Contacts of the strand formed by residues 146 - 151 (chain A) in PDB entry 1OWH
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 SER 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A GLY 3.7 1.1 + - - -
145A THR* 1.3 78.6 - - - +
147A CYS* 1.3 64.9 + - - +
171A VAL* 3.9 19.2 - - - +
172A VAL 3.4 5.2 - - - -
173A LYS* 3.6 27.3 + - - +
217A CYS* 4.8 2.9 - - - -
218A SER* 5.0 3.1 + - - -
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Residues in contact with CYS 147 (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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145A THR* 4.0 4.9 - - - -
146A SER* 1.3 78.5 - - - +
148A GLU* 1.3 60.8 + - - +
171A VAL* 3.4 6.5 - - - -
172A VAL* 2.9 34.6 + - + +
174A LEU* 3.8 24.7 - - + -
215A LEU* 3.8 18.4 - - + -
216A VAL 3.3 8.1 - - - +
217A CYS* 2.2 48.0 - - - +
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Residues in contact with GLU 148 (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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11A ASN 5.1 0.7 - - - +
12A GLN* 3.0 32.7 + - - -
14A TRP* 3.8 13.1 - - - -
147A CYS* 1.3 73.4 - - - +
149A ILE* 1.3 64.1 + - - +
150A THR* 4.7 2.4 + - - +
169A MET* 3.7 12.7 - - + +
170A THR 3.4 10.5 - - - +
171A VAL* 4.3 10.3 - - + -
214A PRO 3.7 0.5 - - - +
215A LEU* 3.5 5.0 - - - +
216A VAL* 3.0 48.8 + - + +
223A MET* 3.6 25.3 - - + +
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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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1A ILE* 3.9 7.0 - - + -
147A CYS 4.3 0.2 + - - -
148A GLU* 1.3 78.3 - - - +
150A THR* 1.3 67.0 + - - +
169A MET* 3.3 5.9 - - - +
170A THR* 3.1 52.2 + - + +
172A VAL* 4.5 12.6 - - + -
205A ASP 4.0 0.9 - - - -
206A SER* 3.5 30.1 - - - +
214A PRO 3.5 13.9 - - - +
215A LEU* 3.6 24.0 - - + -
229A VAL* 4.8 6.1 - - + -
244A TYR* 3.5 31.4 - - + +
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Residues in contact with THR 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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1A ILE* 4.1 6.3 - - - -
12A GLN* 3.1 38.3 + - + +
14A TRP* 5.2 0.2 + - - -
15A PHE* 3.7 22.3 - - + -
148A GLU* 4.7 3.1 + - - +
149A ILE* 1.3 80.8 + - - +
151A GLY* 1.3 58.8 + - - +
167A LEU* 3.8 27.8 - - + -
168A LYS 3.0 22.4 - - - +
169A MET* 4.4 0.2 - - + -
210A ASP* 4.6 5.4 - - - +
213A GLY* 4.5 5.0 - - - -
214A PRO* 3.9 21.2 + - - +
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Residues in contact with GLY 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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1A ILE* 3.9 5.8 + - - +
15A PHE* 4.0 15.7 - - - -
31A TYR* 5.4 0.2 - - - -
150A THR* 1.3 80.9 - - - +
152A PHE* 1.3 57.9 + - - -
153A GLY 3.8 0.7 + - - +
163A PRO* 5.3 0.3 - - - +
167A LEU* 3.8 7.4 - - - -
168A LYS* 3.1 33.1 + - - +
210A ASP* 3.3 20.4 - - - +
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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