Contacts of the helix formed by residues 154 - 173 (chain B) in PDB entry 1BO1
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 154 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER* 1.3 73.6 - - - +
155B GLU* 1.3 70.6 + - - +
157B VAL* 3.6 2.9 + - - +
158B ALA* 3.4 18.0 + - - +
197B TYR* 3.7 40.5 + - - -
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B SER* 3.0 14.6 - - - +
154B SER* 1.3 85.9 + - - +
156B ASP* 1.3 61.2 + - - +
158B ALA* 2.9 25.7 + - - +
159B GLU* 3.0 10.2 + - - +
372B THR* 6.4 0.7 - - - -
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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
----------------------------------------------------------
150B LYS* 5.0 5.0 + - - -
152B VAL* 3.6 20.7 - - + +
153B SER* 2.8 33.3 + - - +
155B GLU* 1.3 79.0 - - - +
157B VAL* 1.3 50.6 + - - +
159B GLU* 2.6 29.7 + - - +
160B MET* 2.8 17.3 + - - +
186B MET* 4.7 0.2 - - - -
371B LEU* 3.9 17.8 - - + +
372B THR* 3.0 39.4 + - - +
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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
----------------------------------------------------------
98B TYR* 3.5 36.8 - - + +
152B VAL* 3.6 12.3 - - + -
153B SER 3.1 3.4 + - - +
154B SER 3.8 8.1 - - - +
156B ASP* 1.3 75.5 - - - +
158B ALA* 1.3 59.7 + - - +
160B MET* 3.7 2.3 + - - +
161B HIS* 2.9 35.9 + - + +
186B MET* 3.4 20.2 - - + -
187B TYR 5.4 0.2 - - - +
197B TYR* 3.0 43.7 - - + -
198B MET 5.4 0.2 - - - +
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER 3.4 10.3 + - - +
155B GLU* 2.9 15.3 + - - +
157B VAL* 1.3 76.4 - - - +
159B GLU* 1.3 64.5 + - - +
161B HIS* 3.5 7.3 + - - +
162B ASN* 3.3 27.2 + - - +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B GLU 3.0 7.3 + - - +
156B ASP* 2.6 20.1 + - - +
158B ALA* 1.3 70.7 - - - +
160B MET* 1.3 65.4 + - - +
162B ASN* 2.9 17.6 + - + +
163B ILE* 3.0 20.8 + - + +
276B ILE* 3.4 15.4 - - - +
277B MET* 4.4 12.8 - - + +
370B ILE 3.2 7.3 - - - +
371B LEU* 2.8 42.6 - - + +
372B THR* 2.7 27.9 + - - -
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Residues in contact with MET 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.3 34.5 - - + -
156B ASP 2.8 6.0 + - - +
157B VAL 3.8 1.8 - - - +
159B GLU* 1.3 75.9 - - - +
161B HIS* 1.3 54.4 + - + +
163B ILE* 4.1 6.5 - - - -
164B LEU* 2.7 64.6 + - + +
167B TYR* 6.0 0.4 - - - -
183B PHE* 3.8 36.1 - - + -
186B MET* 3.4 37.0 - - + -
199B VAL* 4.8 4.3 - - + -
371B LEU* 3.6 24.3 - - + +
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Residues in contact with HIS 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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71B PHE 3.8 13.0 - - - +
72B LYS* 5.5 2.4 - - - -
73B ALA 5.1 1.6 + - - -
98B TYR* 3.5 41.7 - + + +
99B CYS* 3.5 32.5 + - - -
103B PHE* 6.1 0.2 - + - -
157B VAL* 2.9 23.2 + - + +
158B ALA* 3.5 11.7 + - - +
159B GLU 3.1 1.0 - - - -
160B MET* 1.3 79.1 - - - +
162B ASN* 1.3 64.9 + - - +
164B LEU* 3.7 15.0 + - + +
165B LYS* 4.5 15.8 - - - +
186B MET* 4.3 7.6 - - - -
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Residues in contact with ASN 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ALA* 3.3 17.7 + - - +
159B GLU* 2.9 13.1 + - + +
161B HIS* 1.3 81.9 - - - +
163B ILE* 1.3 65.0 + - + +
165B LYS* 4.6 7.1 + - - +
166B LYS* 5.3 5.7 + - - +
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLU* 3.0 28.8 + - + +
160B MET* 3.6 13.9 - - - +
162B ASN* 1.3 81.0 - - + +
164B LEU* 1.3 68.2 + - - +
165B LYS 2.9 5.5 + - - -
166B LYS* 3.1 7.8 + - - +
167B TYR* 3.0 26.6 + - + -
183B PHE* 5.0 2.5 - - + -
270B PHE* 6.1 0.4 - - + -
274B LEU* 4.8 22.2 - - + -
276B ILE* 4.5 14.1 - - + -
370B ILE* 3.7 32.3 - - + -
371B LEU* 3.9 21.8 - - + -
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Residues in contact with LEU 164 (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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71B PHE* 4.0 8.2 - - + +
99B CYS* 3.9 22.9 - - - -
102B VAL* 4.1 16.2 - - + -
103B PHE* 3.8 25.1 - - + -
106B LEU* 3.9 25.8 - - + -
160B MET* 2.7 42.3 + - + +
161B HIS* 4.0 14.1 - - + +
162B ASN 3.5 1.4 - - - -
163B ILE* 1.3 73.8 - - - +
165B LYS* 1.3 57.1 + - + +
167B TYR* 4.2 12.3 - - + -
168B HIS* 3.0 28.1 + - - +
