Contacts of the strand formed by residues 196 - 204 (chain A) in PDB entry 2BBV
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 LYS 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A PRO* 3.2 23.3 - - + +
195A VAL* 1.3 77.9 - - - +
197A LEU* 1.3 59.7 + - - +
198A SER 3.7 0.4 - - - -
217A LEU* 3.4 6.5 - - - -
218A VAL* 2.6 49.6 + - + +
246A ASN* 4.5 22.9 + - - +
247A GLU* 4.1 18.1 + - - -
291A TRP* 4.4 5.2 - - - -
293A ASN* 5.4 5.8 - - - +
164B SER* 3.6 12.3 - - - +
165B SER* 3.0 26.0 + - - +
252B PHE* 4.2 7.7 + - - +
254B ASP* 3.2 29.6 + - - +
322B ARG* 5.1 5.9 - - - +
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LYS* 1.3 71.0 - - - +
198A SER* 1.3 59.5 + - - +
215A HIS* 3.9 27.8 - - + +
216A THR 3.5 9.9 - - - +
217A LEU* 3.6 6.1 - - + -
256A LEU* 3.4 33.2 - - + -
259A ILE* 5.2 1.1 - - + -
262A LEU* 3.5 32.8 - - + -
288A ILE* 6.2 2.0 - - + -
291A TRP* 3.6 33.2 - - + +
254B ASP* 3.5 13.5 - - - +
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Residues in contact with SER 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LYS 3.5 0.2 + - - -
197A LEU* 1.3 75.8 - - - +
199A ASN* 1.3 74.1 + - - +
215A HIS* 3.6 7.6 + - - +
216A THR* 2.5 29.2 + - - -
218A VAL* 3.4 27.6 - - - -
254B ASP* 4.0 9.8 - - - +
255B ILE 2.6 30.6 + - - -
256B LEU* 3.8 10.3 - - - +
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Residues in contact with ASN 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A SER* 1.3 84.3 + - - +
200A VAL* 1.3 58.1 + - - +
213A LEU* 3.6 23.5 - - + +
214A VAL 3.2 15.0 - - - +
215A HIS* 4.7 2.9 - - - +
216A THR* 3.3 10.5 - - - +
215B HIS* 3.0 35.0 + - - -
256B LEU* 3.6 15.0 - - - +
257B GLU 3.2 21.5 + - - +
213C LEU* 6.0 2.0 - - + -
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ASN* 1.3 74.9 - - - +
201A GLN* 1.3 66.3 + - - +
202A PHE* 4.1 13.7 - - + -
212A ALA 3.4 1.7 - - - +
213A LEU* 3.3 5.1 - - - -
214A VAL* 2.8 54.9 + - + +
216A THR* 4.1 13.9 - - - -
267A VAL* 6.1 0.2 - - + -
271A THR* 3.0 27.8 - - - +
272A SER* 3.9 11.2 - - - +
157B ALA* 4.8 4.5 - - + -
257B GLU* 3.3 22.4 - - + +
258B GLY* 4.8 0.7 - - - +
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Residues in contact with GLN 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 1.3 76.1 - - - +
202A PHE* 1.3 64.6 - - - +
203A PRO* 4.7 1.7 - - + +
211A SER* 5.1 2.9 - - - +
212A ALA 2.9 8.7 - - - +
213A LEU* 4.5 11.5 - - + +
214B VAL* 5.2 1.6 - - - +
215B HIS* 3.8 18.2 + - - +
257B GLU 3.0 8.1 + - - +
258B GLY* 3.2 34.4 + - - +
259B ILE* 3.6 29.1 - - + +
260B GLN 4.5 0.8 - - - +
261B THR 3.3 14.5 + - - -
264B PRO* 2.9 47.5 - - + +
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Residues in contact with PHE 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A VAL* 4.1 24.0 - - + -
201A GLN* 1.3 78.1 - - - +
203A PRO* 1.3 80.1 - - + +
204A VAL* 3.2 12.4 + - + -
211A SER* 4.4 1.7 + - - -
212A ALA* 2.8 60.8 + - + +
214A VAL* 4.3 14.4 - - + -
266A ASN 5.8 2.5 - - - -
267A VAL* 5.1 11.9 - - + -
271A THR* 3.9 33.7 - - + +
210C THR* 6.1 2.7 - - + -
211C SER* 6.0 2.5 - - - -
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Residues in contact with PRO 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A GLN* 4.6 2.9 - - + +
202A PHE* 1.3 91.3 - - + +
204A VAL* 1.3 67.2 + - - +
210A THR 3.5 8.1 - - - +
211A SER* 3.9 14.3 - - - +
258B GLY 5.8 1.3 - - - +
264B PRO* 6.4 0.4 - - + -
265B ALA* 4.8 15.0 - - + +
266B ASN* 4.1 18.6 - - - +
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A PHE* 3.2 18.5 + - + +
203A PRO* 1.3 81.4 - - - +
205A ALA* 1.3 70.1 + - - +
206A THR* 3.3 25.1 - - + +
209A ALA* 5.1 1.7 - - - +
210A THR* 2.8 47.7 + - - +
212A ALA* 4.8 6.7 - - + -
266B ASN* 4.8 5.5 + - - -
208C PRO* 3.8 14.1 - - + -
209C ALA 5.1 2.2 - - - +
210C THR* 3.8 20.9 - - + -
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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