Contacts of the strand formed by residues 166 - 171 (chain A) in PDB entry 5UV6
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 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A GLU 4.8 3.6 - - - +
165A PRO* 1.3 78.1 - - + +
167A VAL* 1.3 62.9 + - - +
168A THR* 5.6 2.2 - - - +
183A GLU 6.1 0.4 - - - -
204A ALA* 3.3 3.3 - - - -
205A LEU* 2.9 53.7 + - - +
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Residues in contact with VAL 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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157A CYS* 4.2 13.2 - - + +
159A ALA* 5.9 2.7 - - + -
165A PRO 5.3 2.0 - - - +
166A THR* 1.3 79.4 - - - +
168A THR* 1.3 72.4 + - - +
169A TRP* 4.9 0.9 - - - +
183A GLU* 3.1 31.4 + - - +
184A ASP* 3.6 11.0 - - - +
185A GLU* 3.5 36.6 - - + +
202A CYS* 3.4 32.5 - - - -
203A SER 3.3 5.4 - - - +
204A ALA* 4.7 6.5 - - + -
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Residues in contact with THR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A THR* 5.6 1.3 - - - +
167A VAL* 1.3 82.8 - - - +
169A TRP* 1.3 63.7 + - - +
170A ARG* 5.4 0.9 - - - +
180A PHE* 3.9 29.8 - - + -
182A SER 3.6 9.0 - - - -
183A GLU* 4.3 12.3 - - + +
184A ASP 5.1 0.2 - - - +
201A GLU 3.3 3.1 - - - +
202A CYS* 3.5 1.2 - - - -
203A SER* 2.9 43.4 + - - +
205A LEU* 5.4 9.6 - - + -
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Residues in contact with TRP 169 (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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141A ILE* 3.5 22.0 - - + -
142A SER* 5.4 0.2 - - - -
155A LEU* 3.8 20.0 - - + -
156A LEU 3.9 1.8 - - - -
157A CYS* 3.4 31.7 - - + +
167A VAL* 4.9 2.0 - - + +
168A THR* 1.3 76.3 - - - +
170A ARG* 1.3 59.7 + - - +
180A PHE* 3.5 7.8 - - - -
181A VAL* 3.2 20.2 + - + -
182A SER* 2.9 23.9 + - - +
184A ASP 3.3 27.4 + - - -
185A GLU 3.3 9.7 + - - -
187A LEU* 3.6 37.4 - - + +
200A TYR* 3.8 23.3 - - + -
201A GLU 3.2 15.9 - - - -
202A CYS* 4.0 9.4 - - + -
214A ARG 5.2 0.7 - - - -
216A VAL* 3.5 29.6 - - + -
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Residues in contact with ARG 170 (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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168A THR* 5.4 0.7 - - - +
169A TRP* 1.3 76.4 - - - +
171A HIS* 1.3 72.3 + - - +
172A LEU* 3.5 20.5 + - - +
179A GLY 3.5 25.8 - - - +
180A PHE* 4.2 32.1 - - + +
200A TYR* 4.4 2.2 - - - -
201A GLU* 2.9 73.7 + - - +
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Residues in contact with HIS 171 (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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170A ARG* 1.3 79.8 - - - +
172A LEU* 1.3 68.5 - - - +
173A SER* 3.3 34.2 + - - +
179A GLY* 3.1 18.6 + - - +
181A VAL* 3.8 13.9 - - + +
195A ASP 3.5 19.5 - - - -
196A GLN* 3.7 5.6 + - + +
197A SER 2.7 29.0 + - - -
199A GLU 3.7 9.6 - - - -
200A TYR* 3.4 44.8 + + + -
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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