Contacts of the strand formed by residues 192 - 200 (chain B) in PDB entry 3BRW
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 ASN 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 SER* 3.2 18.8 + - - +
191B ASN* 1.3 89.3 - - - +
193B PHE* 1.3 73.6 + - - +
239B PHE* 3.6 44.4 - - + +
263B GLU* 3.5 22.3 + - - +
373B GLU* 4.8 1.9 - - - +
377B TYR* 5.6 0.3 + - - -
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Residues in contact with PHE 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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190B SER 3.9 17.5 - - - -
191B ASN 4.2 0.4 - - - -
192B ASN* 1.3 78.2 - - - +
194B LYS* 1.3 62.4 + - - +
195B PHE* 3.8 26.5 - + + -
239B PHE* 3.2 11.7 - - - -
262B LYS* 3.6 34.3 - - + -
263B GLU 3.1 8.8 + - - +
264B ILE* 3.7 6.6 - - + -
265B MET 3.1 23.5 + - - -
370B ILE* 3.6 26.9 - - + -
373B GLU* 3.3 44.2 - - + -
374B TYR* 3.4 28.3 - + - -
377B TYR* 4.1 7.6 - - - -
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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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193B PHE* 1.3 78.2 - - - +
195B PHE* 1.3 70.0 + - - +
239B PHE* 4.4 13.5 - - + -
241B GLY* 4.0 17.5 - - - +
242B GLY* 6.2 0.4 - - - -
265B MET 3.2 8.5 - - - +
267B HIS* 3.6 22.0 - - + +
287B HIS 5.3 0.2 + - - -
290B ASN* 2.8 29.3 + - - +
291B ASP* 3.2 28.0 + - - +
292B ILE* 4.6 1.8 + - - +
293B VAL 4.2 0.2 - - - +
373B GLU* 4.2 8.8 + - - +
61D THR* 3.1 22.2 + - - -
62D GLU 5.5 0.9 - - - +
63D GLN* 3.8 22.7 + - - +
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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
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193B PHE* 3.8 21.5 - + + -
194B LYS* 1.3 78.8 - - - +
196B GLY* 1.3 58.2 + - - +
264B ILE* 3.5 33.9 - - + -
265B MET 3.2 6.1 + - - -
266B PHE* 3.4 18.8 - + + -
267B HIS* 2.8 33.6 + - - +
291B ASP* 3.6 5.2 - - - -
293B VAL* 3.2 30.5 - - + +
295B VAL* 5.0 0.2 - - + -
369B LEU* 3.5 57.7 - - + -
370B ILE* 3.9 14.6 - - + -
373B GLU* 3.5 17.9 - - + -
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Residues in contact with GLY 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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195B PHE* 1.3 70.0 - - - +
197B VAL* 1.3 64.8 + - - +
267B HIS 3.7 5.6 - - - -
288B ILE* 4.0 10.5 - - - -
291B ASP* 3.6 12.7 + - - -
293B VAL 3.1 11.5 + - - -
294B ALA* 3.8 12.6 - - - -
295B VAL* 2.4 36.7 + - - +
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Residues in contact with VAL 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 GLY* 1.3 78.6 - - - +
198B ILE* 1.3 68.3 + - - +
220B PHE* 4.1 27.0 - - + -
223B PHE* 4.9 8.1 - - + -
224B LEU* 4.7 7.9 - - + -
227B LEU* 4.5 7.2 - - + -
266B PHE* 3.7 28.7 - - + -
267B HIS 2.9 12.8 + - - +
268B VAL* 4.0 23.7 - - + +
269B SER* 3.0 28.1 + - - -
288B ILE* 4.3 1.6 - - - +
295B VAL* 3.2 18.4 - - + +
297B PHE* 5.2 1.3 - - + -
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Residues in contact with ILE 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 VAL* 1.3 78.9 - - - +
199B TYR* 1.3 61.1 + - - +
200B GLN 3.9 0.2 + - - -
210B LEU* 4.2 18.8 - - + +
211B PHE* 4.0 29.8 - - + -
220B PHE* 4.7 4.7 - - - -
269B SER* 3.9 10.8 - - - -
288B ILE* 4.2 13.0 - - + -
294B ALA* 5.7 3.6 - - + -
295B VAL 3.0 11.1 + - - +
296B VAL* 3.9 28.9 - - + -
297B PHE* 3.0 28.9 + - - +
304B PHE* 4.4 7.4 - - + -
309B ILE* 4.1 24.9 - - + -
317B TYR* 5.2 3.8 - - + -
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Residues in contact with TYR 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 ILE* 1.3 74.6 - - - +
200B GLN* 1.3 76.0 + - - +
201B LYS* 3.2 48.7 + - + +
209B GLU 4.5 4.7 - - - +
210B LEU* 3.9 16.4 + - - +
213B THR* 4.0 32.1 + - + +
215B GLU 5.6 1.3 - - - -
217B SER* 3.6 20.1 - - - -
220B PHE* 3.5 35.6 - + + -
269B SER* 4.0 6.1 + - - -
270B THR* 4.8 3.1 - - + -
297B PHE* 3.5 14.6 - + - -
299B ASP* 2.7 43.7 + - + +
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Residues in contact with GLN 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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198B ILE 3.9 1.4 + - - -
199B TYR* 1.3 79.8 - - - +
201B LYS* 1.3 65.8 + - - +
204B ALA* 3.4 22.3 + - + +
210B LEU* 3.9 15.3 - - + -
296B VAL* 4.0 12.9 - - + +
297B PHE 3.0 9.7 + - - +
298B GLN* 2.5 56.0 + - + +
299B ASP* 4.1 3.6 + - - +
300B GLU* 4.7 4.5 + - - +
302B THR* 3.6 10.4 + - - +
303B PRO 3.2 24.9 + - - -
304B PHE* 3.6 17.6 - - - +
308B MET* 3.7 10.5 - - - +
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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