Contacts of the strand formed by residues 200 - 207 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A SO4 2.8 14.7 + - - -
118A ARG* 3.4 15.7 + - - +
119A LEU 3.8 2.6 + - - -
120A PRO* 3.4 23.3 - - + +
121A SER 4.8 0.7 + - - -
122A ARG 5.6 0.2 - - - +
124A GLU* 4.3 8.7 - - - +
196A VAL* 3.2 5.0 - - - +
197A CYS 3.0 47.6 + - - +
198A ARG 4.0 3.1 - - - +
199A GLY* 1.3 69.9 + - - -
201A LEU* 1.3 58.3 + - - +
202A GLN* 3.1 26.4 + - + +
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Residues in contact with LEU 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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7A SO4 4.8 0.6 + - - -
44A VAL* 3.8 26.9 - - + -
52A LEU* 4.3 7.9 - - + -
117A VAL* 4.5 17.7 - - + -
118A ARG 3.1 16.1 + - - +
119A LEU* 4.3 9.9 - - + -
120A PRO* 3.1 26.5 - - + +
194A PRO* 3.7 27.8 - - + -
195A LEU 3.8 4.9 - - - +
196A VAL* 3.8 6.3 - - + +
200A THR* 1.3 70.4 + - - +
202A GLN* 1.3 60.8 + - - +
203A GLY 3.4 21.3 - - - +
204A LEU* 4.5 0.9 - - + -
224A VAL* 3.7 29.9 - - + +
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Residues in contact with GLN 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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120A PRO* 3.2 18.3 - - - +
122A ARG 3.5 8.8 + - - +
123A CYS* 3.9 5.3 - - - +
124A GLU* 3.1 39.5 + - + +
156A LEU* 5.1 1.9 - - + +
175A LEU* 3.7 19.9 - - + +
195A LEU* 2.9 7.4 + - + +
196A VAL 3.4 1.2 - - - +
197A CYS* 3.5 37.0 - - + -
200A THR* 3.1 25.9 - - + +
201A LEU* 1.3 74.1 - - - +
203A GLY* 1.3 57.5 + - - +
223A GLN* 3.4 10.6 + - - +
224A VAL* 3.1 20.3 + - - -
225A CYS* 4.1 12.4 + - - +
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Residues in contact with GLY 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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175A LEU* 4.6 2.9 - - - -
193A GLY 3.8 0.9 - - - +
195A LEU* 2.6 40.8 + - - +
201A LEU* 3.4 16.4 - - - +
202A GLN* 1.3 76.8 - - - +
204A LEU* 1.3 63.9 + - - -
221A TYR* 4.4 2.9 - - - -
222A THR 2.9 14.4 - - - -
224A VAL* 3.9 3.9 - - - +
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Residues in contact with LEU 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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44A VAL* 3.7 25.1 - - + -
52A LEU* 3.7 22.2 - - + +
53A THR 3.5 26.0 - - - +
54A ALA* 5.1 0.9 - - + +
98A ASP 4.6 4.3 - - - +
99A LEU* 3.9 16.6 - - + -
192A GLY* 3.6 25.6 - - - +
193A GLY 3.3 7.2 - - - +
201A LEU* 4.5 1.6 - - + -
203A GLY* 1.3 80.0 - - - +
205A VAL* 1.3 64.3 + - - +
206A SER 3.3 0.2 + - - -
221A TYR* 2.9 23.1 + - - -
222A THR* 3.2 16.4 + - + +
224A VAL* 3.9 13.0 - - + -
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Residues in contact with VAL 205 (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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54A ALA* 4.1 6.6 - - - +
132A VAL* 4.2 16.8 - - + -
133A SER 5.3 0.4 - - - +
186A ALA* 3.9 20.2 - - + -
187A CYS 5.2 1.3 - - - +
190A ASP* 3.2 21.5 - - + +
191A SER* 3.5 25.5 - - - +
192A GLY* 2.9 24.5 + - - +
193A GLY* 3.1 22.3 + - - +
204A LEU* 1.3 70.1 - - - +
206A SER* 1.3 61.0 - - - +
207A TRP* 5.0 2.0 - - - +
220A VAL 4.0 2.5 - - - +
221A TYR* 3.6 20.6 - - + -
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Residues in contact with SER 206 (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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56A HIS* 3.2 22.8 + - - -
95A HIS* 4.1 4.5 + - - +
98A ASP* 2.6 35.9 + - - +
174A MET* 6.1 1.0 - - - +
191A SER* 4.4 3.4 + - - -
204A LEU 4.1 0.2 - - - -
205A VAL* 1.3 77.6 - - - +
207A TRP* 1.3 79.3 + - - +
220A VAL 2.8 8.9 + - - -
221A TYR 3.2 16.5 - - - +
222A THR* 4.0 15.7 - - - -
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Residues in contact with TRP 207 (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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95A HIS* 3.7 33.2 + + + +
166A TYR* 3.9 35.2 - + - -
169A LEU* 3.9 30.5 - - + -
170A LEU* 4.3 4.7 - - + -
174A MET* 4.1 18.8 - - + +
205A VAL* 5.0 3.1 - - - +
206A SER* 1.3 93.5 + - - +
208A GLY* 1.3 69.6 + - - +
219A GLY* 3.9 1.2 - - - -
220A VAL* 2.9 69.2 + - + +
210B PHE* 4.1 18.2 - + - -
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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