Contacts of the strand formed by residues 192 - 199 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C SER* 3.4 9.7 - - - -
191C ASN* 1.3 92.8 - - - +
193C PHE* 1.3 68.8 + - - +
194C LYS* 5.8 0.3 - - - +
239C PHE* 3.6 40.2 - - + -
263C GLU* 3.7 25.3 + - - +
373C GLU* 5.2 1.0 - - - +
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Residues in contact with PHE 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C SER* 3.3 33.7 - - - -
192C ASN* 1.3 76.6 - - - +
194C LYS* 1.3 62.4 + - - +
195C PHE* 3.9 21.3 - + + -
239C PHE* 3.2 17.6 - - - -
262C LYS* 3.4 36.6 - - + -
263C GLU 3.1 10.3 + - - +
264C ILE* 3.7 6.0 - - + -
265C MET 3.4 13.4 + - - -
370C ILE* 3.5 42.6 - - + -
373C GLU* 3.2 35.2 - - + +
374C TYR* 3.9 14.1 - + - -
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Residues in contact with LYS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ASN 5.8 0.4 - - - +
193C PHE* 1.3 78.9 - - - +
195C PHE* 1.3 72.5 + - - +
239C PHE* 4.2 10.3 - - + -
241C GLY* 3.4 34.5 - - - +
265C MET* 3.5 14.8 - - + +
267C HIS* 4.0 8.1 - - + -
290C ASN* 2.7 31.7 + - - +
291C ASP* 3.1 29.3 + - + +
292C ILE* 4.7 3.3 + - - +
293C VAL 4.1 0.7 + - - +
373C GLU* 4.9 5.3 + - - +
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Residues in contact with PHE 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C PHE* 3.9 20.9 - + + -
194C LYS* 1.3 79.4 - - - +
196C GLY* 1.3 60.2 + - - +
264C ILE* 3.6 31.9 - - + -
265C MET 3.7 4.8 + - - -
266C PHE* 3.4 28.4 - + + -
267C HIS 2.8 29.8 + - - -
291C ASP* 3.9 4.9 - - - -
293C VAL* 3.3 32.1 - - + +
295C VAL* 4.8 0.9 - - + -
366C LEU* 5.3 0.7 - - + -
369C LEU* 3.7 55.9 - - + -
370C ILE* 3.9 14.4 - - + -
373C GLU* 4.1 15.0 - - - -
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Residues in contact with GLY 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C PHE* 1.3 72.9 - - - +
197C VAL* 1.3 57.9 + - - -
198C ILE* 5.0 0.2 - - - -
267C HIS 3.4 6.3 - - - -
288C ILE* 3.7 23.3 - - - -
291C ASP* 3.8 8.1 + - - +
293C VAL 3.3 10.9 + - - -
294C ALA* 4.1 6.1 - - - -
295C VAL* 2.6 39.0 + - - +
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Residues in contact with VAL 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C GLY* 1.3 77.7 - - - +
198C ILE* 1.3 73.9 + - - +
220C PHE* 4.6 16.2 - - + -
223C PHE* 5.8 3.4 - - + -
224C LEU* 6.2 1.3 - - + -
227C LEU* 5.2 11.0 - - + -
266C PHE* 3.8 36.3 - - + -
267C HIS 2.5 18.0 + - - +
268C VAL* 3.7 25.8 - - + -
269C SER* 3.0 28.4 + - - -
288C ILE* 3.9 3.0 - - - +
295C VAL* 3.6 13.0 - - + +
297C PHE* 6.2 0.2 - - + -
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Residues in contact with ILE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C GLY 5.0 0.7 - - - -
197C VAL* 1.3 84.5 - - - +
199C TYR* 1.3 68.2 + - - +
210C LEU* 3.5 42.8 - - + +
211C PHE* 4.9 12.3 - - + +
220C PHE* 4.6 3.6 - - - -
269C SER* 3.9 20.9 - - - +
288C ILE* 4.7 18.2 - - + -
294C ALA* 5.2 6.3 - - + -
295C VAL* 2.9 11.1 + - - +
296C VAL* 4.2 24.7 - - + -
297C PHE* 3.0 28.9 + - - +
304C PHE* 5.8 1.6 - - + -
309C ILE* 5.4 10.1 - - + -
317C TYR* 5.4 5.4 - - + -
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Residues in contact with TYR 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C ILE* 1.3 80.9 - - - +
200C GLN* 1.3 82.7 + - - +
201C LYS* 5.9 1.5 - - + -
210C LEU* 3.5 23.9 + - - +
213C THR* 3.6 41.7 + - + +
215C GLU* 4.2 12.6 - - + +
216C GLU 3.4 13.0 + - - -
217C SER* 2.9 28.5 + - - -
220C PHE* 4.6 18.2 - + + -
269C SER* 4.4 4.2 + - - +
270C THR* 5.8 2.7 - - + -
296C VAL* 5.1 1.1 - - - -
297C PHE* 3.3 20.9 - + + +
298C GLN* 5.3 0.4 - - - -
299C ASP* 3.3 13.8 + - - -
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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