Contacts of the strand formed by residues 141 - 147 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B GLU 5.8 0.2 - - - -
140B THR* 1.3 77.8 - - - +
142B GLU* 1.3 64.9 + - - -
143B LYS 3.4 3.1 - - - -
144B ILE* 3.1 10.7 - - - +
157B GLY 3.5 1.7 - - - +
158B LYS* 3.3 4.4 - - - +
159B PHE 3.1 29.3 + - - +
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Residues in contact with GLU 142 (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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141B GLY* 1.3 72.6 - - - -
143B LYS* 1.3 67.1 + - + +
156B TYR* 4.5 4.3 - - - -
157B GLY* 3.2 24.3 - - - +
158B LYS* 3.3 41.5 + - - +
166B GLU* 5.2 2.8 - - - +
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Residues in contact with LYS 143 (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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130B VAL 4.4 0.5 - - - +
131B GLY* 4.3 9.9 - - - -
132B GLU 5.1 1.2 + - - -
141B GLY* 3.4 1.2 - - - -
142B GLU* 1.3 88.8 - - + +
144B ILE* 1.3 63.5 + - - +
145B ALA 4.3 0.2 + - - -
156B TYR* 3.1 36.3 - - + +
182B PHE* 5.7 0.9 - - - -
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Residues in contact with ILE 144 (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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129B LEU* 5.4 0.2 - - + -
130B VAL 3.5 3.1 - - - -
131B GLY* 4.3 12.1 - - - -
132B GLU 4.7 6.5 - - - +
139B MET* 3.3 47.3 - - + +
140B THR 3.2 9.2 - - - +
141B GLY* 3.1 35.2 - - - +
143B LYS* 1.3 83.2 - - - +
145B ALA* 1.3 67.3 + - - +
156B TYR* 3.5 2.4 - - - -
157B GLY 2.8 31.4 + - - +
159B PHE* 3.4 38.6 - - + -
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Residues in contact with ALA 145 (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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128B SER 3.8 0.2 - - - +
129B LEU* 3.4 3.8 - - - +
130B VAL* 2.8 41.0 + - + +
144B ILE* 1.3 79.0 - - - +
146B TYR* 1.3 64.5 + - - +
147B VAL* 4.0 1.3 + - + -
155B LEU 3.3 10.5 - - - +
156B TYR* 3.8 9.4 - - + -
159B PHE* 4.1 4.9 - - - -
182B PHE* 3.5 40.6 - - + -
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Residues in contact with TYR 146 (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 TYR* 4.0 14.8 - + - -
127B GLY* 3.7 8.8 - - - -
128B SER 3.3 20.4 - - - -
129B LEU* 3.5 18.4 - - + -
145B ALA* 1.3 73.6 - - - +
147B VAL* 1.3 70.4 + - - +
148B TYR* 3.6 41.8 - + - -
149B PRO* 4.0 0.2 - - - +
154B ALA* 3.1 4.9 - - - +
155B LEU* 2.8 40.2 + - + +
159B PHE* 3.7 8.9 - - + -
308B PHE* 3.2 31.5 - - - -
309B VAL 4.0 3.7 + - - -
311B PRO* 3.6 48.7 - - + -
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Residues in contact with VAL 147 (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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120B TRP* 4.7 6.1 - - + -
122B TYR* 6.5 0.4 - - + -
127B GLY* 3.2 1.7 - - - -
128B SER* 2.7 47.1 + - - +
130B VAL* 3.9 23.6 - - + -
145B ALA* 4.5 1.3 - - + -
146B TYR* 1.3 81.5 - - - +
148B TYR* 1.3 74.4 + - - +
151B GLU* 3.7 26.9 - - + -
152B ARG 4.0 1.3 - - - +
153B THR 3.6 10.1 - - - +
154B ALA* 4.1 0.7 - - + -
172B LEU* 5.3 5.8 - - + -
182B PHE* 4.1 27.8 - - + -
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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