Contacts of the strand formed by residues 179 - 184 (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 ARG 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLY 4.7 12.8 - - - +
118A VAL* 3.8 23.8 - - + +
132A GLU* 5.1 9.0 + - - -
175A THR* 3.1 1.5 - - - -
176A GLU* 2.6 41.9 + - + +
177A GLU* 3.8 10.8 + - - +
178A GLY* 1.3 75.8 - - - +
180A PRO* 1.3 66.3 - - + +
181A HIS* 3.0 18.4 + - + +
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Residues in contact with PRO 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A VAL* 4.0 11.2 - - + -
120A TRP* 3.7 10.1 - - + -
130A VAL* 3.5 28.3 - - + -
131A GLY* 5.5 2.0 - - - +
172A LEU* 3.6 20.4 - - + -
174A SER 3.5 6.3 - - - +
175A THR* 4.0 2.7 - - - +
178A GLY 3.6 4.7 - - - +
179A ARG* 1.3 87.6 - - + +
181A HIS* 1.3 70.7 + - - +
182A PHE* 3.7 24.5 + - + -
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Residues in contact with HIS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A LEU* 3.8 2.1 - - - +
173A MET* 2.8 38.5 + - + +
174A SER* 2.8 36.3 + - - +
176A GLU* 3.2 29.5 - - + +
179A ARG* 3.0 36.4 + - + -
180A PRO* 1.3 79.6 + - - +
182A PHE* 1.3 62.2 + - - +
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Residues in contact with PHE 182 (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* 5.3 3.1 - - + -
143A LYS 5.6 1.1 - - - -
145A ALA* 3.5 18.2 - - + -
147A VAL* 4.3 8.7 - - + -
154A ALA* 3.5 30.1 - - + -
156A TYR* 3.4 43.3 - + + -
170A ALA* 4.3 13.0 - - + -
171A THR 3.3 7.2 - - - +
172A LEU* 3.7 28.9 - - + -
173A MET* 3.9 8.6 - - - +
180A PRO* 3.7 36.8 - - + -
181A HIS* 1.3 75.5 - - - +
183A GLU* 1.3 59.8 + - - +
184A LEU* 4.1 1.6 + - + -
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Residues in contact with GLU 183 (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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152A ARG* 5.9 0.3 + - - -
170A ALA* 3.2 6.4 - - - -
171A THR* 2.9 57.0 + - - +
173A MET* 3.7 29.3 - - + +
182A PHE* 1.3 73.9 - - - +
184A LEU* 1.3 60.8 + - - +
185A MET* 3.2 27.1 + - - +
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Residues in contact with LEU 184 (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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156A TYR* 4.5 22.7 - - + -
168A LYS* 3.5 51.1 - - + +
169A LEU 3.6 11.4 - - - +
170A ALA* 4.4 5.2 - - + -
182A PHE* 4.1 1.6 + - + -
183A GLU* 1.3 74.4 - - - +
185A MET* 1.3 69.1 + - - +
186A PRO* 4.0 1.9 - - - +
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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