Contacts of the strand formed by residues 198 - 208 (chain C) in PDB entry 3BZE
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 GLU 198 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193C PRO* 4.0 0.9 - - - +
194C ILE* 3.1 35.3 + - + +
195C SER* 3.2 22.2 + - - +
197C HIS* 1.3 85.6 - - + +
199C ALA* 1.3 65.5 + - - +
248C VAL* 3.6 24.1 - - + +
249C VAL 3.4 10.5 - - - +
250C PRO* 4.9 4.3 - - + -
251C SER* 4.5 4.0 - - - -
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Residues in contact with ALA 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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191C HIS* 3.7 26.5 - - + +
192C HIS 3.6 7.2 - - - -
193C PRO* 3.7 15.5 - - + -
194C ILE* 3.7 6.3 - - - +
198C GLU* 1.3 78.6 - - - +
200C THR* 1.3 63.5 + - - +
201C LEU* 5.6 0.4 - - + -
248C VAL* 3.5 4.0 - - - +
249C VAL* 2.8 35.2 + - + +
251C SER* 5.1 5.8 - - - -
254C GLU* 4.6 7.2 - - + +
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Residues in contact with THR 200 (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 THR 3.6 0.5 - - - +
191C HIS* 3.5 7.1 - - - -
192C HIS* 2.9 44.7 + - + +
194C ILE* 3.3 22.5 - - - +
199C ALA* 1.3 75.0 + - - +
201C LEU* 1.3 78.2 + - - +
202C ARG* 4.2 20.9 - - + +
246C ALA* 4.0 16.4 - - + -
247C VAL 3.6 7.6 - - - +
248C VAL* 4.2 9.0 - - + +
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Residues in contact with LEU 201 (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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189C VAL* 4.4 9.2 - - + -
190C THR 3.5 7.9 - - - +
191C HIS* 4.0 22.2 - - + -
199C ALA 5.4 0.4 - - - +
200C THR* 1.3 81.9 - - - +
202C ARG* 1.3 62.7 + - - +
217C TRP* 3.5 24.7 - - + -
246C ALA* 3.3 3.1 - - - -
247C VAL* 3.1 32.4 + - + -
249C VAL* 3.8 26.7 - - + -
254C GLU* 3.8 37.0 - - + +
257C TYR* 3.8 14.4 - - + +
273C ARG 5.6 1.8 - - - +
274C TRP* 4.6 9.0 - - + -
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Residues in contact with ARG 202 (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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189C VAL* 3.3 4.9 - - - +
190C THR* 3.0 40.1 + - - +
192C HIS* 3.7 24.7 + - + +
200C THR* 4.0 11.3 - - + +
201C LEU* 1.3 73.2 - - - +
203C CYS* 1.3 61.1 + - - +
204C TRP* 3.4 23.2 - - + +
217C TRP* 4.1 2.0 - - - -
229C GLU* 4.8 2.6 + - - -
244C TRP* 3.2 63.5 - - + +
245C ALA 3.6 2.5 - - - -
246C ALA* 4.0 9.3 - - + +
98D ASP* 2.9 31.2 + - - +
99D MET* 3.6 22.3 - - - +
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Residues in contact with CYS 203 (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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187C THR* 4.2 18.6 - - - -
188C HIS 3.8 2.2 - - - -
189C VAL* 4.4 5.8 - - - -
202C ARG* 1.3 71.8 - - - +
204C TRP* 1.3 63.3 + - - +
215C LEU* 4.0 4.9 - - - +
217C TRP* 3.6 16.4 - - + +
244C TRP* 3.0 7.7 - - - +
245C ALA* 2.8 44.3 + - + +
259C CYS* 2.0 49.4 - - - -
261C VAL* 4.4 3.8 - - - -
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Residues in contact with TRP 204 (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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186C LYS 4.3 0.7 - - - -
187C THR* 3.1 31.4 + - - +
188C HIS* 2.9 49.8 + + + +
190C THR* 3.0 28.1 + - + +
202C ARG* 3.4 23.4 - - + +
203C CYS* 1.3 75.5 - - - +
205C ALA* 1.3 60.4 + - - +
206C LEU* 4.1 24.9 - - + -
215C LEU* 5.1 0.7 - - - -
234C ARG* 3.5 16.6 - - - -
243C LYS 4.0 4.7 - - - -
244C TRP* 3.5 24.9 - + + -
97D ARG 4.5 5.8 - - - -
98D ASP* 3.4 26.7 - - - -
99D MET* 3.7 25.6 - - - -
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Residues in contact with ALA 205 (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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185C PRO* 4.1 7.0 - - + -
186C LYS 3.7 3.8 - - - -
187C THR* 4.1 4.5 - - - +
204C TRP* 1.3 74.6 - - - +
206C LEU* 1.3 62.2 + - - +
208C PHE* 3.0 29.0 - - + -
213C ILE* 3.8 18.8 - - + -
215C LEU* 4.0 16.2 - - + -
242C GLN* 3.2 1.9 - - - -
243C LYS* 3.0 28.9 + - + +
261C VAL* 5.0 0.2 - - + -
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Residues in contact with LEU 206 (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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185C PRO* 3.4 0.7 - - - +
186C LYS* 2.8 54.9 + - + +
188C HIS* 3.9 28.5 - - + +
204C TRP* 4.1 21.8 - - + -
205C ALA* 1.3 80.2 - - - +
207C GLY* 1.3 65.9 + - - +
208C PHE* 3.5 3.1 - - - -
241C PHE 4.0 0.9 - - - -
242C GLN* 3.7 40.2 - - + +
14D PRO* 4.1 24.9 - - + -
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Residues in contact with GLY 207 (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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183C GLU* 3.1 23.7 - - - +
184C PRO 3.6 5.2 - - - +
186C LYS* 5.1 8.6 - - - +
206C LEU* 1.3 76.5 - - - +
208C PHE* 1.3 58.5 + - - -
236C ALA* 5.6 0.8 - - - +
240C THR* 3.4 25.7 - - - +
241C PHE 2.9 10.1 + - - -
242C GLN* 4.9 3.2 - - - +
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Residues in contact with PHE 208 (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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183C GLU* 3.1 14.8 - - - +
184C PRO 4.2 0.4 - - - -
185C PRO* 3.6 29.4 - - + -
205C ALA* 3.0 35.4 - - + -
207C GLY* 1.3 75.7 - - - +
209C TYR* 1.3 64.7 + - - +
210C PRO 3.5 17.9 - - - -
211C ALA 3.4 21.3 - - - -
213C ILE* 3.8 18.2 - - + -
233C THR* 4.5 1.3 - - + -
240C THR* 3.4 3.0 - - - -
241C PHE* 2.9 46.0 + - + -
242C GLN* 3.5 21.3 - - - -
243C LYS* 4.0 8.3 - - + -
263C HIS* 3.5 14.4 - + + -
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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