Contacts of the strand formed by residues 147 - 151 (chain A) in PDB entry 2C0O
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 PHE 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A TRP* 3.5 27.4 - + + -
137A LEU* 3.7 6.6 - - - +
145A GLY 3.7 9.9 - - - -
146A SER* 1.3 76.3 - - - +
148A MET* 1.3 72.6 + - - +
149A ILE* 4.8 2.9 - - + -
161A LEU* 4.1 7.0 - - + -
162A SER 3.0 14.4 - - - +
163A VAL* 4.5 0.2 - - - -
202A VAL* 3.8 31.9 - - + -
206A LYS* 4.5 3.1 - - - -
216A LEU* 3.6 37.0 - - + -
217A SER 3.2 25.4 - - - -
218A VAL 3.2 19.5 + - - -
219A PRO* 3.6 13.9 - - + +
220A CYS* 2.8 24.8 + - - +
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Residues in contact with MET 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TRP 3.3 7.0 - - - -
125A PHE* 3.4 47.1 - - + -
128A ILE* 4.2 6.7 - - - -
133A ALA* 3.8 28.7 - - + +
136A GLN* 4.2 12.8 - - + +
137A LEU* 4.1 11.2 - - + -
147A PHE* 1.3 78.6 - - - +
149A ILE* 1.3 67.2 + - - +
150A ARG* 4.3 6.1 - - + -
160A SER 3.5 0.7 - - - +
161A LEU* 3.5 5.2 - - - +
162A SER* 2.9 41.5 + - - -
220A CYS* 3.8 30.1 - - + -
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A TRP* 2.9 36.5 + - + +
124A PHE* 3.4 14.5 - - + -
125A PHE* 3.0 24.3 + - - -
147A PHE* 4.8 5.4 - - + -
148A MET* 1.3 74.7 - - - +
150A ARG* 1.3 66.6 + - - +
159A TYR* 3.9 15.3 - - + -
160A SER 3.2 2.9 - - - +
161A LEU* 3.8 24.9 - - + -
179A ILE* 3.7 31.4 - - + -
198A LEU* 4.6 13.5 - - + +
201A LEU* 4.5 14.8 - - + -
202A VAL* 4.9 7.9 - - + -
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Residues in contact with ARG 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 4.3 3.8 - - - -
125A PHE 3.4 17.3 - - - +
128A ILE* 3.5 22.6 + - + +
130A ARG* 3.7 16.7 - - - +
133A ALA* 3.3 21.9 - - - +
148A MET* 4.3 11.2 - - + -
149A ILE* 1.3 77.9 - - - +
151A ASP* 1.3 67.2 + - - +
159A TYR* 3.1 14.3 - - - +
160A SER* 2.9 48.4 + - - +
162A SER* 3.1 14.3 + - - -
176A HIS* 2.8 37.2 + - - +
501A PTR 2.6 41.4 + - - -
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Residues in contact with ASP 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 4.2 7.8 - - - -
125A PHE 3.8 3.4 + - - -
126A LYS* 3.7 18.5 - - - +
127A GLY* 3.3 29.8 + - - +
128A ILE 3.4 18.1 + - - +
150A ARG* 1.3 75.7 + - - +
152A SER* 1.3 68.6 + - - +
153A GLU* 3.2 4.5 + - - +
157A GLY* 6.0 0.5 - - - -
158A SER 3.8 4.4 + - - +
159A TYR* 3.4 23.7 - - - -
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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