Contacts of the helix formed by residues 173 - 183 (chain B) in PDB entry 1BMO
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 GLU 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B ASN* 4.0 22.8 + - - +
172B THR* 1.3 74.5 - - - +
174B LYS* 1.3 67.3 + - + +
176B LYS* 2.9 19.6 + - - +
177B LEU* 3.0 12.3 + - - +
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Residues in contact with LYS 174 (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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172B THR* 3.8 4.0 + - - +
173B GLU* 1.3 81.9 - - + +
175B GLN* 1.3 63.4 + - + +
177B LEU* 3.3 30.4 + - + +
178B ARG* 3.0 55.1 + - - +
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Residues in contact with GLN 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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170B LEU 4.7 2.1 - - - +
171B LEU* 3.6 22.6 - - + +
172B THR* 3.1 45.3 + - - +
173B GLU 3.1 1.0 - - - -
174B LYS* 1.3 76.2 - - + +
176B LYS* 1.3 65.7 + - - +
178B ARG* 3.1 7.0 + - - +
179B VAL* 2.9 27.7 + - - +
212B PHE* 3.9 20.8 - - + -
216B TRP* 3.8 21.2 + - - +
220B GLN* 5.6 1.9 + - - +
284B LEU 5.6 0.8 + - - -
285B VAL 4.9 2.4 + - - -
286B ILE* 3.8 25.0 + - - +
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Residues in contact with LYS 176 (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 TYR* 3.8 34.6 + - + -
165B ASP* 2.7 48.1 + - - +
166B GLU* 5.2 0.6 - - - +
167B ASP 5.4 0.4 - - - +
168B ASN* 3.1 15.0 - - - +
171B LEU* 3.4 25.1 - - + +
172B THR 2.9 16.6 + - - +
173B GLU* 2.9 12.6 + - - +
175B GLN* 1.3 73.4 - - - +
177B LEU* 1.3 54.7 + - - +
179B VAL 3.1 1.6 + - - -
180B LYS* 2.7 38.4 + - - +
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Residues in contact with LEU 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 GLU* 3.0 13.1 + - - +
174B LYS* 3.5 37.7 - - + +
176B LYS* 1.3 76.1 - - - +
178B ARG* 1.3 64.7 + - + +
180B LYS* 3.0 38.3 + - + +
181B LYS* 3.1 21.5 + - + +
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Residues in contact with ARG 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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174B LYS* 3.0 48.6 + - + +
175B GLN* 3.3 9.9 - - - +
177B LEU* 1.3 78.7 - - + +
179B VAL* 1.3 62.2 + - - +
180B LYS 3.2 0.7 + - - -
181B LYS* 3.4 13.4 + - - +
182B ILE* 3.5 17.2 + - - +
212B PHE* 3.5 44.9 - - + -
283B ASP* 5.5 4.4 + - - -
284B LEU* 3.3 34.2 - - - +
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Residues in contact with VAL 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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158B LEU* 3.2 58.8 - - + +
159B VAL* 3.9 11.4 - - + +
162B TYR* 3.5 20.6 - - + -
171B LEU* 3.9 8.5 - - + -
175B GLN 2.9 16.3 + - - +
176B LYS 4.0 2.9 - - - +
178B ARG* 1.3 74.9 - - - +
180B LYS* 1.3 56.4 + - - +
181B LYS 3.4 0.2 - - - -
182B ILE* 3.4 10.9 - - + +
183B HIS* 2.8 27.4 + - + +
212B PHE* 3.7 13.7 - - + -
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Residues in contact with LYS 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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162B TYR* 3.6 25.9 + - + +
176B LYS 2.7 17.5 + - - +
177B LEU* 3.0 30.5 + - + +
179B VAL* 1.3 71.2 - - - +
181B LYS* 1.3 72.7 + - - +
182B ILE 3.0 1.9 + - - -
183B HIS* 3.1 1.0 + - - +
184B GLU* 2.6 74.3 + - - +
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Residues in contact with LYS 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 LEU* 3.1 23.4 + - + +
178B ARG* 3.4 8.9 + - - +
180B LYS* 1.3 92.6 - - - +
182B ILE* 1.3 64.7 + - + +
184B GLU* 4.2 14.5 + - - +
185B ASN* 3.5 19.6 + - - +
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Residues in contact with ILE 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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155B LYS* 4.4 7.6 - - + -
158B LEU* 5.5 0.7 - - + -
159B VAL* 4.2 14.6 - - + -
178B ARG 3.6 15.5 - - - +
179B VAL* 3.4 17.4 + - + +
180B LYS 3.0 0.2 - - - -
181B LYS* 1.3 80.9 - - + +
183B HIS* 1.3 69.1 + - - +
185B ASN* 3.3 14.5 - - - +
188B ARG* 3.4 21.5 - - - +
208B ASN* 5.6 1.6 - - - +
209B MET* 3.7 47.1 - - + +
212B PHE* 4.7 9.2 - - + -
213B PRO* 3.8 23.1 - - + -
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Residues in contact with HIS 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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159B VAL* 3.9 17.3 - - + -
162B TYR* 3.2 37.8 + + + -
163B GLU* 2.9 35.9 + - + -
179B VAL* 2.8 20.9 + - + +
180B LYS 3.1 4.0 + - - +
182B ILE* 1.3 73.8 - - - +
184B GLU* 1.3 68.5 + - + +
185B ASN 3.2 3.3 + - - +
188B ARG* 2.9 40.1 + - - +
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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