Contacts of the helix formed by residues 189 - 198 (chain M) in PDB entry 3J8B
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 LEU 189 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188M LEU* 1.3 74.5 - - - +
190M GLY* 1.3 57.4 + - - +
192M TYR* 3.2 6.2 + - - +
193M THR* 2.8 33.2 + - - -
219M LEU 5.7 4.7 - - - +
222M HIS* 5.7 9.4 - - + -
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Residues in contact with GLY 190 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LEU 3.2 3.8 - - - +
189M LEU* 1.3 78.8 - - - +
191M SER* 1.3 59.9 + - - +
193M THR* 3.3 4.3 + - - -
194M GLU* 3.0 25.7 + - - +
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Residues in contact with SER 191 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LEU* 3.2 16.8 + - - +
190M GLY* 1.3 75.9 - - - +
192M TYR* 1.3 58.2 + - - +
194M GLU* 3.6 4.9 + - - +
195M ASP* 3.1 27.9 + - - +
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Residues in contact with TYR 192 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188M LEU 2.9 17.0 + - - +
189M LEU* 3.2 6.0 + - - +
191M SER* 1.3 75.6 - - - +
193M THR* 1.3 59.8 + - - +
195M ASP* 3.3 5.0 + - - +
196M ASN* 2.8 31.5 + - - +
207M CYS* 6.1 1.7 - - + +
211M ALA* 5.7 9.2 - - + -
223M LEU* 6.0 6.1 - - + -
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Residues in contact with THR 193 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189M LEU 2.8 17.7 + - - -
190M GLY* 3.9 4.5 - - - -
192M TYR* 1.3 73.3 - - - +
194M GLU* 1.3 65.7 + - - +
196M ASN* 3.4 6.7 + - - +
197M ALA* 3.1 26.7 + - - +
222M HIS* 6.5 1.8 - - - -
223M LEU* 6.3 3.6 - - - +
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Residues in contact with GLU 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M GLY 3.0 17.9 + - - +
191M SER* 3.9 6.1 - - - +
193M THR* 1.3 74.6 - - - +
195M ASP* 1.3 62.8 + - - +
197M ALA* 3.3 5.9 + - - +
198M SER* 3.2 23.9 + - - -
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Residues in contact with ASP 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191M SER 3.1 18.8 + - - +
192M TYR* 3.7 5.6 - - - +
194M GLU* 1.3 77.1 - - - +
196M ASN* 1.3 61.0 + - - +
198M SER* 3.2 3.1 + - - -
199M GLN* 2.8 39.7 + - + +
207M CYS* 6.3 2.9 - - + -
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Residues in contact with ASN 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192M TYR 2.8 17.7 + - - +
193M THR* 3.8 7.6 - - - +
195M ASP* 1.3 78.0 - - - +
197M ALA* 1.3 58.4 + - - +
198M SER 3.6 0.5 + - - -
199M GLN* 4.0 13.3 - - - +
204M ALA* 6.4 2.9 - - + +
207M CYS* 5.8 9.3 - - + +
226M LEU* 5.5 11.2 - - + -
228M PRO* 4.5 18.4 - - + +
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Residues in contact with ALA 197 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193M THR 3.1 17.4 + - - +
194M GLU* 3.7 5.2 - - - +
195M ASP 3.2 0.2 - - - -
196M ASN* 1.3 76.0 - - - +
198M SER* 1.3 58.0 + - - +
199M GLN 5.2 0.2 - - - -
228M PRO* 6.0 1.3 - - - -
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Residues in contact with SER 198 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194M GLU 3.2 13.3 + - - -
195M ASP* 3.2 4.9 + - - -
197M ALA* 1.3 81.1 - - - +
199M GLN* 1.3 62.9 + - - +
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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