Contacts of the strand formed by residues 178 - 182 (chain A) in PDB entry 2ASB
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 LEU 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLY 6.1 0.4 - - - -
145A VAL* 3.8 24.7 - - + -
169A GLY 3.5 1.4 - - - +
170A VAL* 3.2 5.4 - - - +
171A THR* 2.4 63.6 + - - +
173A GLY* 4.2 2.7 - - - +
176A GLU 3.7 2.2 + - - -
177A PRO* 1.3 69.8 - - - +
179A ILE* 1.3 63.6 + - - +
180A THR* 3.5 20.2 - - - +
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A SER* 5.8 3.6 - - - +
109A THR* 4.8 15.7 - - - +
135A ILE* 3.8 21.8 - - + -
142A SER* 3.5 26.5 - - - +
143A GLU 3.9 13.0 + - - +
144A GLY* 3.2 2.0 - - - -
145A VAL* 3.0 28.9 + - - +
167A VAL* 4.2 13.9 - - + -
169A GLY 3.4 6.3 - - - +
170A VAL* 4.4 16.4 - - + -
177A PRO* 3.6 11.7 + - + +
178A LEU* 1.3 78.9 - - - +
180A THR* 1.3 59.9 + - - +
181A LEU* 3.8 24.9 - - + -
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Residues in contact with THR 180 (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 VAL* 3.6 5.5 - - + +
147A PRO* 3.7 30.5 - - + -
150A GLU* 5.2 0.7 - - + -
167A VAL* 3.7 4.5 - - - +
168A VAL* 2.8 45.9 + - + -
169A GLY* 2.6 23.1 + - - +
171A THR* 5.1 0.9 + - - -
178A LEU* 3.5 23.9 - - - +
179A ILE* 1.3 71.4 - - - +
181A LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 181 (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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115A VAL* 3.7 24.2 - - + -
133A VAL* 3.7 37.9 - - + -
135A ILE* 4.5 7.6 - - + -
144A GLY* 3.9 21.3 - - - -
145A VAL 2.8 13.0 + - - +
146A ILE* 3.5 12.5 - - + +
147A PRO* 3.4 22.2 - - - +
150A GLU* 3.6 2.8 - - - +
165A CYS* 3.9 16.8 - - + -
166A TYR 3.3 5.4 - - - +
167A VAL* 3.9 13.0 - - + -
168A VAL* 4.2 2.0 - - - +
179A ILE* 3.8 20.0 - - + -
180A THR* 1.3 75.4 - - - +
182A SER* 1.3 62.7 + - - +
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Residues in contact with SER 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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146A ILE* 4.3 1.6 - - - -
150A GLU* 2.7 32.1 + - - -
165A CYS* 3.8 6.2 - - - -
166A TYR* 2.8 36.9 + - - +
168A VAL* 3.5 20.6 - - - -
181A LEU* 1.3 76.6 - - - +
183A ARG* 1.3 65.7 + - - +
184A THR* 3.1 2.1 + - - -
185A HIS* 3.1 25.2 + - - +
188A LEU* 4.0 1.7 - - - +
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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