Contacts of the strand formed by residues 200 - 207 (chain C) in PDB entry 3BSQ
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 THR 200 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ARG* 3.4 19.1 + - - +
119C LEU 3.7 2.9 + - - -
120C PRO* 3.3 23.4 - - + +
121C SER 4.8 0.7 + - - -
124C GLU* 4.2 8.5 - - - +
196C VAL* 3.2 11.1 - - - +
197C CYS 2.9 41.7 + - - +
198C ARG 3.9 4.7 - - - +
199C GLY* 1.3 76.0 - - - +
201C LEU* 1.3 58.4 + - - +
202C GLN* 3.3 23.8 - - - +
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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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44C VAL* 3.9 26.7 - - + -
52C LEU* 4.3 4.9 - - + -
117C VAL* 4.5 15.5 - - + +
118C ARG 3.0 16.4 + - - +
119C LEU* 4.2 13.9 - - + -
120C PRO* 3.1 26.4 - - + +
194C PRO* 3.7 26.9 - - + -
195C LEU 3.7 6.3 - - - +
196C VAL* 4.3 6.7 - - + +
200C THR* 1.3 71.5 + - - +
202C GLN* 1.3 61.2 + - - +
203C GLY 3.4 21.3 - - - +
204C LEU* 4.5 0.7 - - + -
224C VAL* 3.7 30.2 - - + +
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Residues in contact with GLN 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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120C PRO* 3.3 17.1 - - - +
122C ARG 3.4 9.5 + - - +
123C CYS* 4.0 5.5 - - - +
124C GLU* 3.2 38.0 + - + +
156C LEU* 5.1 0.6 - - + +
175C LEU* 3.7 19.7 - - + +
195C LEU* 2.7 14.2 + - + +
197C CYS* 3.5 34.3 - - + -
200C THR* 3.3 25.4 + - + +
201C LEU* 1.3 73.5 - - - +
203C GLY* 1.3 54.3 + - - +
223C GLN* 3.4 9.9 + - - -
224C VAL* 3.0 22.1 + - - -
225C CYS* 4.0 12.8 + - - +
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Residues in contact with GLY 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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175C LEU* 4.5 0.9 - - - -
193C GLY 3.8 0.2 - - - +
194C PRO 3.8 0.7 - - - -
195C LEU* 2.9 42.9 + - - +
201C LEU* 3.4 12.4 - - - +
202C GLN* 1.3 79.5 - - - +
204C LEU* 1.3 63.6 + - - -
221C TYR* 4.3 6.7 - - - -
222C THR 3.0 13.2 - - - -
224C VAL* 4.0 3.1 - - - -
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Residues in contact with LEU 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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44C VAL* 3.7 25.1 - - + -
52C LEU* 3.7 20.6 - - + -
53C THR 3.4 28.5 - - - +
54C ALA* 4.4 1.3 - - + +
98C ASP 4.6 3.6 - - - +
99C LEU* 3.9 17.3 - - + -
192C GLY* 3.6 27.1 - - - +
193C GLY 3.3 6.1 - - - +
201C LEU* 4.5 2.0 - - + -
203C GLY* 1.3 80.8 - - - +
205C VAL* 1.3 66.8 + - - +
206C SER* 3.3 1.2 + - - -
221C TYR* 3.0 20.5 - - - -
222C THR* 3.1 18.1 + - + +
224C VAL* 3.9 13.2 - - + -
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Residues in contact with VAL 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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54C ALA* 4.0 7.3 - - - +
132C VAL* 4.3 14.8 - - + -
133C SER 5.3 0.7 - - - +
186C ALA* 3.9 21.8 - - + -
187C CYS 5.2 1.3 - - - +
190C ASP* 3.1 23.8 - - + +
191C SER* 3.6 23.4 - - - +
192C GLY* 2.8 22.6 + - - +
193C GLY* 3.1 22.4 + - - +
204C LEU* 1.3 70.5 - - - +
206C SER* 1.3 62.6 + - - +
207C TRP* 5.0 2.5 - - - +
220C VAL 3.9 1.8 - - - +
221C TYR* 3.6 20.2 - - + -
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Residues in contact with SER 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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56C HIS* 3.2 23.3 + - - -
95C HIS* 4.1 4.7 + - - +
98C ASP* 2.8 33.7 + - - +
174C MET* 6.0 2.0 - - - +
191C SER* 4.4 3.0 + - - -
204C LEU 4.0 0.9 - - - -
205C VAL* 1.3 78.4 - - - +
207C TRP* 1.3 80.9 + - - +
220C VAL* 2.7 21.5 + - - -
221C TYR 3.9 3.4 - - - -
222C THR* 3.9 14.7 + - - -
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Residues in contact with TRP 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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95C HIS* 3.7 34.5 - + + +
166C TYR* 3.9 34.5 - + - -
169C LEU* 4.0 32.3 - - + -
170C LEU* 4.3 4.3 - - + -
174C MET* 4.0 19.5 - - - +
205C VAL* 5.0 3.0 - - - +
206C SER* 1.3 97.7 + - - +
208C GLY* 1.3 78.7 + - - +
219C GLY* 3.9 1.2 - - - -
220C VAL* 2.9 65.9 + - + +
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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