Contacts of the strand formed by residues 143 - 150 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A MET* 5.7 0.4 - - - -
194A TYR* 4.6 5.8 - - - -
63B NRQ 2.6 30.7 + - - -
141B GLU 3.5 1.5 + - - -
142B ALA* 1.3 75.1 - - - +
144B THR* 1.3 66.1 + - - +
158B SER* 4.1 2.2 - - - -
159B ASP 3.7 11.7 - - - -
160B MET* 3.7 22.2 - - - -
196B ASP* 3.7 0.7 - - - +
197B ARG* 2.8 50.7 + - - +
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Residues in contact with THR 144 (chain B).
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* 3.8 35.0 - - - +
194A TYR* 4.8 6.0 - - - -
220A ARG* 3.2 14.7 + - - -
143B SER* 1.3 76.9 + - - +
145B GLU* 1.3 70.6 + - - +
146B MET* 4.0 1.3 + - + -
157B ARG 4.1 0.2 - - - +
158B SER* 3.3 15.7 + - - -
159B ASP 4.6 4.0 + - - +
194B TYR* 4.3 8.3 - - + -
195B VAL 3.2 9.9 - - - +
196B ASP* 3.0 23.2 + - - +
197B ARG* 3.6 2.0 - - - -
220B ARG* 4.2 5.8 - - - +
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Residues in contact with GLU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 2.7 24.2 + - - -
92B ARG* 5.0 1.0 + - - -
144B THR* 1.3 74.8 - - - +
146B MET* 1.3 65.7 + - - +
147B LEU* 3.5 25.8 - - + +
156B GLY* 3.8 8.3 - - - -
157B ARG 3.4 15.9 - - - +
158B SER* 3.9 1.3 - - - -
176B THR* 4.4 4.2 + - - -
178B TYR* 2.6 32.1 + - - -
194B TYR* 3.2 7.4 - - - +
195B VAL* 2.8 40.4 + - + +
197B ARG* 3.2 30.5 + - - +
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Residues in contact with MET 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU* 5.1 0.7 - - - -
142A ALA 4.2 9.9 - - - +
143A SER* 5.6 0.4 - - - -
159A ASP* 4.0 25.4 - - + +
160A MET 3.8 14.1 - - - +
161A ALA* 3.8 33.7 - - + -
171A ILE* 4.3 11.2 - - + -
144B THR 4.0 1.2 + - - -
145B GLU* 1.3 73.7 - - - +
147B LEU* 1.3 65.6 + - - +
148B TYR* 4.2 9.0 - - + -
156B GLY* 3.3 3.3 - - - -
157B ARG* 2.8 44.9 + - + +
192B VAL* 4.3 11.9 - - + -
193B TYR 3.6 4.9 - - - +
194B TYR* 3.6 31.9 - - + -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LYS* 5.2 1.1 - - - -
70B ILE* 6.2 0.2 - - + -
80B PHE* 4.2 8.3 - - + -
145B GLU* 3.5 31.9 - - + +
146B MET* 1.3 75.5 - - - +
148B TYR* 1.3 63.0 + - - +
154B LEU* 3.7 18.8 - - + -
155B GLU 3.4 7.9 - - - +
178B TYR* 4.0 21.5 - - + -
191B GLY 4.1 0.2 - - - +
192B VAL* 3.3 5.5 - - - +
193B TYR* 2.8 70.7 + - + +
195B VAL* 3.5 32.8 - - + +
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ALA* 5.5 1.6 - - + -
169A HIS* 4.2 26.7 - + + +
171A ILE* 3.0 42.5 - - + +
146B MET* 4.2 13.2 - - + -
147B LEU* 1.3 78.7 - - - +
149B PRO* 1.3 81.4 - - + +
150B ALA* 3.7 4.7 + - + -
154B LEU* 3.7 5.1 - - - +
155B GLU* 3.0 73.7 + - + +
157B ARG* 3.4 25.7 + - + -
192B VAL* 4.0 16.4 - - + -
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Residues in contact with PRO 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A GLY* 5.2 7.1 - - - -
169A HIS* 4.8 11.2 + - + -
148B TYR* 1.3 95.0 - - + +
150B ALA* 1.3 60.4 + - - +
153B GLY 3.4 7.4 - - - +
154B LEU* 3.9 6.0 - - + -
189B MET* 4.0 16.8 - - + -
190B PRO 3.8 18.6 - - - +
191B GLY* 3.8 25.4 - - - +
192B VAL* 3.9 5.4 - - + +
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Residues in contact with ALA 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B TYR* 4.2 8.7 - - + +
149B PRO* 1.3 76.6 - - - +
151B ASP* 1.3 76.2 + - - +
152B GLY 3.4 1.8 - - - -
153B GLY* 2.7 38.0 + - - +
155B GLU* 4.0 31.9 - - + +
189B MET* 4.8 0.6 - - - +
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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