Contacts of the helix formed by residues 182 - 192 (chain c) in PDB entry 5M32
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 182 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180c CYS 2.7 10.9 + - - +
181c LYS* 1.3 75.7 - - + +
183c GLN* 1.3 63.4 + - - +
184c ILE 3.1 4.9 - - - +
185c GLU* 2.9 32.1 + - - +
186c LYS* 3.0 49.1 + - - +
409g ARG* 4.5 12.1 + - - -
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Residues in contact with GLN 183 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180c CYS* 3.0 41.4 + - + +
182c GLU* 1.3 81.9 + - - +
184c ILE* 1.3 64.5 + - - +
186c LYS* 4.0 11.2 - - + +
187c LEU* 3.5 19.4 + - - +
341c ILE* 3.7 21.2 - - + +
342c GLU 2.9 26.4 + - - +
343c PHE* 3.3 36.2 - - + +
344c SER* 4.5 4.9 + - - +
431g LYS* 5.9 1.4 - - - -
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Residues in contact with ILE 184 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174c TYR* 4.4 31.0 - - + +
177c VAL* 4.4 24.9 - - + +
178c GLY* 5.9 0.2 - - - -
179c GLY 5.8 0.2 - - - +
180c CYS* 3.6 14.1 - - + +
181c LYS* 3.5 31.9 - - - +
182c GLU 3.1 0.6 - - - -
183c GLN* 1.3 78.3 - - + +
185c GLU* 1.3 50.5 + - - +
187c LEU* 2.9 12.8 + - + +
188c ARG* 2.5 52.6 + - + +
225c CYS* 4.6 17.7 - - - -
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Residues in contact with GLU 185 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181c LYS 4.3 10.9 + - - +
182c GLU* 2.9 25.4 + - + +
184c ILE* 1.3 80.7 - - + +
186c LYS* 1.3 58.8 + - - +
188c ARG* 3.9 13.6 - - + +
189c GLU* 3.3 24.8 + - + +
409g ARG* 4.6 25.0 - - + +
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Residues in contact with LYS 186 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182c GLU* 3.0 47.2 + - - +
183c GLN* 4.3 8.3 - - + +
184c ILE 3.2 0.2 - - - -
185c GLU* 1.3 79.0 - - - +
187c LEU* 1.3 62.8 + - - +
188c ARG 3.5 0.2 + - - -
189c GLU* 3.5 8.4 - - - +
190c VAL* 3.5 21.8 - - - +
339c ARG* 3.5 25.2 - - - +
340c LYS 5.7 0.9 - - - +
341c ILE* 3.7 26.9 - - + -
406g ILE* 6.1 1.8 - - - +
409g ARG* 5.2 8.4 - - - +
426g GLU* 4.1 27.2 - - - +
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Residues in contact with LEU 187 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174c TYR* 6.2 1.1 - - + -
183c GLN 3.5 13.4 + - - +
184c ILE* 2.9 12.6 + - + +
186c LYS* 1.3 78.9 - - - +
188c ARG* 1.3 62.5 + - - +
190c VAL* 3.4 3.8 + - - +
191c VAL* 3.3 20.9 + - + +
212c VAL* 3.8 35.7 - - + -
214c LEU* 4.5 16.8 - - + -
225c CYS* 3.7 33.7 - - + +
229c VAL* 4.3 20.9 - - + -
318c LEU* 4.4 20.6 - - + -
341c ILE* 4.6 5.7 - - + +
343c PHE* 4.9 2.0 - - + -
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Residues in contact with ARG 188 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174c TYR* 3.5 33.7 - - - +
184c ILE* 2.5 28.9 + - + +
185c GLU* 3.9 13.7 - - + +
186c LYS 3.2 0.4 - - - -
187c LEU* 1.3 75.9 - - - +
189c GLU* 1.3 58.0 + - - +
191c VAL* 3.9 6.3 - - - -
192c GLU* 3.1 63.6 + - - +
197c HIS* 5.9 1.1 - - + -
232c ARG* 4.3 16.4 - - - +
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Residues in contact with GLU 189 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185c GLU* 3.3 19.2 + - + +
186c LYS* 3.5 5.6 - - - +
188c ARG* 1.3 79.6 - - - +
190c VAL* 1.3 68.7 + - - +
192c GLU 4.3 1.3 - - - -
193c THR* 4.1 8.8 - - - +
197c HIS* 3.9 26.6 + - + -
201c PHE* 4.5 5.2 - - + -
208c PRO* 5.4 0.3 - - - +
209c PRO* 5.2 0.3 - - - +
339c ARG* 3.0 38.6 + - - +
405g MET* 3.2 36.3 - - - +
409g ARG* 6.3 3.1 - - + -
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Residues in contact with VAL 190 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186c LYS 3.5 11.9 - - - +
187c LEU 3.4 3.3 + - - +
188c ARG 3.2 0.6 - - - -
189c GLU* 1.3 102.8 - - - +
191c VAL* 1.3 64.0 + - - +
192c GLU 3.3 0.2 - - - -
193c THR* 3.3 18.6 - - - +
208c PRO* 5.7 0.9 - - - -
209c PRO* 3.3 42.4 - - + +
210c LYS 4.3 5.8 - - - +
211c GLY 4.3 0.2 - - - +
212c VAL* 3.6 28.5 - - + -
316c LYS* 3.6 11.9 - - + +
339c ARG* 3.7 15.5 - - + +
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Residues in contact with VAL 191 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174c TYR* 4.2 1.6 - - - +
187c LEU* 3.3 17.4 + - + +
188c ARG* 3.5 10.8 - - - +
190c VAL* 1.3 79.3 - - - +
192c GLU* 1.3 71.7 + - + +
193c THR 3.5 2.7 + - - -
194c PRO* 3.8 11.1 - - - +
195c LEU* 4.9 1.0 - - - +
212c VAL* 5.5 0.6 - - + +
229c VAL* 3.8 36.3 - - + +
232c ARG 5.9 1.3 - - - +
233c THR* 5.0 5.6 - - - +
271c LEU* 3.9 25.8 - - + +
316c LYS* 5.0 8.1 - - + +
318c LEU* 3.7 30.1 - - + -
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Residues in contact with GLU 192 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174c TYR* 2.7 33.5 + - - +
188c ARG* 3.1 41.1 + - - +
189c GLU 4.6 0.2 - - - -
190c VAL 3.3 0.4 - - - -
191c VAL* 1.3 86.6 - - + +
193c THR* 1.3 52.8 + - - +
194c PRO* 3.8 2.5 - - - -
195c LEU* 3.7 43.5 - - + +
197c HIS* 2.5 41.8 + - + +
232c ARG* 3.3 19.8 + - - +
233c THR* 6.4 0.9 - - - -
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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