Contacts of the strand formed by residues 192 - 200 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A SER* 3.5 11.8 + - - -
191A ASN* 1.3 90.3 - - - +
193A PHE* 1.3 73.4 + - - +
194A LYS* 5.9 0.2 - - - +
239A PHE* 3.6 46.1 - - + +
263A GLU* 3.1 20.7 - - + +
373A GLU* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A SER* 3.2 32.8 - - - -
192A ASN* 1.3 78.1 - - - +
194A LYS* 1.3 56.8 + - - +
195A PHE* 3.7 28.7 - + + -
239A PHE* 3.8 6.1 - - - -
262A LYS* 3.6 28.7 - - + -
263A GLU 2.8 9.7 + - - +
264A ILE* 3.4 11.7 - - + +
265A MET* 2.8 32.1 + - - +
370A ILE* 3.6 40.4 - - + -
373A GLU* 3.3 37.7 - - + -
374A TYR* 3.8 13.7 - + - -
377A TYR* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PHE* 1.3 73.6 - - - +
195A PHE* 1.3 66.5 + - - +
239A PHE* 4.5 15.3 - - + -
241A GLY* 4.3 18.4 - - - +
265A MET* 3.2 6.5 - - + +
267A HIS* 3.7 24.5 - - + +
287A HIS* 5.0 1.3 - - - +
290A ASN* 3.1 29.4 + - - +
291A ASP* 2.8 41.3 + - - +
292A ILE* 4.8 10.5 + - + +
293A VAL 4.5 0.3 - - - +
373A GLU* 4.4 8.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A PHE* 3.7 19.5 - + + -
194A LYS* 1.3 78.0 - - - +
196A GLY* 1.3 61.7 + - - +
264A ILE* 3.5 38.4 - - + -
265A MET 3.0 6.7 + - - +
266A PHE* 3.4 18.9 - + + -
267A HIS* 2.8 25.6 + - - +
291A ASP* 2.9 9.9 - - - +
293A VAL* 3.7 27.1 - - + +
294A ALA* 5.0 1.1 - - - -
369A LEU* 3.5 59.9 - - + -
370A ILE* 3.7 10.5 - - + -
373A GLU* 3.7 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A PHE* 1.3 73.4 - - - +
197A VAL* 1.3 63.2 + - - +
198A ILE* 5.1 0.4 - - - -
267A HIS 3.7 7.4 - - - -
288A ILE* 4.5 7.6 - - - -
291A ASP* 3.0 13.5 + - - -
293A VAL 3.3 8.5 + - - -
294A ALA* 3.7 13.7 - - - -
295A VAL* 2.6 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A GLY* 1.3 77.6 - - - +
198A ILE* 1.3 68.5 + - - +
220A PHE* 4.0 25.6 - - + -
223A PHE* 4.9 8.5 - - + -
224A LEU* 4.6 8.5 - - + -
227A LEU* 5.6 4.9 - - + -
266A PHE* 3.5 29.6 - - + -
267A HIS 3.0 7.5 + - - +
268A VAL* 3.9 28.9 - - + +
269A SER* 3.2 24.4 + - - -
288A ILE* 3.6 3.3 - - - +
295A VAL* 3.7 17.9 - - + -
297A PHE* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 1.3 81.1 - - - +
199A TYR* 1.3 65.0 + - - +
200A GLN 4.0 0.3 + - - -
210A LEU* 4.0 36.6 - - + -
211A PHE* 5.0 9.2 - - + -
220A PHE* 4.3 4.4 - - - -
269A SER* 4.4 9.4 - - - +
288A ILE* 4.2 28.5 - - + -
294A ALA* 4.4 9.9 - - + -
295A VAL 3.2 9.7 + - - +
296A VAL* 3.6 24.7 - - + +
297A PHE* 3.0 28.2 + - - +
304A PHE* 6.2 0.9 - - + -
309A ILE* 4.0 24.2 - - + -
314A LEU* 5.7 0.2 - - + -
317A TYR* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 1.3 74.5 - - - +
200A GLN* 1.3 67.3 + - - +
201A LYS* 3.5 30.5 + - + +
202A LEU 5.1 0.7 + - - -
210A LEU* 4.0 16.9 + - - +
213A THR* 3.6 37.4 + - + -
215A GLU 5.2 2.7 - - - -
216A GLU* 5.6 0.9 - - - -
217A SER* 3.3 26.7 - - - -
220A PHE* 3.7 33.5 - + + -
269A SER* 4.3 6.6 + - - +
270A THR* 4.7 11.0 - - + -
297A PHE* 3.1 27.4 - + - -
299A ASP* 2.4 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 4.0 1.2 + - + -
199A TYR* 1.3 82.1 - - - +
201A LYS* 1.3 62.2 + - - +
204A ALA* 3.3 25.7 + - + +
210A LEU* 3.7 20.6 - - + -
296A VAL* 3.7 8.9 - - + +
297A PHE 3.0 12.7 + - - +
298A GLN* 3.1 39.2 + - + +
299A ASP* 4.1 5.0 + - - +
302A THR* 3.5 19.5 + - - +
303A PRO 3.3 23.8 + - - -
304A PHE* 3.5 18.3 - - - -
308A MET* 3.8 7.3 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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