Contacts of the strand formed by residues 197 - 204 (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 197 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C THR* 3.9 35.2 - - + +
167C GLY* 3.9 27.4 - - - +
168C TYR 3.6 2.9 - - - +
169C PHE* 4.0 7.6 - - + -
192C VAL 3.9 0.5 - - - +
193C LEU* 3.6 4.8 - - - +
194C GLN* 2.9 33.8 + - - +
195C SER* 4.0 8.3 - - - +
196C GLY* 1.3 87.7 - - - +
198C TYR* 1.3 62.1 + - - +
199C THR* 5.0 1.3 + - - -
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Residues in contact with TYR 198 (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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167C GLY* 2.9 22.3 + - - -
168C TYR* 2.7 53.3 + + + +
169C PHE* 3.9 27.2 - + - -
171C GLU* 3.6 50.0 + - + +
191C ALA* 4.0 7.2 - - + -
192C VAL 3.2 14.8 - - - +
193C LEU* 3.9 35.4 - - + +
197C LEU* 1.3 75.0 - - - +
199C THR* 1.3 61.7 + - - +
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Residues in contact with THR 199 (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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164C LEU* 3.5 30.3 - - + -
165C VAL 3.3 7.9 - - - +
166C LYS* 3.6 12.3 - - + +
167C GLY* 3.2 19.6 + - - -
168C TYR* 4.1 0.7 - - - -
191C ALA* 3.2 2.3 - - - -
192C VAL* 2.9 42.6 + - - +
197C LEU 4.1 1.2 + - - -
198C TYR* 1.3 72.3 + - - +
200C LEU* 1.3 64.3 + - - +
153D THR* 5.5 3.1 - - + -
198D PHE* 4.2 17.4 - - + -
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Residues in contact with LEU 200 (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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164C LEU* 3.6 2.9 - - - +
165C VAL* 2.8 51.7 + - + +
168C TYR* 3.4 24.4 - - + +
171C GLU* 4.9 2.0 - - - +
173C VAL* 3.6 24.5 - - + +
175C VAL* 4.2 2.5 - - + -
188C THR* 4.2 18.4 - - + -
189C PHE 3.4 20.6 - - - +
190C PRO* 5.1 1.3 - - + -
191C ALA* 3.7 12.3 - - + +
199C THR* 1.3 76.5 - - - +
201C THR* 1.3 81.7 + - - +
202C SER 4.1 1.1 - - - +
198D PHE* 4.2 7.2 - - - -
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Residues in contact with THR 201 (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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147C LEU* 3.6 19.6 - - + +
163C CYS 3.3 13.3 + - - +
164C LEU* 3.6 10.0 - - - +
189C PHE* 3.0 34.3 + - - +
200C LEU* 1.3 84.4 + - - +
202C SER* 1.3 75.0 + - - +
155D VAL* 3.8 4.9 - - - +
157D LEU* 4.0 31.9 - - + -
198D PHE* 3.5 24.3 - - - -
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Residues in contact with SER 202 (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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162C GLY* 3.1 3.5 - - - -
163C CYS* 2.8 33.9 + - - -
175C VAL* 3.5 32.9 - - - +
177C TRP* 3.1 21.9 + - - -
186C VAL* 4.2 0.3 - - - +
187C HIS 3.4 6.6 + - - -
188C THR* 2.8 24.7 + - - +
189C PHE* 5.0 0.2 - - - -
200C LEU* 4.1 0.8 - - - +
201C THR* 1.3 78.4 - - - +
203C SER* 1.3 61.2 + - - +
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Residues in contact with SER 203 (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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160C THR* 3.8 18.5 - - - +
161C LEU 3.2 11.4 - - - -
162C GLY* 4.6 0.2 - - - -
177C TRP* 3.9 3.8 - - - -
185C GLY 3.9 1.0 + - - +
186C VAL* 3.4 7.6 - - - +
187C HIS* 2.8 39.4 + - - +
189C PHE* 3.5 18.0 - - - -
202C SER* 1.3 75.7 - - - +
204C VAL* 1.3 62.0 + - - +
205C THR* 5.6 1.0 + - - -
157D LEU* 3.9 18.5 - - - +
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Residues in contact with VAL 204 (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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159C VAL 3.8 0.3 - - - +
160C THR* 3.3 4.5 - - - -
161C LEU* 2.9 45.6 + - + +
177C TRP* 3.6 39.0 - - + -
182C LEU* 4.2 28.0 - - + -
184C SER 4.3 4.7 - - - +
185C GLY 3.4 7.9 - - - +
186C VAL* 3.6 23.1 - - + -
203C SER* 1.3 74.5 - - - +
205C THR* 1.3 70.9 + - - +
216C VAL* 5.2 1.3 - - + -
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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