Contacts of the strand formed by residues 192 - 200 (chain D) in PDB entry 5BUG
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 ALA 192 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D PRO 4.0 2.8 + - - -
191D VAL* 1.3 75.2 - - - +
193D LEU* 1.3 66.3 + - - +
249D VAL 3.7 7.6 - - - +
250D CYS* 4.3 13.8 - - + -
349D LYS* 4.5 1.0 - - - +
350D THR* 3.7 33.0 + - + +
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191D VAL* 4.1 19.7 - - + +
192D ALA* 1.3 81.5 - - - +
194D LEU* 1.3 64.7 + - - +
248D PRO* 3.7 3.8 - - - +
249D VAL* 3.0 39.9 + - + +
277D THR* 3.5 33.4 - - + +
280D ILE* 3.9 20.9 - - + +
316D LEU* 4.2 12.1 - - + -
347D PHE* 4.1 17.0 - - + -
348D THR 3.4 15.9 - - - +
349D LYS* 3.8 16.2 - - + -
350D THR* 4.1 7.0 - - - +
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Residues in contact with LEU 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D LEU* 1.3 76.9 - - - +
195D PHE* 1.3 59.9 + - - +
196D HIS* 3.4 7.8 - - + +
246D PRO* 4.0 22.4 - - + +
247D LEU 3.6 2.2 - - - -
248D PRO* 4.0 32.1 - - + -
347D PHE* 3.1 8.1 - - - +
348D THR* 2.7 54.5 + - - +
349D LYS 5.6 0.9 - - - +
350D THR* 4.1 21.1 - - + +
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Residues in contact with PHE 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D LEU* 1.3 71.9 - - - +
196D HIS* 1.3 59.4 + - - +
197D LYS 3.4 22.2 - - - -
198D MET* 3.6 26.9 - - + -
217D VAL* 4.7 5.2 - - + -
243D PHE* 3.5 32.2 - + - -
246D PRO* 3.4 2.3 - - - +
247D LEU* 2.7 50.0 + - + +
249D VAL* 3.9 20.9 - - + -
253D ILE* 5.2 4.0 - - + -
255D VAL* 4.2 20.2 - - + -
345D LEU* 4.1 8.1 - - + -
346D TYR 3.4 15.0 - - - -
347D PHE* 3.5 33.2 - + + -
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Residues in contact with HIS 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194D LEU* 3.4 23.8 - - + +
195D PHE* 1.3 72.6 - - - +
197D LYS* 1.3 70.3 + - + +
242D GLU* 3.8 1.7 - - - +
243D PHE* 3.2 27.4 + - - +
246D PRO* 3.4 32.1 - - + +
315D TYR* 3.6 27.7 + + + +
346D TYR 2.9 11.4 + - - +
347D PHE 4.0 1.3 - - - -
348D THR* 2.6 46.7 + - + +
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Residues in contact with LYS 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D PHE* 3.4 8.3 - - - -
196D HIS* 1.3 87.3 - - + +
198D MET* 1.3 66.1 + - - +
233D ARG* 5.8 1.3 - - - +
240D TYR* 4.5 24.5 - - + -
241D PHE 3.2 14.4 - - - +
242D GLU* 3.8 24.0 - - + +
243D PHE* 3.8 5.2 - - - -
315D TYR* 3.7 32.3 + - + +
346D TYR* 3.0 61.6 + - + +
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Residues in contact with MET 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D PHE* 3.6 23.3 - - + -
197D LYS* 1.3 81.7 - - - +
199D MET* 1.3 60.4 + - - +
200D PHE* 5.8 0.2 - - + -
215D PHE* 3.6 35.9 - - + -
240D TYR* 3.5 4.3 - - - +
241D PHE* 2.8 44.8 + - + +
243D PHE* 4.5 4.0 - - + -
255D VAL* 4.0 13.0 - - + -
257D PHE* 3.6 35.4 - - + -
273D PHE* 4.4 1.1 - - - -
343D VAL* 4.4 7.2 - - + -
344D LYS 3.1 8.1 - - - +
345D LEU* 3.7 23.3 - - + -
346D TYR* 4.4 2.5 - - - -
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Residues in contact with MET 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D MET* 1.3 76.0 - - - +
200D PHE* 1.3 69.7 + - - +
201D GLU* 3.7 36.3 - - + +
238D PHE* 3.9 15.7 - - + -
239D MET 3.1 15.5 - - - +
240D TYR* 3.5 42.2 - - + -
241D PHE* 5.0 0.2 - - - -
342D LYS 3.7 0.3 - - - +
343D VAL* 3.3 4.2 - - - -
344D LYS* 2.8 46.1 + - + +
346D TYR* 4.1 28.7 - - + +
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Residues in contact with PHE 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D MET* 1.3 82.4 - - - +
201D GLU* 1.3 61.1 + - - +
202D THR 3.5 12.3 - - - +
204D PRO* 3.8 32.3 - - + -
213D PRO* 4.4 4.9 - - + -
238D PHE* 3.4 8.7 - - - -
239D MET* 2.7 42.0 + - + +
241D PHE* 3.7 24.0 - + - -
257D PHE* 3.5 41.5 - + - -
270D MET* 4.3 6.7 - - + -
271D PHE* 3.8 27.4 - + - -
341D PHE* 3.8 11.4 - + + -
342D LYS 3.4 3.4 - - - -
343D VAL* 4.1 11.2 - - + -
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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