Contacts of the helix formed by residues 143 - 161 (chain B) in PDB entry 3BQM
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 GLN 143 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B SER 3.4 7.9 + - - +
142B LEU* 1.3 73.1 - - - +
144B PRO* 1.4 81.3 - - + +
145B ASP* 3.6 18.6 - - - +
146B GLU* 2.9 37.9 + - - +
147B PHE* 3.1 11.1 + - - +
201B HIS* 5.1 0.2 - - - -
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Residues in contact with PRO 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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142B LEU 4.0 2.0 - - - +
143B GLN* 1.4 94.6 - - + +
145B ASP* 1.3 57.4 + - - +
147B PHE* 3.4 7.7 + - + +
148B GLN* 3.0 27.8 + - - +
201B HIS* 5.1 6.9 - - - +
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Residues in contact with ASP 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLN* 3.1 17.3 + - - +
144B PRO* 1.3 77.2 - - - +
146B GLU* 1.3 70.4 + - - +
148B GLN* 3.6 7.9 + - - +
149B LYS* 2.5 66.6 + - - +
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Residues in contact with GLU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B SER 3.9 3.5 - - - +
142B LEU* 3.6 12.8 - - + +
143B GLN* 2.9 40.4 + - + +
145B ASP* 1.3 87.5 - - - +
147B PHE* 1.3 65.1 + - - +
149B LYS* 3.2 9.5 + - - +
150B ILE* 3.2 16.6 + - - +
239B ASP* 4.8 1.6 - - - +
292B PHE* 3.4 56.3 - - + -
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Residues in contact with PHE 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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136B PHE* 3.6 20.6 - + - -
137B ASP 3.6 25.8 - - - -
138B GLY* 3.9 1.8 - - - -
142B LEU* 4.2 6.5 - - + +
143B GLN 3.1 10.2 + - - +
144B PRO* 3.6 9.0 - - + +
146B GLU* 1.3 76.7 - - - +
148B GLN* 1.3 63.2 + - - +
150B ILE* 3.1 21.0 + - + +
151B LEU* 3.1 28.6 + - + +
172B GLN* 3.6 23.6 - - - -
199B VAL* 3.6 34.1 - - + -
201B HIS* 3.6 46.2 - + + +
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Residues in contact with GLN 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PRO 3.0 17.3 + - - +
145B ASP* 3.6 10.1 - - - +
146B GLU 3.3 0.2 - - - -
147B PHE* 1.3 77.9 - - - +
149B LYS* 1.3 55.9 + - + +
151B LEU* 3.2 26.3 + - - +
152B ASP* 2.8 59.1 + - - +
155B LYS* 4.8 5.5 - - - +
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ASP* 2.5 50.1 + - - +
146B GLU* 3.2 5.8 + - - +
148B GLN* 1.3 73.3 - - + +
150B ILE* 1.3 60.3 + - - +
152B ASP* 3.8 7.4 - - - +
153B PHE* 2.9 29.5 + - - +
292B PHE* 3.8 37.6 - - + +
293B GLU* 2.5 33.5 + - - +
295B LEU* 3.7 7.7 - - + +
296B LYS* 5.6 4.9 - - + +
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Residues in contact with ILE 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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136B PHE* 3.8 31.6 - - + -
137B ASP* 4.0 24.5 - - + +
142B LEU* 4.1 12.3 - - + -
146B GLU 3.2 12.6 + - - +
147B PHE* 3.1 10.6 + - + +
149B LYS* 1.3 72.8 - - - +
151B LEU* 1.3 65.0 + - - +
153B PHE* 3.1 5.5 + - - +
154B MET* 3.0 25.6 + - + +
237B ILE* 4.1 33.9 - - + -
238B THR* 6.1 0.9 - - - -
239B ASP* 6.1 0.7 - - + -
261B ILE* 5.1 0.2 - - + -
292B PHE* 3.8 26.7 - - + -
295B LEU* 4.1 8.1 - - + -
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Residues in contact with LEU 151 (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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136B PHE* 3.8 23.6 - - + -
147B PHE* 3.1 34.4 + - + +
148B GLN* 3.4 33.0 - - - +
150B ILE* 1.3 74.4 - - - +
152B ASP* 1.3 63.2 + - - +
154B MET* 3.3 26.4 + - + +
155B LYS* 3.2 29.3 + - - +
196B LEU* 4.1 16.2 - - + +
199B VAL* 4.3 22.2 - - + +
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Residues in contact with ASP 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLN* 2.8 47.5 + - - +
149B LYS* 4.0 8.0 - - - +
151B LEU* 1.3 69.8 - - - +
153B PHE* 1.3 60.4 + - - +
155B LYS* 3.2 27.5 + - - +
156B ASP* 2.9 40.1 + - - +
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Residues in contact with PHE 153 (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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1B BQM 3.4 42.4 - - + -
134B PHE* 5.1 2.0 - + - -
149B LYS 2.9 19.5 + - - +
150B ILE* 3.4 4.0 - - - +
152B ASP* 1.3 75.9 - - - +
154B MET* 1.3 65.8 + - + +
156B ASP* 3.4 8.4 + - - +
157B VAL* 3.1 32.0 + - + +
237B ILE* 4.0 20.9 - - + -
