Contacts of the strand formed by residues 141 - 147 (chain A) in PDB entry 1O9S
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 GLY 141 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A GLU 5.6 0.7 - - - -
140A THR* 1.3 76.8 - - - +
142A GLU* 1.3 64.1 + - - -
143A LYS 3.4 2.9 - - - -
144A ILE* 3.3 10.1 - - - +
157A GLY 3.6 1.6 - - - +
158A LYS* 3.5 5.5 - - - +
159A PHE 3.1 30.1 + - - +
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Residues in contact with GLU 142 (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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141A GLY* 1.3 71.7 - - - -
143A LYS* 1.3 67.9 + - + +
156A TYR* 5.0 2.1 - - - -
157A GLY* 3.1 26.4 - - - +
158A LYS* 3.2 45.7 + - - +
166A GLU* 5.5 1.0 - - - +
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Residues in contact with LYS 143 (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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130A VAL 4.5 0.5 - - - +
131A GLY* 4.4 9.2 - - - -
132A GLU 5.0 1.6 + - - -
141A GLY* 3.4 1.0 - - - -
142A GLU* 1.3 88.9 - - + +
144A ILE* 1.3 62.1 + - - +
145A ALA 4.3 0.2 + - - -
156A TYR* 3.3 37.7 - - + +
157A GLY 3.9 0.4 - - - -
182A PHE* 5.6 1.0 - - - -
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Residues in contact with ILE 144 (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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129A LEU* 5.2 0.9 - - + -
130A VAL 3.5 11.2 - - - +
131A GLY* 4.4 9.6 - - - -
132A GLU 4.3 8.3 - - - +
139A MET* 3.1 57.2 - - + +
140A THR 3.2 6.5 - - - +
141A GLY* 3.3 22.4 - - - +
143A LYS* 1.3 81.1 - - - +
145A ALA* 1.3 69.4 + - - +
156A TYR* 3.5 0.6 - - - -
157A GLY 2.9 30.6 + - - +
159A PHE* 3.3 35.3 - - + -
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Residues in contact with ALA 145 (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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128A SER 3.9 0.2 - - - +
129A LEU* 3.3 5.2 - - - +
130A VAL* 2.8 42.3 + - + +
144A ILE* 1.3 77.9 - - - +
146A TYR* 1.3 64.1 + - - +
147A VAL* 4.1 2.0 + - + -
155A LEU 3.2 11.4 - - - +
156A TYR* 3.9 10.8 - - + -
159A PHE* 3.9 6.5 - - - -
182A PHE* 3.5 36.3 - - + -
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Residues in contact with TYR 146 (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 TYR* 4.2 13.5 - + - -
127A GLY* 3.7 10.0 - - - -
128A SER 3.1 27.1 - - - -
129A LEU* 3.6 20.9 - - + -
145A ALA* 1.3 74.5 - - - +
147A VAL* 1.3 66.7 + - - +
148A TYR* 3.5 42.2 - + - -
154A ALA* 3.1 4.9 - - - +
155A LEU* 2.8 39.4 + - + +
159A PHE* 3.7 8.5 - - + -
308A PHE* 3.2 32.1 - - - -
309A VAL 4.1 3.6 + - - -
311A PRO* 3.7 44.0 - - + -
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Residues in contact with VAL 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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120A TRP* 4.9 1.3 - - + -
127A GLY* 3.2 1.6 - - - -
128A SER* 2.7 52.2 + - - +
130A VAL* 4.3 16.4 - - + -
145A ALA* 4.6 1.6 - - + -
146A TYR* 1.3 83.8 - - - +
148A TYR* 1.3 76.5 + - - +
151A GLU* 3.8 21.8 - - + -
152A ARG 3.9 4.3 - - - +
153A THR 3.5 12.3 - - - +
154A ALA* 4.1 11.2 - - + -
172A LEU* 4.2 15.7 - - + -
182A PHE* 4.3 16.4 - - + -
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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