Contacts of the strand formed by residues 193 - 205 (chain A) in PDB entry 3BX9
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 TYR 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A HIS* 3.0 34.9 + + - -
76A ILE* 3.9 16.6 - - + -
77A PRO 4.7 2.1 + - - -
79A PHE 5.1 1.0 + - - -
80A PHE* 4.0 16.6 - - - -
146A MET* 3.6 2.1 - - - +
147A LEU* 2.9 56.5 + - + +
154A LEU* 4.1 6.1 - - + +
190A PRO* 3.7 24.0 - - + -
191A GLY 3.4 12.8 - - - -
192A VAL* 1.3 75.8 - - - +
194A TYR* 1.3 95.0 + - - +
195A VAL* 3.8 12.9 - - + +
219A ALA* 3.7 16.8 - - + -
220A ARG 3.6 8.5 - - - +
221A TYR* 3.9 15.3 - - + -
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Residues in contact with TYR 194 (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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144A THR* 4.1 11.4 - - + -
145A GLU 3.3 5.2 - - - +
146A MET* 3.5 37.5 - - + -
192A VAL* 3.7 21.6 - - + +
193A TYR* 1.3 90.9 - - - +
195A VAL* 1.3 63.6 + - - +
219A ALA* 3.2 3.3 - - - +
220A ARG* 2.8 67.2 + - - +
222A CYS* 3.8 38.0 - - + +
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Residues in contact with VAL 195 (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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70A ILE* 4.0 31.2 - - + -
144A THR* 3.2 3.7 - - - -
145A GLU* 2.8 43.8 + - + +
147A LEU* 3.5 24.5 - - + -
193A TYR* 3.8 14.4 - - + +
194A TYR* 1.3 80.5 - - - +
196A ASP* 1.3 75.9 + - - +
197A ARG* 3.7 14.5 + - - +
217A ALA* 4.1 10.8 - - + -
218A VAL 3.4 7.4 - - - +
219A ALA* 3.9 7.9 - - + -
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Residues in contact with ASP 196 (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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143A SER 3.5 4.7 - - - +
144A THR* 2.7 26.8 + - - +
195A VAL* 1.3 72.7 - - - +
197A ARG* 1.3 61.1 + - - +
217A ALA* 3.3 2.4 - - - -
218A VAL* 2.9 40.0 + - + +
220A ARG* 2.6 44.4 + - - +
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Residues in contact with ARG 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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63A NRQ 3.2 42.5 - - - +
67A LYS* 3.7 4.2 - - - +
142A ALA* 3.4 7.5 - - - +
143A SER* 3.0 58.6 + - - +
144A THR 4.2 0.2 - - - -
145A GLU* 2.8 43.8 + - - +
160A MET* 5.5 1.8 - - + -
195A VAL* 3.7 19.1 + - - +
196A ASP* 1.3 76.9 - - - +
198A ARG* 1.3 67.2 + - - +
199A LEU* 5.0 9.4 - - + +
215A GLU* 3.3 27.9 + - - +
216A VAL 3.2 12.6 - - - +
217A ALA* 4.0 4.0 - - + -
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Residues in contact with ARG 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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142A ALA* 4.1 26.9 - - + +
197A ARG* 1.3 78.2 - - - +
199A LEU* 1.3 60.6 + - - +
200A GLU* 3.6 30.7 + - + +
214A HIS 3.9 0.2 - - - +
215A GLU* 3.3 10.3 - - - +
216A VAL* 2.9 46.5 + - + +
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Residues in contact with LEU 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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59A ALA* 3.7 27.8 - - + +
60A THR* 3.8 26.0 - - + -
63A NRQ 4.0 28.0 - - + +
140A TRP* 3.9 42.5 + - + +
141A GLU 5.5 3.0 + - - +
142A ALA* 5.5 0.2 - - - +
160A MET* 4.5 7.6 - - + -
197A ARG* 5.0 9.1 - - + +
198A ARG* 1.3 73.3 - - - +
200A GLU* 1.3 62.3 + - - +
201A ARG 4.4 0.3 + - - -
213A GLN* 3.4 31.0 - - + +
214A HIS 3.6 2.7 - - - +
215A GLU* 4.4 6.5 - - + +
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Residues in contact with GLU 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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198A ARG* 3.6 30.1 + - + +
199A LEU* 1.3 85.0 - - - +
201A ARG* 1.3 61.6 + - - +
202A ILE* 3.6 16.1 + - + +
213A GLN* 3.3 7.2 - - - +
214A HIS* 2.7 66.4 + - - +
216A VAL* 5.1 2.3 - - - +
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Residues in contact with ARG 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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55A PHE* 3.3 31.8 - - - +
56A ASP* 3.0 38.0 + - - +
59A ALA* 5.6 1.4 - - - +
139A GLY* 6.2 3.4 - - - -
199A LEU 4.4 0.4 + - - -
200A GLU* 1.3 71.9 - - - +
202A ILE* 1.3 66.4 + - - +
203A LYS* 3.9 16.6 - - - +
204A GLU* 4.1 21.1 - - - +
208A GLU* 3.4 30.8 + - - +
211A VAL* 3.9 9.8 - - + +
212A GLU 3.6 6.5 - - - +
213A GLN* 4.5 6.4 + - + +
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Residues in contact with ILE 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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40A THR* 5.7 0.2 - - - +
200A GLU* 4.1 16.2 - - + +
201A ARG* 1.3 79.0 - - - +
203A LYS* 1.3 63.1 + - + +
212A GLU* 2.8 49.2 + - + +
214A HIS* 3.7 34.8 - - + +
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Residues in contact with LYS 203 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A ARG* 6.4 1.1 - - - +
201A ARG* 3.6 8.6 - - - +
202A ILE* 1.3 83.9 - - + +
204A GLU* 1.3 65.1 + - - +
205A ALA* 6.4 2.2 - - - -
211A VAL* 3.5 2.3 - - - -
212A GLU* 2.8 57.3 + - + +
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Residues in contact with GLU 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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201A ARG* 4.1 13.5 - - - -
203A LYS* 1.3 82.1 - - - +
205A ALA* 1.3 73.6 + - - +
206A ASP 4.7 0.5 + - - -
207A LYS* 3.4 6.1 + - - +
208A GLU* 2.6 61.9 + - + +
210A TYR 3.1 11.4 - - - +
211A VAL* 4.4 2.0 - - + -
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Residues in contact with ALA 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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203A LYS* 6.4 2.0 - - - -
204A GLU* 1.3 81.4 + - - +
206A ASP* 1.3 74.4 + - - +
209A THR 3.1 2.9 + - - -
210A TYR* 2.8 50.2 + - + -
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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