Contacts of the strand formed by residues 143 - 150 (chain F) in PDB entry 3BXB
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 SER 143 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E MET* 5.7 0.7 - - - -
194E TYR* 4.6 6.5 - - - -
63F NRQ 2.7 30.2 + - - -
141F GLU 4.7 0.4 - - - -
142F ALA* 1.3 77.2 - - - +
144F THR* 1.3 65.0 + - - +
158F SER* 4.0 1.3 - - - -
159F ASP 3.8 9.4 - - - -
160F MET* 3.8 24.5 - - - -
196F ASP* 3.7 1.7 - - - +
197F ARG* 2.7 49.8 + - - +
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Residues in contact with THR 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E THR* 3.7 35.0 - - - +
194E TYR* 5.0 5.6 - - - -
220E ARG* 3.5 10.7 + - - -
143F SER* 1.3 74.9 + - - +
145F GLU* 1.3 70.6 + - - +
146F MET 4.9 0.2 - - - +
157F ARG 4.2 0.5 - - - +
158F SER* 3.0 19.4 + - - -
159F ASP 4.4 3.8 + - - +
194F TYR* 4.6 10.1 - - + -
195F VAL 3.3 6.1 - - - +
196F ASP* 2.7 22.9 + - - +
197F ARG* 3.3 4.7 - - - -
220F ARG* 4.2 9.4 - - - +
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Residues in contact with GLU 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F LYS* 3.1 21.5 + - - -
92F ARG* 5.2 1.1 + - - -
144F THR* 1.3 76.0 - - - +
146F MET* 1.3 67.1 + - - +
147F LEU* 3.8 24.8 + - + +
156F GLY* 3.7 7.4 - - - -
157F ARG 3.4 14.8 - - - +
158F SER* 4.6 0.7 - - - -
176F THR* 4.2 5.0 + - - -
178F TYR* 2.5 32.9 + - - -
194F TYR* 3.2 8.3 - - - +
195F VAL* 2.9 36.6 + - + +
197F ARG* 3.2 30.9 + - - +
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Residues in contact with MET 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E GLU* 4.9 0.2 - - - -
142E ALA 4.1 19.7 - - - +
143E SER* 5.4 0.4 - - - -
159E ASP* 4.0 26.7 - - + +
160E MET 4.0 7.2 - - - -
161E ALA* 3.7 39.5 - - + +
171E ILE* 4.2 11.7 - - + -
144F THR* 4.3 1.2 + - + +
145F GLU* 1.3 71.2 - - - +
147F LEU* 1.3 64.8 + - - +
148F TYR* 4.2 8.6 - - + -
155F GLU 3.8 0.3 - - - +
156F GLY* 3.3 4.2 - - - -
157F ARG* 2.9 39.6 + - + +
192F VAL* 4.2 12.8 - - + -
193F TYR 3.4 4.5 - - - +
194F TYR* 3.7 22.0 - - + -
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Residues in contact with LEU 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F LYS* 5.3 1.3 - - - -
70F ILE* 6.3 0.7 - - + -
80F PHE* 4.3 8.3 - - + -
145F GLU* 3.8 27.8 - - + +
146F MET* 1.3 75.5 - - - +
148F TYR* 1.3 61.9 - - - +
154F LEU* 3.8 25.4 - - + -
155F GLU 3.3 7.0 - - - +
178F TYR* 3.8 28.9 - - + -
191F GLY 4.1 1.9 - - - +
192F VAL* 3.2 6.4 - - - +
193F TYR* 2.7 63.8 + - + +
195F VAL* 3.8 29.6 - - + -
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Residues in contact with TYR 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E ALA* 5.4 1.8 - - + -
169E HIS* 4.2 27.1 - - + +
171E ILE* 3.2 34.8 - - + +
146F MET* 4.2 12.3 - - + -
147F LEU* 1.3 78.9 - - - +
149F PRO* 1.4 81.8 - - + +
150F ALA* 5.2 1.1 - - + -
154F LEU* 3.6 5.0 - - - -
155F GLU* 2.9 69.8 + - + -
157F ARG* 3.1 43.1 + - + -
192F VAL* 4.0 15.9 - - + -
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Residues in contact with PRO 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E GLY* 5.6 4.9 - - - -
169E HIS* 4.9 9.7 + - + -
148F TYR* 1.4 98.8 - - + +
150F ALA* 1.3 60.3 + - - +
153F GLY 3.5 6.1 - - - +
154F LEU* 4.1 8.7 - - + -
189F MET* 4.4 14.4 - - + -
190F PRO 3.4 24.9 - - - +
191F GLY* 4.0 13.7 - - - +
192F VAL* 4.1 11.7 - - + +
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Residues in contact with ALA 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F TYR* 4.4 4.0 - - + +
149F PRO* 1.3 78.3 - - - +
151F ASP* 1.3 62.8 + - + +
152F GLY 3.2 1.6 - - - -
153F GLY* 2.6 41.9 + - - +
155F GLU* 3.6 32.5 - - + +
189F MET* 4.6 0.8 - - - +
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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