Contacts of the strand formed by residues 150 - 155 (chain O) in PDB entry 2V16
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 150 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137O PHE* 3.4 7.3 - - - -
148O GLU* 2.5 40.1 + - + +
149O ASP* 1.4 69.9 - - - +
151O PHE* 1.2 71.7 + - - +
168O GLY 3.1 15.4 + - - -
169O GLY* 3.5 28.7 - - - +
312O GLU* 4.0 29.4 - - + +
313O PHE 3.4 9.2 - - - +
314O ASP* 4.0 22.2 - - - +
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Residues in contact with PHE 151 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O THR* 4.1 2.2 - - + -
123O MET* 3.5 44.9 - - + -
137O PHE* 3.8 33.0 - + + -
150O VAL* 1.2 81.3 - - - +
152O SER* 1.4 54.5 + - - +
153O PHE* 3.7 15.5 - + - -
165O ILE* 4.6 0.9 - - + -
166O VAL 3.2 13.9 - - - +
167O LEU* 3.8 18.4 - - + -
169O GLY 4.4 0.4 - - - -
190O TRP* 3.7 21.8 - + - -
312O GLU* 4.7 0.2 - - - -
313O PHE* 2.8 69.9 + + + +
315O ARG* 4.5 3.4 - - + -
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Residues in contact with SER 152 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151O PHE* 1.4 69.6 - - - +
153O PHE* 1.3 64.7 - - - +
164O GLN 4.4 0.2 - - - -
165O ILE* 3.3 10.4 - - - +
166O VAL 2.9 28.3 + - - -
169O GLY 3.3 17.6 + - - -
170O SER* 3.9 1.9 - - - -
310O TYR* 3.6 25.4 - - - -
311O THR 3.0 14.8 + - - -
312O GLU* 3.4 21.0 - - - +
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Residues in contact with PHE 153 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O LEU* 4.9 0.9 - - + -
31O PHE* 3.8 18.8 - - + -
33O THR* 4.4 1.6 - - + -
123O MET* 4.7 2.9 - - + -
151O PHE* 3.7 29.4 - + - -
152O SER* 1.3 79.1 - - - +
154O TYR* 1.3 59.7 + - - +
155O TYR* 3.6 26.5 - + + -
164O GLN 3.5 4.7 - - - -
165O ILE* 3.7 34.8 - - + -
216O THR* 3.3 36.6 - - + -
306O ILE* 4.3 16.9 - - + +
310O TYR* 3.6 12.7 - - - -
311O THR* 3.0 33.5 + - - +
313O PHE* 3.7 15.5 - + - -
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Residues in contact with TYR 154 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153O PHE* 1.3 73.3 - - - +
155O TYR* 1.4 74.2 + - - +
156O ASN* 3.4 33.1 + - + +
161O LEU* 3.3 26.2 - - + -
163O GLY* 2.8 35.4 - - - -
164O GLN* 3.1 20.5 + - + +
174O HIS* 3.3 46.3 + + + -
306O ILE 5.1 0.4 - - - -
310O TYR* 3.8 20.4 - + + +
325O ALA* 4.2 14.4 - - + -
326O ARG* 3.5 20.5 + - - -
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Residues in contact with TYR 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O LEU* 3.6 22.9 - - + -
14O TYR* 3.5 48.1 + + + +
31O PHE 4.1 2.8 + - - -
153O PHE* 3.6 22.2 - + - -
154O TYR* 1.4 77.4 - - - +
156O ASN* 1.6 62.5 + - - +
157O ARG* 5.0 0.7 - - - +
162O GLY 4.0 0.7 - - - -
216O THR* 2.1 42.2 + - - -
303O ALA* 3.9 30.1 - - + -
306O ILE* 4.0 30.8 + - + +
307O ARG* 3.2 26.6 + - - +
1327O C47 5.1 0.2 - - - -
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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