Contacts of the helix formed by residues 188 - 196 (chain J) in PDB entry 2BM8
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 MET 188 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162J HIS* 2.9 41.3 - - + +
185J ILE* 4.4 3.8 - - + +
186J GLU 2.8 6.1 + - - -
187J ASP* 1.3 75.1 - - + +
189J ILE* 1.3 65.7 + - - +
190J PRO 3.5 0.4 - - - -
191J TYR* 3.2 22.8 + - - +
192J TRP* 3.1 55.1 + - + -
13L ASN* 4.0 15.3 - - - +
16L ARG* 3.8 29.6 - - - +
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Residues in contact with ILE 189 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J ILE* 3.6 44.0 + - + +
188J MET* 1.3 76.9 - - - +
190J PRO* 1.3 73.4 - - + +
191J TYR 3.1 0.3 + - - -
192J TRP* 3.2 11.5 + - + +
193J TYR* 3.1 21.3 + - - +
200J PHE* 3.6 26.2 - - + -
204J LEU* 5.2 3.6 - - + -
226J ARG* 3.7 10.5 - - + +
227J GLY* 3.8 22.0 - - - +
229J LEU* 4.9 8.7 - - + -
41K TRP* 3.4 33.0 - - + +
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Residues in contact with PRO 190 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J ASP* 3.6 15.3 - - - +
189J ILE* 1.3 97.9 - - + +
191J TYR* 1.3 63.9 + - + +
193J TYR* 3.7 5.9 + - + +
194J ARG* 3.1 25.8 + - - +
222J SER 5.5 2.0 - - - +
225J ASP* 3.8 37.0 - - + +
226J ARG* 3.7 26.6 + - - +
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Residues in contact with TYR 191 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J ASP* 3.1 33.9 - - + -
188J MET* 3.2 23.2 + - - +
189J ILE 3.1 1.0 - - - -
190J PRO* 1.3 80.3 - - + +
192J TRP* 1.3 67.2 + - + +
194J ARG* 3.1 7.2 + - + +
195J TYR* 3.0 57.1 + + + -
16L ARG* 4.5 14.1 - - - +
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Residues in contact with TRP 192 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J HIS* 3.9 24.0 - - + -
165J THR* 3.8 31.6 - - + -
166J PHE* 4.3 18.4 - + - -
185J ILE* 4.2 19.3 - - + -
188J MET* 3.1 41.9 + - + +
189J ILE* 3.7 11.7 - - + +
191J TYR* 1.3 76.5 - - + +
193J TYR* 1.3 57.0 + - - +
195J TYR* 4.7 5.4 - + - +
196J ALA* 2.8 38.4 + - - +
200J PHE* 3.9 30.5 - + + -
12L LEU* 3.6 39.7 - - + +
13L ASN* 3.3 21.4 + - - -
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Residues in contact with TYR 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189J ILE 3.1 15.5 + - - +
190J PRO 4.0 4.5 - - - +
192J TRP* 1.3 73.4 - - - +
194J ARG* 1.3 68.1 + - - +
197J PRO* 3.4 39.6 - - + +
200J PHE* 3.8 16.1 - + + -
201J SER* 4.1 13.9 - - - -
226J ARG* 4.1 14.4 - - - -
41K TRP* 3.5 36.6 - + + -
42K ALA* 3.7 23.3 - - + +
46K ARG* 6.2 0.9 - - - -
51L SER* 5.7 0.3 + - - -
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Residues in contact with ARG 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J PRO 3.1 15.3 + - - +
191J TYR* 3.1 13.8 + - + +
193J TYR* 1.3 82.0 - - - +
195J TYR* 1.3 69.9 + - + +
197J PRO* 3.9 6.2 - - - +
51L SER* 3.0 32.7 + - - -
52L ASP* 3.4 22.4 + - - -
53L PHE* 3.5 57.2 + - + +
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Residues in contact with TYR 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191J TYR* 3.0 47.9 + + + +
192J TRP* 4.4 5.8 - + - +
194J ARG* 1.3 87.1 - - + +
196J ALA* 1.3 59.7 + - + +
197J PRO* 3.3 7.3 - - - +
12L LEU 5.6 1.6 - - - +
15L PHE* 3.5 18.4 - - + +
16L ARG* 3.6 30.2 + - + +
17L GLY* 3.6 26.8 + - - -
19L GLY* 3.2 24.1 - - - -
20L GLU* 3.6 3.5 + - - +
53L PHE* 3.4 41.6 - + - -
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Residues in contact with ALA 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192J TRP* 2.8 13.2 + - - +
195J TYR* 1.3 77.9 - - + +
197J PRO* 1.3 58.3 - - - +
198J GLN 3.5 0.4 - - - -
199J LEU* 4.5 3.1 - - + -
200J PHE* 3.0 28.9 + - - +
12L LEU* 4.2 15.7 - - + +
15L PHE* 3.8 31.2 - - + -
20L GLU* 3.4 18.4 - - - +
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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