Contacts of the helix formed by residues 196 - 207 (chain A) in PDB entry 1M1B
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 PRO 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ALA 4.8 0.2 - - - +
195A ASP* 1.3 87.1 - - + +
197A SER* 1.3 64.2 + - - -
198A ASP 3.3 1.8 - - - -
199A ILE* 3.0 11.0 + - + -
200A GLU* 2.8 46.3 + - + +
219A TYR* 3.9 24.0 - - + -
222A THR* 3.4 37.5 - - + +
226A HIS* 4.5 2.2 - - - +
227A PHE* 4.8 5.4 - - + -
230A MET* 4.8 2.5 - - + -
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Residues in contact with SER 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 LYS* 3.0 38.4 + - - +
195A ASP* 2.7 25.5 + - - -
196A PRO* 1.3 76.2 - - - +
198A ASP* 1.3 55.1 + - - +
200A GLU* 3.2 17.9 + - - +
201A ALA* 2.9 30.0 + - - +
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Residues in contact with ASP 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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163A PHE* 3.6 47.5 - - + +
191A SER* 2.5 33.7 + - - +
193A LYS* 3.0 39.1 + - - +
195A ASP 4.7 0.8 + - - +
196A PRO 3.3 1.0 - - - -
197A SER* 1.3 76.4 + - - +
199A ILE* 1.3 59.0 + - + +
201A ALA* 3.2 7.6 + - - +
202A PHE* 2.8 30.8 + - - +
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Residues in contact with ILE 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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189A MET* 3.6 35.9 - - + +
190A HIS 4.9 0.2 - - - -
191A SER* 4.6 12.6 - - - -
196A PRO* 3.0 10.5 + - + +
198A ASP* 1.3 77.2 - - + +
200A GLU* 1.3 64.5 - - - +
201A ALA 3.1 0.2 + - - -
202A PHE* 3.1 4.2 + - - +
203A MET* 2.9 47.7 + - + +
214A ILE* 4.1 22.7 - - + -
219A TYR* 3.3 38.4 - - + +
230A MET* 4.3 16.2 - - + -
232A VAL* 4.6 2.9 - - + -
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Residues in contact with GLU 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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195A ASP* 5.2 0.2 - - - +
196A PRO* 2.8 40.8 + - + +
197A SER* 3.4 17.4 + - - +
199A ILE* 1.3 76.7 - - - +
201A ALA* 1.3 57.0 + - - +
203A MET* 4.1 0.9 - - - +
204A LYS* 3.1 30.8 + - - +
226A HIS* 2.8 27.6 - - - +
230A MET* 3.6 23.7 - - - +
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Residues in contact with ALA 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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163A PHE* 4.9 2.5 - - + -
169A LEU* 3.8 23.3 - - + +
197A SER 2.9 13.1 + - - +
198A ASP* 3.4 13.2 - - - +
199A ILE 3.1 0.2 - - - -
200A GLU* 1.3 75.7 - - - +
202A PHE* 1.3 63.9 + - - +
204A LYS* 3.6 7.0 + - - +
205A ALA* 3.2 23.0 + - - +
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Residues in contact with PHE 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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163A PHE* 4.0 5.6 - - + -
169A LEU* 3.7 8.7 - - + +
172A ALA* 5.0 0.2 - - + -
173A LEU* 4.2 22.9 - - + -
176A ALA* 3.6 23.1 - - + -
187A ILE* 4.7 4.0 - - + -
189A MET* 3.7 40.4 - - + -
198A ASP 2.8 19.1 + - - +
199A ILE* 3.8 2.7 - - + +
201A ALA* 1.3 73.3 - - - +
203A MET* 1.3 65.5 + - + +
205A ALA* 2.9 5.0 + - - +
206A TRP* 2.7 79.6 + + + +
212A VAL* 3.8 30.5 - - + -
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Residues in contact with MET 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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199A ILE* 2.9 35.1 + - + +
200A GLU 4.1 2.5 - - - +
202A PHE* 1.3 93.2 - - + +
204A LYS* 1.3 64.0 + - - +
206A TRP* 3.3 19.5 + - + +
207A ASN* 3.7 5.2 + - - -
208A ASN 5.2 0.9 + - - -
212A VAL* 3.8 29.4 - - + -
230A MET* 3.6 33.9 - - + +
231A GLY 3.6 28.5 - - - +
232A VAL* 3.8 13.2 - - + -
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Residues in contact with LYS 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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200A GLU 3.1 21.4 + - - +
201A ALA* 3.7 7.6 - - - +
203A MET* 1.3 77.7 - - - +
205A ALA* 1.3 60.5 + - - +
207A ASN* 4.0 15.4 + - - +
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Residues in contact with ALA 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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169A LEU* 4.1 17.3 - - + -
173A LEU* 3.9 32.7 - - + +
177A GLU* 5.1 0.2 - - - +
201A ALA 3.2 14.0 + - - +
202A PHE 2.9 4.0 + - - +
204A LYS* 1.3 78.7 - - - +
206A TRP* 1.3 62.2 + - - +
207A ASN* 3.3 13.8 + - - +
209A GLN* 4.8 1.9 + - - -
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Residues in contact with TRP 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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173A LEU* 4.2 6.5 - - + +
176A ALA* 3.5 20.4 - - + -
177A GLU* 3.9 9.4 - - + -
180A ARG* 3.9 16.4 - - + -
187A ILE* 3.9 26.2 - - + -
202A PHE* 2.7 47.0 + + + +
203A MET* 3.3 14.7 + - + +
205A ALA* 1.3 72.4 - - - +
207A ASN* 1.3 68.9 + - - +
208A ASN* 3.5 13.0 - - - -
209A GLN* 3.0 69.7 + - + +
210A GLY* 2.7 52.1 + - - +
212A VAL* 3.6 15.6 - - + +
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Residues in contact with ASN 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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203A MET 3.7 7.2 + - - -
204A LYS 4.0 10.4 + - - +
205A ALA* 3.3 22.6 + - - +
206A TRP* 1.3 77.5 - - - +
208A ASN* 1.3 67.7 + - - +
209A GLN* 3.0 7.0 + - + +
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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