Contacts of the helix formed by residues 172 - 184 (chain B) in PDB entry 1BO6
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 TRP 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46B TYR* 3.5 45.2 + + + +
49B SER* 5.0 0.6 + - - -
129B CYS* 5.3 0.6 - - - +
130B ARG 3.4 28.8 + - - +
132B ALA* 3.7 14.1 - - + -
135B VAL* 3.9 17.7 - - + +
162B PHE* 3.5 27.8 + + + -
170B GLY 3.4 4.4 + - - -
171B SER* 1.3 72.5 + - - +
173B TYR* 1.3 98.6 + + + +
175B HIS* 3.3 1.4 + - - +
176B VAL* 2.9 45.7 + - + +
280B TYR* 3.4 34.3 - + - -
284B MET* 3.9 13.7 - - + -
291B PHE* 3.5 28.7 - + - -
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Residues in contact with TYR 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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132B ALA* 4.9 1.3 - - + -
162B PHE* 3.9 20.6 - + - -
163B MET* 3.7 17.5 - - - -
171B SER* 3.1 13.7 - - - +
172B TRP* 1.3 104.8 - + - +
174B ASP* 1.3 62.6 + - - +
176B VAL* 4.0 0.9 - - - +
177B LYS* 3.0 38.8 + - - +
276B PHE* 3.5 28.1 + - - -
279B HIS* 3.4 37.2 + + - -
280B TYR* 4.0 19.3 - + - -
283B GLN* 3.6 37.5 - - + +
284B MET* 4.1 7.1 - - + +
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Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PRO* 6.0 0.9 - - - -
112B LYS* 5.4 10.0 + - - +
171B SER* 2.9 31.1 + - - +
173B TYR* 1.3 76.7 - - - +
175B HIS* 1.3 63.2 + - - +
177B LYS* 4.0 19.6 + - - +
178B ALA* 3.0 28.2 + - - +
283B GLN* 5.0 3.3 - - - +
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Residues in contact with HIS 175 (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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45B THR* 3.7 23.5 + - - -
46B TYR* 3.5 23.9 - + + +
108B HIS 2.8 26.7 + - - -
109B LEU 3.6 5.5 - - - -
110B PRO* 3.9 23.3 - - + +
127B TYR* 2.9 26.5 + + - +
169B TYR 4.1 11.4 - - - -
171B SER 2.9 16.9 + - - +
172B TRP 3.3 5.8 - - - +
174B ASP* 1.3 79.6 - - - +
176B VAL* 1.3 63.1 + - + +
178B ALA* 4.0 0.9 - - - +
179B TRP* 3.2 50.4 + + - -
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B TYR* 5.6 0.4 - - + -
127B TYR* 3.6 19.5 - - - +
129B CYS* 4.3 9.4 - - + -
172B TRP* 2.9 53.4 + - + +
173B TYR 4.1 2.0 - - - +
175B HIS* 1.3 69.1 - - + +
177B LYS* 1.3 56.9 + - - +
179B TRP* 3.4 1.6 + - - +
180B TRP* 2.8 37.3 + - + +
190B PHE* 4.1 20.6 - - + -
284B MET* 4.0 21.3 - - + -
289B VAL* 4.6 6.3 - - + -
291B PHE* 4.3 13.7 - - + -
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Residues in contact with LYS 177 (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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173B TYR* 3.0 36.1 + - - +
174B ASP* 4.0 16.9 + - - +
176B VAL* 1.3 75.5 - - - +
178B ALA* 1.3 62.5 + - - +
180B TRP* 3.2 9.4 + - - +
181B GLU* 3.0 23.6 + - - +
283B GLN* 3.2 35.5 + - - +
284B MET* 4.0 13.7 - - - -
286B ASP 6.1 1.3 - - - -
287B CYS* 3.8 27.8 - - + -
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Residues in contact with ALA 178 (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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110B PRO* 5.7 0.7 - - + -
111B PRO* 3.6 26.2 - - + +
174B ASP 3.0 19.7 + - - +
175B HIS 4.0 0.2 - - - +
177B LYS* 1.3 75.8 - - - +
179B TRP* 1.3 58.4 + - - +
181B GLU* 3.3 10.3 + - - +
182B LYS* 3.0 29.1 + - - +
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Residues in contact with TRP 179 (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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42B VAL* 5.0 0.7 - - + -
44B ALA* 3.5 27.1 - - + +
109B LEU 3.1 25.7 + - - -
111B PRO* 3.2 34.6 - - + +
114B LEU* 4.0 14.4 - - + -
119B TRP* 3.7 20.6 - + - -
125B MET* 3.8 28.3 - - + -
127B TYR* 3.3 48.8 - + + +
175B HIS* 3.2 28.4 + + - +
176B VAL 3.9 0.9 - - - +
178B ALA* 1.3 76.4 - - - +
180B TRP* 1.3 60.4 + - - +
182B LYS* 3.1 10.8 + - + +
183B SER* 2.9 28.1 + - - -
188B VAL* 4.4 12.2 - - + +
190B PHE* 4.0 2.8 - - - -
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Residues in contact with TRP 180 (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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176B VAL 2.8 19.7 + - - +
177B LYS* 3.4 7.4 - - - +
179B TRP* 1.3 75.2 - - - +
181B GLU* 1.3 66.3 + - + +
183B SER* 2.3 34.2 + - - -
184B LYS* 3.8 2.9 + - - +
190B PHE* 3.4 58.9 - + + -
192B PHE* 5.0 3.6 - + - -
287B CYS* 3.7 21.1 - - - -
288B THR* 3.1 32.9 + - - +
289B VAL* 3.5 29.0 - - + +
290B LYS* 4.7 4.0 - - + -
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Residues in contact with GLU 181 (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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177B LYS 3.0 12.3 + - - +
178B ALA* 3.5 12.1 - - - +
180B TRP* 1.3 82.6 - - + +
182B LYS* 1.3 69.7 + - + +
184B LYS* 3.0 52.6 - - - +
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Residues in contact with LYS 182 (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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111B PRO* 4.0 16.4 - - + -
119B TRP* 3.6 57.3 - - + +
178B ALA 3.0 16.8 + - - +
179B TRP* 3.1 17.7 + - + +
181B GLU* 1.3 84.3 - - + +
183B SER* 1.3 58.5 + - - +
184B LYS* 3.0 5.9 + - - +
185B ASN* 3.1 20.6 + - - +
188B VAL* 3.7 7.3 - - + +
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Residues in contact with SER 183 (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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179B TRP 2.9 12.0 + - - -
180B TRP* 2.3 41.5 + - - -
182B LYS* 1.3 73.3 - - - +
184B LYS* 1.3 65.1 + - - +
185B ASN 2.9 12.3 - - - +
188B VAL* 3.6 26.8 - - - +
190B PHE* 3.8 22.2 - - - -
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Residues in contact with LYS 184 (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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180B TRP 4.7 1.3 - - - +
181B GLU* 3.0 47.8 + - - +
182B LYS 3.0 1.0 + - - +
183B SER* 1.3 79.7 + - - +
185B ASN* 1.3 61.5 + - - +
186B SER* 3.4 2.9 + - - -
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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