Contacts of the strand formed by residues 143 - 150 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A NRQ 2.4 30.0 + - - -
141A GLU 4.5 1.3 - - - -
142A ALA* 1.3 78.9 - - - +
144A THR* 1.3 61.8 + - - +
158A SER* 4.3 0.9 - - - -
159A ASP 3.8 19.7 - - - -
160A MET* 3.9 13.5 - - - -
196A ASP* 3.5 2.6 - - - +
197A ARG* 2.7 53.2 + - - -
146B MET* 5.6 0.2 - - - -
194B TYR* 4.5 6.1 - - - -
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Residues in contact with THR 144 (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* 1.3 73.5 - - - +
145A GLU* 1.3 71.9 - - - +
146A MET* 4.7 0.4 - - + +
157A ARG 4.1 0.7 - - - +
158A SER* 3.0 18.0 + - - -
159A ASP 4.4 4.3 + - - +
194A TYR* 4.1 9.4 - - + -
195A VAL 3.2 5.8 - - - +
196A ASP* 2.6 26.2 + - - +
197A ARG* 3.2 3.4 - - - -
220A ARG* 3.9 13.5 - - - +
144B THR* 3.8 26.2 - - - +
194B TYR* 4.7 7.1 - - - -
220B ARG* 3.2 14.2 + - - -
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Residues in contact with GLU 145 (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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67A LYS* 3.0 24.8 + - - -
92A ARG* 5.2 1.0 + - - -
144A THR* 1.3 75.7 - - - +
146A MET* 1.3 68.6 + - - +
147A LEU* 3.6 29.1 - - + +
156A GLY* 3.7 11.8 - - - -
157A ARG 3.4 12.1 - - - +
158A SER* 4.0 2.6 - - - -
176A THR* 4.1 6.4 + - - -
178A TYR* 2.8 21.5 + - - -
194A TYR* 3.1 6.8 - - - +
195A VAL* 2.8 41.2 + - + +
197A ARG* 3.1 27.7 + - - +
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Residues in contact with MET 146 (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* 4.2 1.4 + - + +
145A GLU* 1.3 73.5 - - - +
147A LEU* 1.3 64.2 + - - +
148A TYR* 4.3 14.9 + - + -
155A GLU 3.9 0.5 - - - +
156A GLY* 3.4 2.9 - - - -
157A ARG* 3.0 55.5 + - + +
192A VAL* 4.4 13.0 - - + -
193A TYR 3.3 5.6 - - - +
194A TYR* 3.6 30.5 - - + -
141B GLU* 5.2 0.2 - - - -
142B ALA 4.5 7.4 - - - +
143B SER* 5.7 0.4 - - - -
159B ASP* 4.2 21.8 - - + +
160B MET 4.2 2.7 - - - -
161B ALA* 3.8 40.2 - - + +
171B ILE* 4.3 5.6 - - + -
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Residues in contact with LEU 147 (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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67A LYS* 5.4 0.2 - - - -
80A PHE* 4.2 7.6 - - + -
145A GLU* 3.6 38.8 - - + +
146A MET* 1.3 77.3 - - - +
148A TYR* 1.3 61.4 + - - +
154A LEU* 4.0 15.5 - - + -
155A GLU 3.4 7.0 - - - +
178A TYR* 3.8 22.4 - - + -
192A VAL* 3.2 5.5 - - - +
193A TYR* 2.6 77.1 + - + +
195A VAL* 3.7 25.6 - - + -
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Residues in contact with TYR 148 (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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146A MET* 4.3 13.2 - - + -
147A LEU* 1.3 76.9 - - - +
149A PRO* 1.3 79.8 - - + +
150A ALA* 4.7 7.0 - - + -
154A LEU* 3.6 4.8 - - - -
155A GLU* 2.9 72.0 + - + -
156A GLY 4.7 0.9 - - - -
157A ARG* 3.2 30.9 + - + -
192A VAL* 4.1 16.6 - - + +
97B GLU* 4.8 0.2 + - - -
161B ALA* 5.5 1.8 - - + -
169B HIS* 4.3 22.9 - + + +
171B ILE* 3.1 44.1 - - + +
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Residues in contact with PRO 149 (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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148A TYR* 1.3 92.2 - - + +
150A ALA* 1.3 61.5 + - - +
152A GLY 6.1 0.7 - - - +
153A GLY 3.5 6.5 - - - +
154A LEU* 4.1 9.0 - - + -
189A MET* 3.9 18.8 - - + -
190A PRO 3.2 26.9 - - - +
191A GLY* 4.6 0.9 - - - -
192A VAL* 4.2 17.9 - - + +
168B GLY* 5.5 4.9 - - - -
169B HIS* 4.9 10.5 + - + -
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Residues in contact with ALA 150 (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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148A TYR* 3.6 12.4 + - + +
149A PRO* 1.3 75.0 - - - +
151A ASP* 1.3 76.8 + - - +
152A GLY 3.3 2.0 - - - +
153A GLY* 2.8 29.9 + - - +
154A LEU* 4.4 0.5 - - - +
155A GLU* 4.4 25.4 - - + +
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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