Contacts of the strand formed by residues 193 - 200 (chain B) in PDB entry 5FFO
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 PHE 193 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B TYR* 4.0 7.4 - - - -
121B LEU* 3.9 20.2 - - + -
158B GLY* 4.1 5.4 - - - -
159B SER 3.1 22.9 - - - -
191B PHE* 3.7 3.1 - - - +
192B GLY* 1.3 78.0 - - - +
194B LYS* 1.3 72.2 + - - +
195B HIS* 3.8 22.4 - + + -
227B ASP* 5.3 0.4 - - + -
228B ALA* 3.5 36.1 - - + +
231B GLN* 3.6 34.1 - - + -
232B ALA* 4.6 7.2 - - + -
239B ILE* 5.3 0.7 - - + -
278B LEU* 3.7 22.7 - - + -
283B GLU* 3.3 3.6 - - - +
284B TYR* 2.6 46.4 + - + +
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Residues in contact with LYS 194 (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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158B GLY* 3.5 1.4 - - - -
159B SER* 2.8 45.2 + - - +
188B LEU* 6.0 3.8 - - - +
189B PRO* 5.6 7.3 - - - +
191B PHE* 3.5 47.3 - - + +
193B PHE* 1.3 76.7 - - - +
195B HIS* 1.3 62.0 + - - +
196B ILE* 3.4 11.5 + - + +
281B LYS 5.7 0.2 - - - +
282B ASN 3.7 4.5 - - - +
283B GLU* 3.7 39.2 + - + +
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Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 2.4 42.5 + + - -
157B PHE 3.7 0.4 + - - -
193B PHE* 3.8 14.9 - - + -
194B LYS* 1.3 68.9 - - - +
196B ILE* 1.3 61.9 + - - +
197B LEU 3.3 24.2 - - - -
198B PRO* 3.5 20.9 - - + +
238B LYS 2.6 29.1 + - - -
239B ILE* 3.5 15.9 - - + +
278B LEU* 3.9 14.1 - - + -
281B LYS 4.7 0.5 - - - +
282B ASN* 2.6 53.3 + - - +
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Residues in contact with ILE 196 (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 PHE* 3.3 20.1 + - + -
159B SER* 3.4 21.1 - - - +
194B LYS* 3.4 20.8 + - + +
195B HIS* 1.3 76.7 - - - +
197B LEU* 1.3 61.9 + - - +
198B PRO* 3.5 9.9 - - - +
209B ILE* 3.9 26.6 - - + +
213B GLN* 3.5 26.7 - - - +
282B ASN* 5.2 3.3 + - - -
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Residues in contact with LEU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B TYR* 3.8 0.2 - - - -
155B LEU 4.1 10.1 - - - +
156B GLY* 3.3 3.2 - - - -
157B PHE* 2.8 41.9 + - + +
195B HIS* 3.3 8.0 - - - -
196B ILE* 1.3 77.9 - - - +
198B PRO* 1.3 83.4 - - + +
200B THR* 4.5 10.1 - - + +
202B ASP 5.3 1.8 - - - +
205B ARG* 4.5 13.5 - - + +
206B PHE* 3.7 48.2 - - + +
209B ILE* 3.6 24.2 - - + -
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Residues in contact with PRO 198 (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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156B GLY* 4.1 0.4 - - - -
195B HIS* 3.5 25.6 - - + +
196B ILE 3.5 9.2 - - - +
197B LEU* 1.3 103.0 - - + +
199B LEU* 1.3 68.2 + - - +
200B THR* 3.2 15.8 + - + +
238B LYS 4.0 9.6 - - - +
239B ILE 4.0 7.0 - - - +
282B ASN* 5.5 5.2 - - - +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 3.7 22.9 - - + +
118B LEU 4.9 1.6 - - - +
119B TYR* 5.0 6.1 - - + -
154B ARG* 3.7 28.4 + - + +
155B LEU* 3.1 26.2 - - - -
156B GLY* 3.6 5.3 - - - +
195B HIS* 5.1 0.4 - - - -
197B LEU 3.6 2.0 + - - -
198B PRO* 1.3 71.2 - - - +
200B THR* 1.3 66.1 + - - +
239B ILE* 3.5 27.9 + - + +
240B GLY* 3.1 29.5 - - - +
241B TRP* 4.1 20.6 - - + -
242B ARG* 5.2 2.5 - - + +
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Residues in contact with THR 200 (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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154B ARG* 3.2 13.0 - - - +
155B LEU* 3.0 31.0 + - - +
197B LEU* 4.5 9.2 - - + +
198B PRO* 3.5 17.6 + - + +
199B LEU* 1.3 80.6 - - - +
201B ASN* 1.3 63.5 + - - +
202B ASP* 3.5 24.4 + - - +
205B ARG* 5.8 0.7 - - - +
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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