Contacts of the strand formed by residues 161 - 168 (chain C) in PDB entry 4YO0
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 161 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C LEU 3.5 7.0 - - - +
148C ALA* 5.1 0.2 - - + -
149C PRO* 3.4 32.5 - - + -
159C VAL* 4.1 19.1 - - + +
160C THR* 1.3 78.9 - - - +
162C GLY* 1.3 59.7 + - - +
177C TRP* 4.0 3.4 - - + -
203C SER* 3.2 5.0 - - - -
204C VAL* 2.9 41.6 + - + +
216C VAL* 3.3 35.4 - - + -
233C ILE* 4.0 24.9 - - + +
140D PHE* 4.4 2.0 - - - -
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Residues in contact with GLY 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C LEU* 2.8 46.3 + - - +
161C LEU* 1.3 75.2 - - - +
163C CYS* 1.3 69.2 + - - -
177C TRP* 3.8 3.4 - - - -
201C THR* 4.7 0.7 - - - -
202C SER 3.1 10.8 - - - -
203C SER* 4.2 3.4 - - - -
233C ILE* 3.4 6.9 - - - +
140D PHE* 4.2 3.5 - - - -
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Residues in contact with CYS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C VAL* 4.6 7.6 - - + -
145C TYR 3.5 8.3 - - - +
147C LEU* 3.9 3.1 - - - +
162C GLY* 1.3 79.7 - - - -
164C LEU* 1.3 61.4 + - - +
165C VAL* 3.8 5.1 + - + +
175C VAL* 5.0 3.6 - - + -
177C TRP* 3.8 3.6 - - + -
201C THR* 3.3 5.2 - - - +
202C SER* 2.8 30.8 + - - +
218C CYS* 2.0 52.9 - - + -
220C VAL* 4.8 5.4 - - + -
231C LYS* 4.2 5.6 - - - -
233C ILE* 3.7 16.2 - - - -
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Residues in contact with LEU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143C SER 3.4 1.4 - - - +
144C VAL* 3.3 6.6 - - - +
145C TYR* 2.8 59.0 + - + +
147C LEU* 3.8 20.0 - - + +
163C CYS* 1.3 71.8 - - - +
165C VAL* 1.3 59.6 + - - +
166C LYS* 4.2 10.8 - - + -
199C THR* 3.5 32.3 - - + -
200C LEU 3.6 4.0 - - - +
201C THR* 3.6 16.6 - - - +
146D GLU* 4.4 5.2 - - - +
153D THR* 3.9 28.0 - - + +
155D VAL* 4.5 7.9 - - + -
198D PHE* 3.9 10.3 - - + -
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C PRO* 3.5 25.1 - - + -
143C SER 3.6 2.7 - - - -
144C VAL* 4.5 2.9 - - + -
163C CYS* 4.2 8.7 - - + +
164C LEU* 1.3 75.6 - - - +
166C LYS* 1.3 58.9 + - - +
168C TYR* 3.7 13.9 - - + -
173C VAL* 4.2 7.2 - - + -
175C VAL* 4.3 6.3 - - + -
199C THR* 3.3 4.4 - - - -
200C LEU* 2.8 58.2 + - + +
220C VAL* 3.9 41.5 - - + -
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142C PRO* 3.4 1.6 - - - +
143C SER* 2.8 45.4 + - - +
145C TYR* 4.1 19.0 + - + +
164C LEU* 4.2 15.3 - - + -
165C VAL* 1.3 72.5 - - - +
167C GLY* 1.3 68.6 + - - +
168C TYR 3.8 0.7 - - - -
199C THR* 3.6 16.4 - - + +
146D GLU* 2.7 30.3 + - - +
151D LYS* 3.7 29.6 - - - +
152D ALA 5.1 0.2 - - - +
153D THR* 3.6 13.6 + - + +
200D ARG* 5.8 11.0 - - - +
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Residues in contact with GLY 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C THR* 3.3 22.2 - - - +
141C ALA 3.4 8.3 - - - +
142C PRO* 4.3 0.2 - - - -
166C LYS* 1.3 76.0 - - - +
168C TYR* 1.3 57.3 + - - -
197C LEU* 3.9 25.8 - - - +
198C TYR 2.9 16.2 + - - -
199C THR* 3.2 7.8 + - - -
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Residues in contact with TYR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C THR 3.3 11.7 - - - +
142C PRO* 3.7 20.4 - - + -
165C VAL* 3.7 28.5 - - + -
167C GLY* 1.3 75.2 - - - +
169C PHE* 1.3 64.0 + - - +
170C PRO 3.7 17.5 - - - -
171C GLU* 2.7 29.8 + - - -
173C VAL* 3.3 32.3 - - + +
191C ALA* 3.5 9.4 - - - +
197C LEU* 3.6 2.9 - - - -
198C TYR* 2.7 72.0 + + + -
199C THR* 4.1 2.7 - - - -
200C LEU* 3.4 23.3 - - + +
222C HIS* 3.9 3.4 - - - +
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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