Contacts of the helix formed by residues 196 - 207 (chain A) in PDB entry 3M18
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 GLU 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A SER* 3.8 27.0 - - - +
169A VAL 4.1 17.4 + - - +
170A PRO* 5.5 1.6 - - + -
171A HIS* 5.5 8.3 - - + +
194A ARG* 3.5 27.8 + - + +
195A CYS* 1.3 75.7 + - - +
197A THR* 1.3 63.9 + - - +
198A LEU 3.2 0.7 + - - -
199A TYR* 3.5 15.1 + - - +
200A LEU* 3.7 9.2 + - - +
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Residues in contact with THR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLN 5.4 1.0 + - - -
168A SER* 5.3 2.4 - - - -
190A PHE* 6.0 1.6 - - + +
191A ASP 3.0 21.8 + - - -
192A CYS* 3.3 30.6 - - - -
194A ARG* 2.7 21.4 + - - +
196A GLU* 1.3 77.9 - - - +
198A LEU* 1.3 53.4 + - - +
200A LEU* 2.9 12.3 + - + +
201A SER* 2.7 33.3 + - - -
234A VAL* 4.5 10.1 - - + -
237A VAL* 4.0 23.3 - - + -
242A LEU* 4.4 5.2 - - - -
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Residues in contact with LEU 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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195A CYS* 3.1 16.0 + - + +
197A THR* 1.3 75.8 - - - +
199A TYR* 1.3 63.5 + - - +
201A SER* 3.2 5.0 + - - +
202A GLN* 3.1 25.5 + - - +
205A ARG* 4.7 0.7 + - - -
237A VAL* 4.5 5.6 - - + -
238A THR* 3.2 38.1 - - - +
239A ASN* 3.6 28.9 - - + +
242A LEU* 3.9 19.1 - - + -
246A CYS* 4.0 28.0 - - + -
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Residues in contact with TYR 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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169A VAL* 3.9 18.6 - - + -
170A PRO 3.9 9.9 - - - -
171A HIS* 3.7 30.7 - + + -
172A GLY* 3.3 36.5 - - - -
173A ALA 3.6 7.6 - - - -
174A PHE* 2.9 42.5 + + - +
175A ASP* 3.7 10.0 + - - -
195A CYS 4.4 0.6 + - - -
196A GLU* 3.5 10.2 + - - +
197A THR 3.3 0.4 - - - -
198A LEU* 1.3 78.1 - - - +
200A LEU* 1.3 59.7 + - - +
202A GLN* 3.8 3.4 - - + +
203A TRP* 2.9 46.0 + + + +
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Residues in contact with LEU 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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168A SER* 5.5 0.9 - - - -
169A VAL* 4.3 21.1 - - + +
174A PHE* 4.3 23.3 - - + -
185A LEU* 4.3 10.5 - - + -
190A PHE* 3.9 43.1 - - + -
196A GLU 3.7 5.0 + - - +
197A THR* 2.9 16.2 + - + +
199A TYR* 1.3 80.9 - - - +
201A SER* 1.3 65.3 + - - +
203A TRP* 3.3 4.1 + - + -
204A ILE* 3.0 43.6 + - + +
234A VAL* 4.2 13.7 - - + -
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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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197A THR* 2.7 18.5 + - - -
198A LEU* 3.2 14.9 + - - +
200A LEU* 1.3 73.7 - - - +
202A GLN* 1.3 64.4 + - - +
204A ILE* 3.4 2.4 + - - +
205A ARG* 3.0 34.2 + - - +
234A VAL* 3.4 29.8 - - - +
235A ARG* 4.2 3.3 - - - +
237A VAL* 2.6 32.2 + - - +
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Residues in contact with GLN 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 LEU 3.1 13.5 + - - +
199A TYR* 4.1 3.6 - - + +
201A SER* 1.3 81.2 + - - +
203A TRP* 1.3 57.8 + - - +
205A ARG* 2.6 52.8 + - - +
206A GLU* 2.8 66.3 + - - +
239A ASN* 6.1 0.7 - - - +
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Residues in contact with TRP 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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174A PHE* 3.5 40.6 + + + +
175A ASP* 5.8 0.4 - - - -
180A LEU* 4.0 22.7 - - + -
183A ILE* 3.6 34.5 - - + -
185A LEU* 4.7 4.5 - - + -
199A TYR* 2.9 46.4 + + + +
200A LEU* 3.5 9.0 - - + +
202A GLN* 1.3 78.3 - - - +
204A ILE* 1.3 69.0 + - + +
206A GLU* 3.0 5.1 + - - -
207A ASN* 2.8 76.6 + - + +
210A LYS* 4.2 10.3 - - + -
211A VAL* 4.0 11.9 - - + -
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Residues in contact with ILE 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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185A LEU* 4.3 10.5 - - + -
200A LEU* 3.0 39.3 + - + +
201A SER 3.8 3.1 - - - +
203A TRP* 1.3 89.4 - - + +
205A ARG* 1.3 64.6 + - - +
207A ASN 4.4 0.4 - - - +
208A SER* 3.0 27.5 + - - -
211A VAL* 4.3 15.9 - - + -
223A PRO* 3.9 28.0 - - + +
226A VAL* 4.4 16.4 - - + -
234A VAL* 4.1 21.1 - - + -
235A ARG* 3.5 22.2 - - + +
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Residues in contact with ARG 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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198A LEU 4.7 0.6 + - - -
201A SER* 3.0 20.8 + - - +
202A GLN* 2.6 61.3 - - - +
204A ILE* 1.3 76.8 - - - +
206A GLU* 1.3 62.2 + - - +
208A SER* 4.0 13.4 + - - -
235A ARG* 2.8 58.6 + - + +
237A VAL 3.0 22.2 + - - -
238A THR* 3.7 24.8 - - - +
239A ASN* 5.1 5.7 + - - -
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Residues in contact with GLU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLN* 2.8 56.2 + - - +
203A TRP* 4.4 2.1 - - - -
205A ARG* 1.3 74.0 - - - +
207A ASN* 1.3 74.6 + - - +
208A SER 3.6 1.1 + - - -
209A ASN* 5.2 1.0 - - - +
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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 TRP* 2.8 73.6 + - + +
204A ILE 3.5 2.5 - - - -
206A GLU* 1.3 88.3 + - - +
208A SER* 1.3 59.3 + - - +
209A ASN* 3.2 9.6 - - - -
210A LYS* 2.8 55.1 + - + +
211A VAL* 3.8 7.2 - - - +
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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