259B ILE* 4.1 11.0 - - + -
295B LEU* 3.5 49.6 - - + -
298B LEU* 4.0 13.5 - - + -
299B PHE* 3.9 25.6 - - + -
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Residues in contact with MET 154 (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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134B PHE* 3.5 50.2 - - + -
136B PHE* 3.7 36.8 - - + -
150B ILE* 3.0 14.5 + - - +
151B LEU* 3.6 41.3 - - + +
153B PHE* 1.3 77.0 - - + +
155B LYS* 1.3 62.5 + - - +
157B VAL* 3.4 2.9 + - - +
158B MET* 3.1 40.8 + - + +
170B ALA* 4.8 2.9 - - - -
196B LEU* 4.2 12.1 - - + -
237B ILE* 4.3 10.3 - - + -
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Residues in contact with LYS 155 (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 GLN* 4.8 5.9 - - - +
151B LEU* 3.2 16.2 + - + +
152B ASP* 3.3 31.7 + - - +
154B MET* 1.3 75.1 - - - +
156B ASP* 1.3 59.9 + - - +
158B MET* 3.2 1.3 + - - +
159B LYS* 2.9 44.6 + - - +
192B PRO* 3.9 20.8 - - + +
193B ASP* 3.2 47.6 + - - +
196B LEU* 3.6 21.4 - - + +
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Residues in contact with ASP 156 (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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152B ASP* 2.9 27.7 + - - +
153B PHE* 3.6 8.0 - - - +
155B LYS* 1.3 76.3 - - - +
157B VAL* 1.3 61.7 + - - +
159B LYS* 3.8 13.4 + - - +
160B LYS 3.2 17.0 + - - -
296B LYS* 6.0 1.2 - - - -
299B PHE* 3.4 47.6 - - + +
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Residues in contact with VAL 157 (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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1B BQM 3.3 38.8 - - - -
134B PHE* 3.8 14.6 - - + -
153B PHE* 3.1 24.2 + - + +
154B MET 3.7 7.2 - - - +
155B LYS 3.3 0.2 - - - -
156B ASP* 1.3 77.2 - - - +
158B MET* 1.3 63.1 + - - +
160B LYS* 3.3 5.2 + - - +
161B LEU* 3.1 33.6 + - + +
168B PHE* 4.8 2.2 - - + -
299B PHE* 4.0 10.1 - - + -
302B LEU* 3.5 26.7 - - + -
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Residues in contact with MET 158 (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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134B PHE* 3.6 18.6 - - + -
154B MET* 3.1 33.5 + - + +
155B LYS 3.9 0.4 - - - +
157B VAL* 1.3 75.7 - - - +
159B LYS* 1.3 62.8 + - - +
161B LEU 3.3 3.3 + - - -
162B SER* 3.1 20.8 + - - -
168B PHE* 3.7 37.2 - - + -
170B ALA* 5.7 0.4 - - + -
181B PHE* 3.6 34.3 - - + -
186B TYR* 4.0 13.1 + - + -
192B PRO* 3.7 28.9 - - + -
196B LEU* 3.9 19.5 - - + -
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Residues in contact with LYS 159 (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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155B LYS* 2.9 33.0 + - - +
156B ASP* 3.8 12.8 + - - +
158B MET* 1.3 78.3 - - - +
160B LYS* 1.3 61.5 + - - +
162B SER* 3.3 23.1 + - - -
192B PRO* 4.0 18.8 - - + -
193B ASP* 3.1 38.1 + - - +
160C LYS* 4.3 0.9 + - - -
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Residues in contact with LYS 160 (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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156B ASP 3.2 15.1 + - - +
157B VAL 3.6 5.2 - - - +
158B MET 3.3 0.2 - - - -
159B LYS* 1.3 79.3 - - - +
161B LEU* 1.3 62.1 + - + +
162B SER 3.3 0.2 - - - -
299B PHE* 4.1 9.4 - - + -
302B LEU* 5.9 0.9 - - + -
303B GLN* 3.4 30.1 - - + +
306B ILE* 3.6 32.3 - - + +
159C LYS 4.3 1.2 + - - -
160C LYS* 3.2 45.5 + - - +
162C SER* 2.8 43.2 + - - -
163C ASN* 4.8 0.4 - - - +
164C THR* 4.5 2.9 - - - -
306C ILE* 5.7 0.9 - - - +
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Residues in contact with LEU 161 (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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1B BQM 4.0 17.5 - - - -
157B VAL* 3.1 34.2 + - + +
158B MET 3.3 5.1 + - - -
159B LYS 3.2 0.2 - - - -
160B LYS* 1.3 80.9 - - + +
162B SER* 1.3 62.2 + - - +
163B ASN 3.7 0.5 + - - -
164B THR* 2.8 29.4 + - - +
166B TYR* 4.2 29.0 - - + +
168B PHE* 3.9 24.4 - - + -
186B TYR* 4.2 5.0 + - - -
302B LEU* 5.5 1.3 - - + -
306B ILE* 4.6 10.8 - - + -
306C ILE* 4.3 21.8 - - + +
308C VAL* 4.2 16.8 - - + +
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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
------------------------------------------------------------
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