Contacts of the helix formed by residues 196 - 207 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A TRP* 2.7 17.6 + - - +
195A TYR* 1.3 74.0 - - + +
197A PRO* 1.3 66.3 - - - +
198A GLN 3.2 0.4 + - - -
199A LEU* 3.4 5.3 + - + -
200A PHE* 3.0 21.1 + - - +
12E LEU* 4.0 17.9 - - + +
15E PHE* 3.9 20.0 - - + -
20E GLU* 3.2 24.7 - - + -
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Residues in contact with PRO 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A TYR* 3.4 39.1 - - + +
194A ARG 4.0 6.3 - - - +
195A TYR 3.2 9.4 - - - +
196A ALA* 1.3 89.7 - - - +
198A GLN* 1.3 64.8 + - + +
200A PHE* 4.1 1.6 - - - +
201A SER* 3.5 22.7 + - - -
20E GLU* 3.3 10.3 - - - +
51E SER* 5.7 9.4 - - - +
53E PHE* 5.9 1.3 - - + -
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Residues in contact with GLN 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ALA 3.2 0.8 + - - -
197A PRO* 1.3 84.6 - - + +
199A LEU* 1.3 65.7 + - + +
200A PHE 3.3 0.2 + - - -
201A SER* 3.4 4.1 + - - -
202A GLU* 3.2 24.2 + - - +
20E GLU* 3.4 22.4 + - - +
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Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ALA* 3.4 7.0 + - + +
198A GLN* 1.3 82.2 - - + +
200A PHE* 1.3 56.8 + - - +
202A GLU* 3.8 21.9 - - + +
203A TYR* 3.0 58.7 + - + +
10E GLN* 3.2 38.1 - - + +
12E LEU* 4.5 6.7 - - + -
15E PHE* 4.5 11.9 - - + -
20E GLU* 3.4 16.5 + - + +
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Residues in contact with PHE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.7 30.1 - + - -
189A ILE* 3.6 31.4 - - + -
192A TRP* 4.0 33.0 - + + +
193A TYR* 4.1 23.6 - + + -
196A ALA 3.0 17.4 + - - +
197A PRO 4.1 1.6 - - - +
199A LEU* 1.3 77.5 - - - +
201A SER* 1.3 65.2 + - - +
203A TYR* 3.3 1.5 + - - +
204A LEU* 2.8 51.1 + - + +
41B TRP* 3.9 30.7 - + - -
12E LEU* 4.1 9.1 - - + +
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A TYR* 4.3 14.2 - - - -
197A PRO 3.5 14.9 + - - -
198A GLN* 3.4 5.5 + - - -
200A PHE* 1.3 82.3 - - - +
202A GLU* 1.3 55.1 + - - +
204A LEU* 3.6 3.9 - - - +
205A GLY* 2.6 34.8 + - - -
38B LEU 5.1 2.0 - - - +
39B ASP 6.1 1.3 - - - -
41B TRP* 5.2 5.8 - - - -
42B ALA* 5.1 6.8 - - - +
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLN 3.2 15.7 + - - +
199A LEU* 3.8 22.1 - - + +
201A SER* 1.3 79.4 - - - +
203A TYR* 1.3 61.9 + - - +
205A GLY* 3.8 2.0 + - - -
206A ALA* 3.6 14.0 + - - +
3E ASP* 4.9 4.9 - - - +
7E GLN* 2.9 42.5 + - - +
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.9 24.2 - + + -
199A LEU* 3.0 33.1 + - + +
200A PHE 3.7 3.4 - - - +
201A SER 3.2 0.2 - - - -
202A GLU* 1.3 80.8 - - - +
204A LEU* 1.3 64.5 + - - +
205A GLY 3.1 0.2 - - - -
206A ALA* 3.2 14.5 + - - +
207A PHE* 3.2 20.2 - - - -
7E GLN* 3.4 25.4 - - - -
8E ASN 4.2 6.4 + - - -
9E PHE* 3.4 32.4 - + + -
10E GLN* 3.1 49.0 + - - +
12E LEU* 3.4 33.0 - - + -
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 4.0 20.8 - - + -
169A MET* 4.9 2.9 - - + -
189A ILE* 4.9 6.1 - - + -
200A PHE* 2.8 44.9 + - + +
201A SER* 3.9 4.0 - - - +
203A TYR* 1.3 73.8 - - - +
205A GLY* 1.3 65.5 + - - +
207A PHE* 3.3 21.2 + - + +
229A LEU* 4.8 19.5 - - + -
38B LEU* 3.3 54.2 - - + +
41B TRP* 4.1 21.1 - - + +
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Residues in contact with GLY 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A SER 2.6 20.9 + - - -
202A GLU* 4.1 3.6 - - - -
203A TYR 3.1 0.6 - - - -
204A LEU* 1.3 74.9 - - - +
206A ALA* 1.3 60.2 + - - +
208A ARG* 3.0 35.7 + - - +
38B LEU 4.3 13.4 + - - -
39B ASP* 4.6 7.2 - - - -
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLU 3.6 9.0 + - - +
203A TYR* 3.2 18.1 + - - +
204A LEU 3.2 0.6 - - - -
205A GLY* 1.3 77.8 - - - +
207A PHE* 1.3 60.9 + - + +
208A ARG* 3.2 8.3 + - - +
209A ASP* 4.7 1.4 + - - -
3E ASP* 3.4 44.6 + - + +
4E TYR* 3.4 28.2 + - - +
7E GLN* 4.8 2.9 - - - +
9E PHE* 4.8 4.3 - - + -
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Residues in contact with PHE 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.7 26.0 - + - -
169A MET* 3.3 46.0 - - + -
170A LYS* 4.2 14.4 - - + -
173A VAL* 4.5 7.0 - - + -
203A TYR 3.2 22.2 - - - -
204A LEU* 3.3 11.9 + - + +
205A GLY 3.2 1.4 - - - -
206A ALA* 1.3 74.7 - - + +
208A ARG* 1.3 63.0 + - - +
209A ASP 3.4 2.2 - - - -
210A VAL* 3.3 20.1 - - + +
211A LEU* 3.0 28.8 + - + +
38B LEU* 3.8 8.2 - - + +
4E TYR* 3.8 20.6 - - + -
9E PHE* 3.7 26.5 - + - -
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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