Contacts of the strand formed by residues 147 - 151 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TRP* 3.6 22.0 - + + -
125B PHE* 4.7 0.2 - - - -
137B LEU* 4.0 5.6 - - - +
145B GLY 3.5 15.5 - - - +
146B SER* 1.3 77.3 - - - +
148B MET* 1.3 70.4 + - - +
149B ILE* 5.1 1.3 - - + -
161B LEU* 4.2 7.4 - - + -
162B SER 3.1 13.9 - - - +
163B VAL* 4.1 1.8 - - + -
202B VAL* 4.2 21.1 - - + -
206B LYS* 4.4 5.4 - - - -
216B LEU* 3.7 48.0 - - + -
217B SER 3.7 14.4 - - - -
218B VAL 3.5 9.7 + - - -
219B PRO* 3.4 37.4 - - + +
220B CYS* 2.9 23.3 + - - +
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Residues in contact with MET 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TRP 3.5 6.5 - - - -
125B PHE* 3.5 39.5 - - + -
128B ILE* 4.4 4.7 - - + -
133B ALA* 3.7 27.4 - - - +
136B GLN* 4.1 17.3 - - + +
137B LEU* 4.2 8.1 - - + -
147B PHE* 1.3 83.6 - - - +
149B ILE* 1.3 63.8 + - - +
150B ARG* 4.3 11.0 - - - -
161B LEU* 3.5 7.3 - - - +
162B SER* 3.0 41.7 + - - +
220B CYS* 3.5 34.1 - - + -
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Residues in contact with ILE 149 (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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123B TRP* 2.7 31.7 + - + +
124B PHE* 3.4 20.6 - - + -
125B PHE* 3.0 26.0 + - - -
147B PHE* 5.1 1.6 - - + -
148B MET* 1.3 74.3 - - - +
150B ARG* 1.3 65.2 + - - +
159B TYR* 4.2 17.3 - - + -
160B SER 3.1 9.2 - - - +
161B LEU* 3.4 30.7 - - + -
179B ILE* 3.8 20.2 - - + -
198B LEU* 4.5 14.6 - - + -
201B LEU* 4.4 5.4 - - + -
202B VAL* 4.4 17.7 - - + -
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Residues in contact with ARG 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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124B PHE* 4.3 3.8 - - - -
125B PHE 3.5 16.4 - - - +
128B ILE* 3.4 30.4 + - + +
129B SER* 4.5 0.2 - - - +
130B ARG* 3.6 16.2 - - - +
133B ALA* 3.7 19.2 - - - +
148B MET* 4.3 9.4 - - + -
149B ILE* 1.3 77.9 - - - +
151B ASP* 1.3 69.0 + - - +
153B GLU 4.6 0.4 - - - +
159B TYR* 3.3 10.5 - - - -
160B SER* 2.8 48.2 + - - +
162B SER* 2.9 18.2 + - - +
176B HIS* 3.0 28.7 + - - -
501B PTR 2.6 38.7 + - - -
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Residues in contact with ASP 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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124B PHE* 3.7 17.0 - - - -
125B PHE 4.1 2.6 + - - -
126B LYS* 3.6 13.8 + - - +
127B GLY* 2.8 33.6 + - - +
128B ILE 3.5 18.7 + - - +
150B ARG* 1.3 78.1 + - - +
152B SER* 1.3 69.3 + - - +
153B GLU* 3.6 0.9 + - - -
156B LYS* 6.2 0.7 - - - +
157B GLY 6.3 0.7 - - - +
158B SER 3.8 6.1 - - - +
159B TYR* 3.7 11.5 - - - -
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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