Contacts of the strand formed by residues 143 - 150 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63E NRQ 2.6 26.2 + - - -
141E GLU 4.3 2.0 - - - -
142E ALA* 1.3 76.4 - - - +
144E THR* 1.3 62.5 + - - +
159E ASP 3.7 20.0 - - - -
160E MET* 4.0 10.5 - - - -
196E ASP* 3.5 2.8 - - - +
197E ARG* 2.5 58.3 + - - -
146F MET* 5.4 0.9 - - - -
194F TYR* 4.4 8.3 - - - -
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Residues in contact with THR 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E SER* 1.3 75.7 + - - +
145E GLU* 1.3 73.4 + - - +
146E MET* 4.2 0.4 + - + -
157E ARG 4.1 0.5 - - - +
158E SER* 2.8 18.5 + - - -
159E ASP 4.5 4.0 + - - +
194E TYR* 4.1 10.1 - - + -
195E VAL 3.2 5.4 - - - +
196E ASP* 2.9 26.9 + - - +
197E ARG* 3.1 4.5 - - - -
220E ARG* 3.9 12.6 - - - +
144F THR* 3.7 26.3 - - - +
159F ASP* 5.5 0.3 - - - +
194F TYR* 4.9 4.1 - - - -
220F ARG* 3.7 13.5 + - - -
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Residues in contact with GLU 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E NRQ 6.0 0.2 - - - -
67E LYS* 2.9 23.6 + - - -
92E ARG* 6.1 0.2 - - - -
144E THR* 1.3 77.7 - - - +
146E MET* 1.3 68.7 + - - +
147E LEU* 3.8 17.9 + - + +
156E GLY* 3.3 18.1 - - - -
157E ARG 3.4 16.2 - - - +
158E SER* 3.9 1.3 - - - -
176E THR* 4.3 3.7 + - - -
178E TYR* 2.4 25.8 + - - -
194E TYR* 3.1 8.7 - - - +
195E VAL* 2.9 36.2 + - + +
197E ARG* 3.3 28.4 + - - +
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Residues in contact with MET 146 (chain E).
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 4.2 0.4 - - - -
145E GLU* 1.3 73.8 - - - +
147E LEU* 1.3 66.0 + - - +
148E TYR* 4.3 7.0 + - + -
155E GLU 3.8 0.5 - - - +
156E GLY* 3.4 3.8 - - - -
157E ARG* 3.0 42.0 + - + +
192E VAL* 4.4 13.7 - - + -
193E TYR 3.4 5.8 - - - +
194E TYR* 3.9 28.7 - - + -
141F GLU* 5.0 0.2 - - - -
142F ALA 4.4 9.4 - - - +
143F SER* 5.7 0.2 - - - -
159F ASP* 3.8 34.3 - - + +
160F MET 3.9 9.0 - - - +
161F ALA* 3.9 32.8 - - + -
171F ILE* 4.4 9.6 - - + -
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Residues in contact with LEU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67E LYS* 4.6 1.6 - - - +
70E ILE* 6.4 0.4 - - + -
80E PHE* 4.6 5.4 - - + -
145E GLU* 3.6 33.2 - - - +
146E MET* 1.3 78.4 - - - +
148E TYR* 1.3 61.0 + - - +
154E LEU* 4.4 12.1 - - + -
155E GLU 3.2 6.5 - - - +
178E TYR* 3.6 25.1 - - + -
191E GLY 4.2 0.2 - - - +
192E VAL* 3.4 5.9 - - - +
193E TYR* 2.8 76.5 + - + +
195E VAL* 3.6 30.7 - - + -
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Residues in contact with TYR 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E MET* 4.3 11.9 - - + -
147E LEU* 1.3 76.4 - - - +
149E PRO* 1.3 80.1 - - + +
150E ALA* 3.5 8.5 + - + -
154E LEU* 3.8 4.0 - - - -
155E GLU* 3.0 70.0 + - + -
156E GLY 4.4 0.2 - - - -
157E ARG* 3.0 40.5 + - + -
192E VAL* 4.4 10.1 - - + +
161F ALA* 5.7 2.0 - - + -
169F HIS* 4.3 27.4 - - + +
171F ILE* 3.5 36.8 - - + +
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Residues in contact with PRO 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E LEU 4.5 0.4 - - - +
148E TYR* 1.3 91.2 - - + +
150E ALA* 1.3 62.2 + - - +
153E GLY 3.8 7.2 - - - +
154E LEU* 4.0 7.8 - - + -
189E MET* 4.0 15.9 - - + -
190E PRO 3.1 28.7 - - - +
191E GLY* 4.3 3.8 - - - +
192E VAL* 4.2 17.7 - - + +
168F GLY* 6.1 1.0 - - - -
169F HIS* 4.9 9.2 + - + -
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Residues in contact with ALA 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E TYR* 3.5 19.8 + - + +
149E PRO* 1.3 75.9 - - - +
151E ASP* 1.3 76.8 + - - +
152E GLY 3.6 1.3 - - - +
153E GLY* 3.3 21.0 + - - +
154E LEU* 4.5 1.9 + - - -
155E GLU* 4.1 23.4 - - + +
177E THR* 6.1 1.0 - - - +
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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