Contacts of the strand formed by residues 166 - 171 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLU 4.7 4.5 - - - +
165B PRO* 1.3 77.4 - - - +
167B VAL* 1.3 64.0 + - - +
168B THR* 5.7 1.7 - - - +
183B GLU 6.1 0.4 - - - -
204B ALA* 3.4 2.8 - - - -
205B LEU* 2.9 53.3 + - - +
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Residues in contact with VAL 167 (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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157B CYS* 4.4 11.7 - - + +
159B ALA* 5.9 2.0 - - + -
165B PRO 5.4 1.8 - - - +
166B THR* 1.3 78.6 - - - +
168B THR* 1.3 72.7 + - - +
169B TRP* 4.9 1.1 - - - +
183B GLU* 3.1 30.1 + - - +
184B ASP* 3.6 9.0 - - - +
185B GLU* 3.5 37.9 - - + +
202B CYS* 3.4 32.5 - - - -
203B SER 3.3 7.6 - - - +
204B ALA* 4.5 7.6 - - + -
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Residues in contact with THR 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B THR* 5.5 1.6 - - - +
167B VAL* 1.3 83.4 - - - +
169B TRP* 1.3 63.7 + - - +
170B ARG* 4.2 1.4 + - - +
180B PHE* 4.4 26.2 - - + -
182B SER 3.6 9.0 - - - -
183B GLU* 4.1 11.4 - - + +
201B GLU 3.3 2.9 - - - +
202B CYS* 3.6 0.9 - - - -
203B SER* 2.9 44.2 + - - +
205B LEU* 5.4 9.9 - - + -
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Residues in contact with TRP 169 (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 ILE* 3.6 22.4 - - + -
142B SER* 5.5 0.2 - - - -
155B LEU* 3.8 24.9 - - + -
156B LEU 3.9 1.3 - - - -
157B CYS* 3.4 31.7 - - + +
167B VAL* 4.9 2.2 - - + +
168B THR* 1.3 75.2 - - - +
170B ARG* 1.3 62.5 + - - +
171B HIS 4.3 0.2 - - - -
180B PHE* 3.8 6.8 - - - -
181B VAL* 3.3 20.6 + - + -
182B SER* 2.9 24.3 + - - +
184B ASP 3.2 27.7 + - - -
185B GLU 3.4 8.9 + - - -
187B LEU* 3.6 38.2 - - + +
200B TYR* 3.8 22.7 - - + -
201B GLU 3.2 16.2 - - - -
202B CYS* 3.9 10.1 - - + -
214B ARG 5.3 0.4 - - - -
216B VAL* 3.5 26.0 - - + -
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Residues in contact with ARG 170 (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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168B THR* 5.4 2.2 - - - +
169B TRP* 1.3 75.9 - - - +
171B HIS* 1.3 73.9 + - - +
172B LEU* 3.5 20.2 + - - +
179B GLY 3.6 26.0 - - - +
180B PHE* 4.5 23.1 - - + +
181B VAL* 4.5 0.2 - - - -
200B TYR* 3.5 2.9 - - - -
201B GLU* 2.9 69.3 + - - +
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Residues in contact with HIS 171 (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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170B ARG* 1.3 81.4 - - - +
172B LEU* 1.3 66.3 - - - +
173B SER* 3.2 29.6 + - - +
174B VAL 4.0 22.9 + - - +
179B GLY* 3.3 12.7 + - - +
181B VAL* 3.6 23.0 - - + +
195B ASP 3.5 19.5 - - - -
196B GLN* 4.1 3.9 - - + +
197B SER 2.7 28.5 + - - -
198B GLY* 4.4 0.2 - - - -
199B GLU 3.7 8.3 - - - -
200B TYR* 3.4 38.8 + + + -
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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