Contacts of the strand formed by residues 153 - 160 (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 THR 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B VAL* 3.6 2.6 - - - +
148B TYR* 2.8 54.1 + - + -
150B ASP* 2.7 31.0 + - - -
152B ARG* 1.3 77.5 - - - +
154B ALA* 1.3 57.4 + - - +
169B LEU* 3.8 23.3 - - + -
170B ALA 3.8 4.5 - - - +
171B THR* 5.0 0.9 - - - +
210B PRO* 5.1 0.4 - - + -
211B TYR* 4.4 10.7 - - - +
214B GLU* 3.5 24.7 + - - +
215B ARG* 4.1 0.2 + - - -
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ALA* 4.5 3.6 - - + -
146B TYR 3.1 13.2 - - - +
147B VAL* 4.1 5.2 - - + -
148B TYR* 4.4 2.0 - - - -
152B ARG 4.4 2.0 - - - +
153B THR* 1.3 76.6 - - - +
155B LEU* 1.3 72.7 + - - +
156B TYR 3.9 0.4 - - - -
169B LEU* 3.5 2.9 - - - +
170B ALA* 2.9 36.6 + - + +
182B PHE* 3.6 37.9 - - + -
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Residues in contact with LEU 155 (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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145B ALA* 3.3 2.1 - - - -
146B TYR* 2.8 36.6 + - + +
148B TYR* 3.7 31.9 - - + +
154B ALA* 1.3 82.6 - - - +
156B TYR* 1.3 59.9 + - - +
159B PHE* 3.6 8.0 - - - -
164B MET* 3.6 38.8 - - + -
167B GLY* 4.4 4.3 - - - -
168B LYS 3.5 3.4 - - - -
169B LEU* 4.2 7.6 - - + -
191B TYR* 3.9 36.3 - - + -
210B PRO* 4.3 6.5 - - + -
310B HIS* 5.4 2.5 - - + -
311B PRO* 3.9 13.9 - - + -
312B ARG* 5.7 0.4 - - + -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B GLU 4.5 4.5 - - - -
143B LYS* 3.1 57.6 - - + +
144B ILE 3.5 10.1 - - - -
145B ALA* 3.8 7.9 - - + -
155B LEU* 1.3 73.8 - - - +
157B GLY* 1.3 59.7 + - - +
166B GLU 3.8 0.2 - - - +
167B GLY* 3.6 2.6 - - - -
168B LYS* 2.8 44.6 + - - +
170B ALA* 4.0 15.7 - - + -
182B PHE* 3.3 42.2 - + + -
184B LEU* 4.4 18.6 - - + -
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Residues in contact with GLY 157 (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 3.5 1.4 - - - +
142B GLU 3.2 20.7 - - - +
144B ILE 2.8 36.0 + - - +
156B TYR* 1.3 81.1 - - - +
158B LYS* 1.3 62.7 + - - -
159B PHE* 3.5 4.1 - - - -
166B GLU* 3.3 7.4 - - - -
168B LYS* 5.8 0.9 - - - -
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Residues in contact with LYS 158 (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 3.3 10.3 - - - +
142B GLU* 3.3 34.4 + - - +
157B GLY* 1.3 70.7 - - - -
159B PHE* 1.3 68.3 + - - +
160B ILE* 4.4 22.0 - - + +
165B ILE* 2.9 44.2 + - + +
166B GLU* 3.0 29.3 + - + +
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Residues in contact with PHE 159 (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* 5.0 6.7 - - + -
139B MET 3.8 6.1 - - - +
140B THR* 3.4 1.0 - - - +
141B GLY 3.1 28.2 + - - +
144B ILE* 3.4 52.3 - - + -
145B ALA 4.1 0.7 - - - -
146B TYR* 3.7 22.0 - - + -
155B LEU 3.6 19.7 - - - -
156B TYR 4.6 0.7 - - - -
157B GLY* 3.5 12.6 - - - -
158B LYS* 1.3 83.1 - - - +
160B ILE* 1.3 69.8 + - - +
162B GLY* 3.9 14.1 - - - -
163B GLU 3.0 9.0 - - - +
164B MET* 3.6 45.5 - - + -
165B ILE* 4.3 0.4 - - - -
167B GLY* 5.0 0.7 - - - -
311B PRO* 5.0 2.5 - - + -
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Residues in contact with ILE 160 (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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140B THR* 4.0 16.8 - - + +
158B LYS* 4.4 18.6 - - - -
159B PHE* 1.3 79.3 - - - +
161B ASP* 1.3 77.5 + - + +
162B GLY 3.2 0.4 - - - -
163B GLU* 2.8 27.0 + - - +
165B ILE* 3.7 29.6 - - + +
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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