 1.3 63.1 + - - +
224B VAL* 3.8 22.0 - - + -
226B MET* 3.9 11.0 - - + -
239B SER* 3.8 23.6 - - - +
240B LEU* 3.6 31.6 - - + -
250B TYR* 4.0 24.2 - - + -
251B SER 3.0 18.2 + - - +
252B ALA* 4.2 3.2 - - + -
254B TRP* 2.9 39.4 + - + +
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Residues in contact with ASP 153 (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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151B ILE* 3.2 12.9 + - + +
152B LEU* 1.3 76.9 - - - +
154B ASP* 1.3 71.2 + - - +
155B GLY 3.3 5.8 - - - +
194B HIS* 2.7 41.2 + - - -
195B GLY* 3.1 27.7 + - - -
198B CYS* 4.3 3.8 - - - -
224B VAL 3.0 8.9 + - - +
226B MET* 2.8 32.2 + - - +
227B LEU* 2.9 26.2 + - - +
253B SER* 4.2 11.8 + - - +
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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
------------------------------------------------------------
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