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Residues in contact with LYS 165 (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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68B PRO* 4.3 6.6 + - + +
71B PHE* 3.5 53.0 - - + +
72B LYS* 3.6 30.9 - - - +
161B HIS 4.5 14.1 - - - +
162B ASN 5.0 4.9 - - - +
163B ILE 2.9 3.4 + - - -
164B LEU* 1.3 69.8 - - + +
166B LYS* 1.3 69.0 + - + +
168B HIS* 3.2 5.2 + - - +
169B GLN* 3.1 21.7 + - - +
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Residues in contact with LYS 166 (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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162B ASN 5.5 5.2 - - - +
163B ILE* 3.1 7.6 + - - +
165B LYS* 1.3 77.2 - - + +
167B TYR* 1.3 64.5 + - - +
169B GLN* 2.9 10.4 + - - +
170B PHE* 2.9 22.0 + - - +
270B PHE* 3.9 7.1 - - + -
273B GLN* 2.9 39.6 + - - +
274B LEU* 3.5 26.7 - - + +
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Residues in contact with TYR 167 (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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106B LEU* 4.0 19.1 - - + -
110B PHE* 3.6 5.2 - - - -
160B MET* 5.9 0.4 - - + -
163B ILE* 3.0 24.4 + - + +
164B LEU* 3.9 17.5 - - + +
166B LYS* 1.3 75.7 - - - +
168B HIS* 1.3 62.2 + - - +
170B PHE* 3.2 3.0 - + - +
171B ILE* 3.0 55.6 + - + +
180B LEU* 4.2 24.0 - - + -
181B PRO 2.5 28.8 + - - -
182B GLN* 3.3 5.0 - - - -
183B PHE* 3.1 42.5 + + - -
270B PHE* 3.4 21.4 - + + -
370B ILE* 4.4 8.7 - - + -
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Residues in contact with HIS 168 (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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66B LEU* 3.3 27.9 - - + +
71B PHE* 4.0 18.2 - + + -
102B VAL* 4.1 5.2 - - + -
105B ASN* 3.0 25.2 + - - -
106B LEU* 3.6 32.8 - - + -
109B ARG* 4.6 2.8 + - - -
164B LEU 3.0 21.3 + - - +
165B LYS 3.5 4.2 + - - +
167B TYR* 1.3 84.3 - - + +
169B GLN* 1.3 64.0 + - - +
171B ILE* 3.3 3.9 + - - +
172B VAL* 3.0 52.6 + - + +
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Residues in contact with GLN 169 (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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165B LYS 3.1 11.3 + - - +
166B LYS* 2.9 12.2 + - - +
168B HIS* 1.3 78.9 + - - +
170B PHE* 1.3 65.4 - - - +
172B VAL* 3.1 39.3 - - - +
173B GLU* 3.2 29.9 + - - +
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Residues in contact with PHE 170 (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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166B LYS 2.9 5.1 + - - -
167B TYR* 3.2 10.3 - + - +
169B GLN* 1.3 72.6 - - - +
171B ILE* 1.3 59.4 + - + +
173B GLU* 2.9 27.7 + - + +
174B CYS* 2.8 48.4 - - - -
178B THR* 3.8 9.6 - - + -
180B LEU* 3.5 33.2 - - + -
266B ARG* 3.8 32.1 - - + -
267B ASP* 3.4 23.3 - - - -
270B PHE* 3.6 41.1 - + + -
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Residues in contact with ILE 171 (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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106B LEU* 4.1 9.2 - - + -
109B ARG* 3.6 25.8 - - + -
110B PHE* 3.6 39.3 - - + -
167B TYR* 3.0 45.0 + - + +
168B HIS 3.6 7.6 - - - +
170B PHE* 1.3 78.4 - - + +
172B VAL* 1.3 62.1 + - - +
174B CYS* 4.5 4.0 - - - -
175B HIS* 3.3 17.3 + - - -
176B GLY* 3.4 8.2 + - - -
178B THR* 4.1 24.7 - - + +
180B LEU* 5.4 0.2 - - + -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ARG* 3.0 31.8 + - - +
168B HIS* 3.0 48.0 + - + +
169B GLN* 3.1 31.9 - - - +
170B PHE 3.0 0.2 - - - -
171B ILE* 1.3 79.8 - - - +
173B GLU* 1.3 58.1 + - + +
174B CYS 3.5 2.6 + - - -
175B HIS* 3.8 15.6 + - - -
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Residues in contact with GLU 173 (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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169B GLN* 3.2 33.0 - - - +
170B PHE* 2.9 23.8 + - + +
172B VAL* 1.3 78.0 - - + +
174B CYS* 1.3 57.7 + - - +
175B HIS* 3.7 8.7 - - - -
266B ARG* 3.6 11.3 + - - -
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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
------------------------------------------------------------
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