Contacts of the helix formed by residues 196 - 206 (chain D) 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 ALA 196 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192D TRP 3.1 14.6 + - - +
193D TYR 3.8 0.2 - - - -
195D TYR* 1.3 82.7 - - + +
197D PRO* 1.3 68.9 - - - +
198D GLN 3.3 2.7 - - - -
199D LEU* 4.1 11.2 - - + -
200D PHE* 3.0 24.4 + - - +
12F LEU* 4.5 14.1 - - + -
15F PHE* 4.7 8.7 - - + -
20F GLU* 3.3 22.2 - - + +
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Residues in contact with PRO 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D TYR* 3.3 38.2 - - + +
194D ARG* 3.5 12.3 - - - +
195D TYR 3.9 1.1 - - - -
196D ALA* 1.3 88.9 - - - +
198D GLN* 1.3 58.0 - - - +
201D SER* 3.1 31.7 + - - -
20F GLU* 4.6 4.9 - - + +
51F SER* 4.8 16.2 - - - +
53F PHE* 6.3 0.2 - - + -
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Residues in contact with GLN 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ALA 3.3 0.4 - - - -
197D PRO* 1.3 77.4 - - - +
199D LEU* 1.3 81.0 + - - +
201D SER* 3.1 7.5 + - - -
202D GLU* 3.0 23.7 + - - +
20F GLU* 3.8 12.4 + - - +
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Residues in contact with LEU 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ALA* 4.1 6.5 - - + -
198D GLN* 1.3 88.2 - - - +
200D PHE* 1.3 56.6 + - - +
202D GLU* 3.3 8.6 + - + +
203D TYR* 2.9 74.6 + - + +
10F GLN* 3.6 20.4 - - - +
12F LEU* 3.8 16.4 - - + -
15F PHE* 4.2 9.2 - - + -
20F GLU* 3.2 27.2 + - - +
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Residues in contact with PHE 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE* 3.9 24.2 - + - -
189D ILE* 3.6 35.7 - - + -
192D TRP* 3.9 25.4 - + + +
193D TYR* 3.8 24.5 - + + -
196D ALA* 3.0 22.7 + - + +
197D PRO 4.6 0.2 - - - +
199D LEU* 1.3 73.8 - - - +
201D SER* 1.3 62.2 + - - +
202D GLU 3.0 2.0 - - - -
203D TYR* 4.5 2.9 - - - +
204D LEU* 2.9 63.5 + - + +
41E TRP* 3.6 33.2 - + - -
12F LEU* 4.6 7.6 - - + +
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Residues in contact with SER 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D TYR* 4.0 14.0 - - - -
197D PRO 3.1 20.8 + - - -
198D GLN* 3.1 6.3 + - - -
200D PHE* 1.3 83.0 - - - +
202D GLU* 1.3 56.7 + - - +
204D LEU* 4.5 3.2 - - - +
205D GLY* 3.3 19.4 + - - -
38E LEU 4.9 2.6 - - - +
39E ASP* 5.5 1.7 - - - -
41E TRP* 5.2 4.4 - - - +
42E ALA* 4.4 11.8 + - - +
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Residues in contact with GLU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D GLN* 3.0 14.4 + - + +
199D LEU* 3.7 13.3 - - + +
201D SER* 1.3 73.7 - - - +
203D TYR* 1.3 74.9 + - + +
204D LEU 3.1 1.1 - - - -
205D GLY* 2.8 13.3 + - - -
206D ALA* 3.0 13.5 + - - +
7F GLN* 2.7 41.8 + - - +
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Residues in contact with TYR 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE* 3.9 21.3 - + + -
199D LEU* 2.9 40.7 + - + +
200D PHE* 4.0 1.3 - - - +
202D GLU* 1.3 80.1 - - - +
204D LEU* 1.3 61.2 + - - +
206D ALA* 3.4 7.8 + - - +
207D PHE* 3.3 23.4 - - - -
7F GLN* 4.5 14.4 - - - -
8F ASN 4.3 4.6 + - - -
9F PHE* 3.7 34.6 - + + -
10F GLN* 2.7 58.5 + - - -
12F LEU* 3.7 35.7 - - + -
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D PHE* 4.1 6.5 - - + -
169D MET* 3.9 25.1 - - + -
185D ILE* 5.7 0.7 - - + -
189D ILE* 5.1 7.2 - - + -
200D PHE* 2.9 41.1 + - + +
201D SER* 4.5 2.7 - - - +
203D TYR* 1.3 79.1 - - - +
205D GLY* 1.3 60.2 + - - +
207D PHE* 3.4 13.7 + - - +
229D LEU* 4.2 8.7 - - + -
38E LEU* 3.7 35.1 - - + +
41E TRP* 3.4 50.9 - - + +
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Residues in contact with GLY 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D SER 3.3 12.8 + - - -
202D GLU* 2.8 8.0 + - - -
204D LEU* 1.3 74.9 - - - +
206D ALA* 1.3 55.5 + - - +
207D PHE 3.0 6.3 - - - -
208D ARG* 3.0 31.2 + - - +
38E LEU 3.8 18.1 + - - -
39E ASP* 4.2 8.6 - - - +
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D GLU* 3.0 9.0 + - - +
203D TYR* 3.7 12.3 - - - +
204D LEU 3.3 0.8 - - - -
205D GLY* 1.3 76.4 - - - +
207D PHE* 1.3 56.3 + - + +
208D ARG* 3.2 4.1 + - - +
209D ASP 5.1 1.0 + - - -
3F ASP* 3.0 37.1 - - - +
4F TYR* 3.2 35.8 + - + +
7F GLN* 3.5 16.4 - - - +
9F PHE* 5.4 1.6 - - + -
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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