Contacts of the strand formed by residues 152 - 155 (chain B) in PDB entry 2ERY
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 THR 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B MET 4.6 2.6 + - - -
123B ILE* 3.3 21.3 - - + +
124B LEU* 3.0 25.3 + - - +
146B ALA* 4.2 0.9 - - - -
151B VAL* 1.3 78.3 - - - +
153B TYR* 1.3 73.5 + - - +
154B MET* 5.4 3.8 - - + -
170B GLU* 4.7 19.8 + - + +
174B VAL* 4.8 8.9 - - - +
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Residues in contact with TYR 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 3.6 28.4 - + - -
95B VAL* 4.1 2.6 - - - +
124B LEU* 3.4 25.1 - - + -
126B GLY* 3.7 22.4 - - - -
135B ARG* 4.7 0.3 + - - -
137B VAL* 5.3 0.5 - - - +
138B THR 4.7 1.2 + - - -
139B GLN* 3.8 18.6 - - + -
142B GLY* 3.7 13.4 - - - +
143B GLN* 3.8 26.7 - - + -
146B ALA* 3.7 15.5 - - + +
151B VAL 4.0 0.6 + - - -
152B THR* 1.3 84.1 - - - +
154B MET* 1.3 62.4 + - - +
155B GLU* 2.7 46.3 + - + +
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Residues in contact with MET 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASP* 5.9 0.4 - - - +
123B ILE* 4.7 4.0 - - + +
124B LEU 3.0 6.9 + - - -
125B ILE* 3.3 18.9 - - + +
126B GLY 3.0 21.9 + - - -
152B THR* 5.4 3.8 - - + -
153B TYR* 1.3 78.9 - - - +
155B GLU* 1.3 78.2 + - - +
156B ALA* 5.3 0.4 - - + -
163B ASN* 3.7 25.1 - - + +
166B GLN* 4.0 20.2 - - + +
167B ALA* 3.6 31.2 - - - -
170B GLU* 4.3 20.9 - - + +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 4.2 3.1 - - - +
126B GLY 3.2 7.9 - - - +
129B ALA* 4.1 11.0 - - + +
135B ARG* 2.8 42.6 + - - -
139B GLN* 3.5 28.4 - - + +
153B TYR* 2.7 39.7 + - + +
154B MET* 1.3 74.3 - - - +
156B ALA* 1.3 61.9 + - - +
162B MET* 3.9 5.4 - - + +
163B ASN* 2.8 31.4 + - - +
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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