Contacts of the strand formed by residues 160 - 167 (chain A) in PDB entry 3THY
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 GLN 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A MET* 3.0 6.1 - - - +
153A SER 2.7 51.6 + - - +
155A VAL* 4.0 24.7 - - + +
158A GLN* 4.9 2.3 - - - +
159A ARG* 1.3 75.4 - - - +
161A VAL* 1.3 62.7 + - - +
162A GLY 4.0 0.4 + - - -
177A GLU* 3.3 40.3 + - + +
178A PHE* 3.6 13.4 - - - +
179A PRO* 3.4 27.0 - - - +
265A VAL* 4.6 2.1 - - + +
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 4.3 9.9 - - + -
151A LYS 3.7 7.2 - - - +
152A MET* 4.0 22.7 - - + -
159A ARG* 4.7 3.1 - - + -
160A GLN* 1.3 75.0 - - - +
162A GLY* 1.3 61.7 + - - +
163A VAL* 4.1 13.5 - - + -
176A CYS 3.9 1.2 - - - +
177A GLU* 3.5 3.4 - - - -
178A PHE* 2.6 68.0 + - + +
180A ASP* 4.4 15.5 - - + +
184A PHE* 4.6 11.4 - - + -
187A LEU* 4.3 7.2 - - + -
213A LEU* 5.2 4.0 - - + -
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Residues in contact with GLY 162 (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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150A VAL* 3.5 1.6 - - - +
151A LYS 2.9 32.8 + - - +
161A VAL* 1.3 73.1 - - - +
163A VAL* 1.3 64.8 + - - +
176A CYS 3.7 3.1 - - - -
177A GLU* 4.2 3.4 - - - -
265A VAL* 3.4 25.2 - - - +
266A ALA* 3.6 12.8 - - - -
269A SER* 3.2 5.0 + - - -
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Residues in contact with VAL 163 (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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148A VAL* 3.6 26.2 - - + -
149A GLY 3.2 3.4 - - - +
150A VAL* 4.1 8.7 - - + -
161A VAL* 4.1 9.4 - - + -
162A GLY* 1.3 80.8 - - - +
164A GLY* 1.3 61.9 + - - +
165A TYR* 4.8 1.3 - - + -
175A LEU 3.7 1.0 - - - -
176A CYS* 2.6 45.7 + - + +
178A PHE* 4.3 1.1 - - + -
187A LEU* 3.9 21.8 - - + -
190A LEU* 3.7 31.2 - - + -
191A LEU* 5.7 0.9 - - + -
194A ILE* 4.7 6.7 - - + -
266A ALA* 3.5 7.8 - - - +
269A SER* 3.9 2.9 - - - -
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Residues in contact with GLY 164 (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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148A VAL* 3.2 4.5 - - - +
149A GLY* 2.6 39.4 + - - -
163A VAL* 1.3 75.9 - - - +
165A TYR* 1.3 62.4 + - - -
174A GLY 3.5 6.5 - - - -
266A ALA 4.2 0.4 - - - -
269A SER* 3.3 3.4 - - - -
270A LEU* 3.6 24.2 - - - -
273A VAL* 3.7 7.1 - - - +
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Residues in contact with TYR 165 (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 ILE* 3.4 34.1 - - + -
147A VAL 3.6 7.9 - - - +
148A VAL* 3.7 8.5 - - + +
163A VAL* 4.8 5.4 - - + -
164A GLY* 1.3 75.7 - - - +
166A VAL* 1.3 67.9 + - - +
167A ASP* 4.6 13.5 - - + -
172A LYS* 5.1 3.0 - - + +
173A LEU* 3.6 1.7 - - - -
174A GLY* 2.7 68.6 + - - +
175A LEU* 4.1 3.6 - - - -
176A CYS* 5.4 0.7 - - + -
194A ILE* 3.5 28.3 - - + -
270A LEU* 3.8 4.7 - - - +
273A VAL* 4.7 3.4 - - - -
292A THR* 4.3 8.6 + - - -
294A PHE* 3.4 34.4 - + + +
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Residues in contact with VAL 166 (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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144A SER 3.9 0.3 - - - +
145A ILE* 2.9 24.3 - - - +
146A GLY 4.4 1.4 + - - -
147A VAL* 4.2 2.4 + - - +
165A TYR* 1.3 80.7 - - - +
167A ASP* 1.3 59.9 + - - +
168A SER* 3.5 18.2 + - - +
172A LYS 3.8 2.7 - - - -
173A LEU* 3.7 25.8 - - + -
270A LEU* 4.2 9.2 - - + -
273A VAL* 4.0 13.0 - - + +
274A ILE* 4.6 2.2 - - + -
277A LEU* 3.5 33.8 - - + +
279A LEU* 4.1 16.4 - - + -
289A PHE* 4.1 10.8 - - + -
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Residues in contact with ASP 167 (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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144A SER* 3.0 37.7 + - - +
145A ILE* 4.0 13.3 - - + +
165A TYR* 4.2 9.6 - - + -
166A VAL* 1.3 70.5 - - - +
168A SER* 1.3 56.6 + - - +
170A GLN* 3.1 34.0 + - - +
171A ARG* 2.9 24.4 + - - -
172A LYS* 2.8 33.0 + - + +
289A PHE* 4.1 0.5 - - - -
344A GLN* 5.2 3.8 - - - +
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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