Contacts of the strand formed by residues 192 - 200 (chain B) in PDB entry 5BZZ
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B PRO 4.0 2.4 + - - -
191B VAL* 1.3 73.7 - - - +
193B LEU* 1.3 69.3 + - - +
249B VAL 3.7 7.6 - - - +
250B CYS* 4.2 12.7 - - + -
349B LYS* 4.4 1.4 - - - +
350B THR* 3.4 25.9 + - + +
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Residues in contact with LEU 193 (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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191B VAL* 3.5 15.7 + - + +
192B ALA* 1.3 81.6 - - - +
194B LEU* 1.3 65.2 + - - +
248B PRO* 3.6 3.6 - - - +
249B VAL* 2.8 42.4 + - + +
277B THR* 3.6 32.1 - - + +
280B ILE* 3.9 17.9 - - + +
316B LEU* 4.4 5.6 - - + -
347B PHE* 4.1 22.9 - - + -
348B THR 3.3 17.0 - - - +
349B LYS* 3.8 23.1 - - + -
350B THR* 3.8 8.4 + - - -
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Residues in contact with LEU 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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193B LEU* 1.3 76.2 - - - +
195B PHE* 1.3 59.0 + - - +
196B HIS* 3.5 8.2 - - + +
246B PRO* 3.9 24.9 - - + +
247B LEU 3.4 2.5 - - - -
248B PRO* 3.8 34.5 - - + -
347B PHE* 3.2 10.3 - - - +
348B THR* 2.8 50.9 + - - +
349B LYS 5.5 0.2 - - - +
350B THR* 4.3 26.2 - - + +
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Residues in contact with PHE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B LEU* 1.3 72.5 - - - +
196B HIS* 1.3 60.6 + - - +
197B LYS 3.3 20.9 - - - -
198B MET* 3.4 29.6 - - + -
217B VAL* 4.8 3.8 - - + -
243B PHE* 3.2 34.7 - + - -
246B PRO* 3.5 0.7 - - - +
247B LEU* 2.7 47.3 + - + +
249B VAL* 4.0 17.0 - - + -
253B ILE* 5.5 2.5 - - + -
255B VAL* 4.2 21.8 - - + -
345B LEU* 4.0 11.2 - - + -
346B TYR 3.4 19.5 - - - -
347B PHE* 3.4 33.4 - + + -
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Residues in contact with HIS 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 LEU* 3.5 23.4 - - + +
195B PHE* 1.3 72.7 - - - +
197B LYS* 1.3 69.5 + - + +
242B GLU* 3.7 2.1 - - - +
243B PHE* 3.0 34.1 + - - +
246B PRO* 3.5 32.2 - - + +
315B TYR* 3.8 26.2 + + + +
346B TYR 3.0 11.4 + - - +
347B PHE 4.0 2.9 - - - -
348B THR* 2.6 43.6 + - + +
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Residues in contact with LYS 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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195B PHE* 3.3 8.2 - - - -
196B HIS* 1.3 85.1 - - + +
198B MET* 1.3 64.7 + - - +
233B ARG* 5.9 1.4 - - - +
240B TYR* 4.6 23.4 - - + -
241B PHE 3.0 15.7 - - - +
242B GLU* 3.7 24.7 - - + -
243B PHE* 3.8 5.5 - - - -
315B TYR* 4.1 31.8 - - - -
346B TYR* 3.0 61.9 + - + -
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Residues in contact with MET 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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195B PHE* 3.4 32.8 - - + -
197B LYS* 1.3 76.2 - - - +
199B MET* 1.3 63.5 + - - +
200B PHE* 5.7 0.2 - - + -
215B PHE* 3.6 44.2 - - + -
240B TYR* 3.6 4.0 - - - +
241B PHE* 2.9 42.3 + - + +
243B PHE* 4.6 2.5 - - + -
255B VAL* 3.8 13.5 - - + -
257B PHE* 3.7 29.6 - - + -
273B PHE* 4.4 8.7 - - - -
343B VAL* 4.4 9.0 - - + -
344B LYS 3.1 12.6 - - - +
345B LEU* 4.4 5.4 - - + -
346B TYR* 4.5 1.8 - - - -
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Residues in contact with MET 199 (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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198B MET* 1.3 77.5 - - - +
200B PHE* 1.3 69.6 + - - +
201B GLU* 3.6 32.3 + - + +
238B PHE* 3.8 17.5 - - + -
239B MET 3.1 15.7 - - - +
240B TYR* 3.5 41.7 - - + -
241B PHE* 4.9 0.2 - - - -
342B LYS 3.6 0.3 - - - +
343B VAL* 3.2 4.3 - - - -
344B LYS* 2.8 52.1 + - + +
346B TYR* 4.1 21.5 - - + +
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Residues in contact with PHE 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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199B MET* 1.3 86.7 - - - +
201B GLU* 1.3 60.6 + - - +
202B THR 3.5 13.2 - - - +
204B PRO* 3.6 33.2 - - + -
211B CYS* 4.7 0.4 - - - -
213B PRO* 4.3 10.1 - - + -
238B PHE* 3.4 8.0 - - - -
239B MET* 2.8 41.4 + - + +
241B PHE* 3.7 22.4 - + - -
257B PHE* 3.5 45.5 - + - -
270B MET* 4.5 2.9 - - + -
271B PHE* 3.8 23.6 - + - -
341B PHE* 3.8 9.9 - + + -
342B LYS 3.3 2.9 - - - -
343B VAL* 4.1 9.0 - - + -
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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