Contacts of the strand formed by residues 193 - 198 (chain B) in PDB entry 3K74
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 MET 193 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163B LEU* 3.8 28.5 - - + -
181B CYS* 5.5 0.4 - - - -
186B PHE* 4.1 16.6 - - + -
188B PHE* 3.8 19.1 - - + -
191B TYR* 3.7 3.3 + - - -
192B TRP* 1.3 79.8 - - - +
194B TYR* 1.3 65.5 + - - +
209B MET* 3.2 4.7 - - - +
210B ILE* 2.9 36.3 + - + +
229B ILE* 4.0 0.6 - - - +
231B ARG* 3.6 24.5 - - - +
238B LEU* 3.7 30.3 - - + -
255B CYS* 4.9 1.8 - - + -
256B ALA 3.5 24.7 - - - +
257B LYS* 4.1 13.5 - - + +
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Residues in contact with TYR 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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21A PRO* 3.8 14.6 - - + -
148A SER* 3.6 15.8 + - - -
149A HIS* 3.2 25.3 + + - -
192B TRP* 3.8 27.6 - - + +
193B MET* 1.3 76.7 - - - +
195B TRP* 1.3 64.7 + - - +
196B VAL* 4.3 7.6 - - + -
206B TRP* 5.6 2.5 - + + -
208B SER 3.2 8.7 - - - +
209B MET* 3.6 34.5 - - + +
229B ILE* 4.7 0.2 - - - -
238B LEU* 3.8 4.4 - - - +
255B CYS* 3.2 5.9 - - - -
256B ALA* 2.9 44.5 + - + +
258B ASP* 4.3 4.2 - - - -
259B TRP* 3.5 50.0 + + + -
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Residues in contact with TRP 195 (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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165B GLU* 4.0 10.3 - - + -
179B LEU* 3.8 24.0 - - + -
180B SER 3.8 22.7 - - - -
181B CYS* 3.9 11.9 - - + -
194B TYR* 1.3 73.0 - - - +
196B VAL* 1.3 65.6 + - - +
206B TRP* 3.8 0.5 - - - +
207B VAL* 2.8 28.3 + - + -
208B SER* 2.8 18.5 + - - +
229B ILE* 3.6 28.3 - - + -
238B LEU* 3.4 35.1 - - + +
239B TYR 3.1 17.8 + - - -
240B LEU* 3.6 39.3 - - + -
253B TYR* 4.4 8.5 - - + -
254B TYR 3.4 27.4 - - - -
255B CYS 3.8 12.8 - - - -
270B THR* 5.1 0.2 - - + -
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Residues in contact with VAL 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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194B TYR* 4.3 9.2 - - + -
195B TRP* 1.3 81.7 - - - +
197B ARG* 1.3 61.8 + - - +
204B LEU* 4.0 18.6 - - + -
205B GLU 3.4 13.5 - - - +
206B TRP* 3.9 11.2 - - + -
207B VAL* 4.2 1.8 - - - +
253B TYR* 3.4 6.9 - - - +
254B TYR* 2.8 50.1 + - + +
256B ALA* 4.7 4.3 - - + -
259B TRP* 3.8 48.5 - - + -
266B LYS* 4.5 4.0 - - + -
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Residues in contact with ARG 197 (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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196B VAL* 1.3 77.4 - - - +
198B ARG* 1.3 59.7 + - - +
199B ALA* 4.1 5.4 + - + +
203B GLY 3.8 0.7 - - - +
204B LEU* 3.4 5.9 - - - -
205B GLU* 2.8 68.2 + - + +
207B VAL* 3.6 18.9 - - + +
222B SER* 3.5 20.8 + - - -
223B VAL* 4.1 11.4 - - - +
227B PHE* 4.2 2.0 - - - -
248B GLU* 4.1 14.3 + - - +
249B ASP* 3.0 27.2 + - - +
251B ALA* 3.8 13.7 - - + -
252B VAL 3.2 10.3 - - - +
253B TYR* 2.8 51.0 + - + -
254B TYR* 4.5 0.4 - - - -
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Residues in contact with ARG 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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197B ARG* 1.3 72.3 - - - +
199B ALA* 1.3 65.8 + - - +
200B PRO* 4.0 0.7 - - - +
201B GLY 6.2 0.4 - - - +
202B LYS 3.4 23.2 + - - +
203B GLY 4.0 6.0 - - - +
204B LEU* 3.9 18.3 - - + +
251B ALA* 3.4 3.4 - - - -
252B VAL* 2.7 39.3 + - + +
254B TYR* 2.0 38.0 + - + -
266B LYS* 3.2 25.3 - - - +
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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