Contacts of the helix formed by residues 188 - 196 (chain F) in PDB entry 2BM9
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D ASN* 5.4 7.0 - - - +
161F ALA 5.5 1.1 - - - +
162F HIS* 2.8 50.9 - - + +
185F ILE* 5.0 1.5 - - + +
186F GLU 3.0 6.2 + - - +
187F ASP* 1.3 80.6 - - + +
189F ILE* 1.3 67.7 + - - +
190F PRO* 3.3 0.7 - - - -
191F TYR* 2.8 41.0 + - + +
192F TRP* 3.1 29.0 + - + +
301F SAM 6.1 0.4 - - - +
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Residues in contact with ILE 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C TRP* 3.5 20.4 - - + +
166F PHE* 6.4 0.7 - - + -
185F ILE* 4.1 38.0 + - + +
187F ASP 3.6 0.6 - - - -
188F MET* 1.3 73.0 - - - +
190F PRO* 1.3 74.2 - - + +
192F TRP* 3.1 15.9 + - + +
193F TYR* 3.1 17.3 + - - +
200F PHE* 3.7 28.5 - - + -
204F LEU* 4.6 13.5 - - + -
226F ARG 3.2 29.2 - - - +
227F GLY* 4.0 15.9 - - - -
229F LEU* 5.3 6.7 - - + -
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Residues in contact with PRO 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TRP* 4.9 1.1 - - + -
187F ASP 3.5 12.8 - - - +
188F MET 3.3 4.9 - - - -
189F ILE* 1.3 98.8 - - + +
191F TYR* 1.3 63.9 + - + +
193F TYR* 3.1 10.5 + - + +
194F ARG* 2.9 26.9 + - - +
223F GLN 6.0 0.2 - - - +
225F ASP* 3.8 28.5 - - + +
226F ARG* 3.8 28.3 - - - +
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Residues in contact with TYR 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187F ASP* 4.5 13.5 - - + -
188F MET* 2.8 40.7 + - + +
190F PRO* 1.3 81.3 - - + +
192F TRP* 1.3 61.1 + - + +
194F ARG* 3.2 8.8 + - + +
195F TYR* 3.0 55.8 + + + -
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Residues in contact with TRP 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 3.5 50.7 - - + -
13D ASN* 3.4 27.1 + - - +
162F HIS* 3.7 30.1 - - + -
165F THR* 3.9 13.2 - - - -
166F PHE* 5.0 11.4 - + - -
185F ILE* 4.0 27.8 - - + -
188F MET* 3.1 19.7 + - + -
189F ILE* 3.1 19.3 + - + +
191F TYR* 1.3 76.8 - - + +
193F TYR* 1.3 57.7 + - - +
195F TYR* 4.7 5.6 - + + +
196F ALA* 3.0 34.7 + - + +
200F PHE* 3.6 31.5 - + + +
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Residues in contact with TYR 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C TRP* 3.6 36.1 - + + -
42C ALA* 3.9 21.8 - - + +
189F ILE 3.1 7.3 + - - +
190F PRO* 3.1 10.3 + - + +
192F TRP* 1.3 73.0 - - - +
194F ARG* 1.3 66.2 + - - +
196F ALA 4.3 2.2 - - - -
197F PRO* 3.4 37.7 - - + +
200F PHE* 4.4 12.7 - + + -
201F SER* 4.0 19.1 - - - -
226F ARG* 4.6 8.3 - - - -
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Residues in contact with ARG 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D SER* 5.0 3.3 - - - +
52D ASP* 3.1 33.3 + - - +
53D PHE* 3.5 56.0 + - + +
190F PRO 2.9 13.1 + - - +
191F TYR* 3.4 17.5 - - + +
193F TYR* 1.3 81.7 - - - +
195F TYR* 1.3 81.6 + - + +
197F PRO* 3.9 7.8 - - - +
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Residues in contact with TYR 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU 5.6 2.5 - - - +
15D PHE* 3.5 23.6 - - + +
16D ARG* 3.5 27.8 - - + -
17D GLY* 3.7 16.6 + - - -
19D GLY* 3.4 21.7 - - - +
20D GLU* 3.7 3.8 + - - +
53D PHE* 3.4 37.7 - + - -
191F TYR* 3.0 46.0 + + + +
192F TRP* 4.6 5.8 - + + +
194F ARG* 1.3 93.7 - - + +
196F ALA* 1.3 57.3 + - + +
197F PRO* 3.4 8.1 - - - +
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Residues in contact with ALA 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.6 16.6 - - + +
15D PHE* 3.9 29.2 - - + -
20D GLU* 3.4 13.9 - - - +
192F TRP* 3.0 15.3 + - - +
195F TYR* 1.3 80.9 - - + +
197F PRO* 1.3 65.2 - - - +
198F GLN 3.4 2.5 - - - -
199F LEU* 5.0 2.9 - - + -
200F PHE* 3.2 22.9 + - - +
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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