Contacts of the helix formed by residues 193 - 200 (chain M) in PDB entry 5D4C
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 193 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M LEU* 3.8 22.2 - - + -
182M VAL* 2.9 45.6 + - + +
184M MET* 3.5 35.9 - - + -
191M PHE* 3.4 5.0 + - - -
192M PRO* 1.3 71.1 - - - +
194M VAL* 1.3 59.0 + - - +
195M LEU 3.2 0.2 - - - -
196M LEU* 3.1 16.1 + - + +
197M LEU* 2.9 38.8 + - + +
303M PHE* 4.5 11.0 - - + +
307M LEU* 3.7 25.6 - - + -
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Residues in contact with VAL 194 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181M VAL* 4.8 3.8 - - + -
182M VAL* 4.6 5.8 - - + -
192M PRO* 3.1 10.0 - - + -
193M LEU* 1.3 81.7 - - - +
195M LEU* 1.3 56.8 + - - +
197M LEU* 3.3 11.7 + - + +
198M ARG* 2.9 23.2 + - - +
207M LEU* 5.3 0.4 - - + -
220M GLY 4.6 4.7 - - - +
221M LEU* 3.2 46.0 - - + +
223M ASP* 4.5 10.5 - - + -
226M VAL* 3.5 29.8 - - + +
227M PHE* 4.1 19.6 - - + -
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Residues in contact with LEU 195 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191M PHE* 4.7 2.5 - - + -
192M PRO* 3.4 18.2 + - + +
193M LEU 3.2 0.2 - - - -
194M VAL* 1.3 78.9 - - - +
196M LEU* 1.3 56.6 + - - +
198M ARG* 3.0 6.1 + - - +
199M VAL* 2.9 29.5 + - - +
226M VAL* 4.0 12.6 - - + +
229M MET* 3.7 20.6 - - + -
234M ALA* 3.3 36.8 - - + +
237M ARG* 3.7 9.6 - - + +
238M LEU* 3.6 37.9 - - + +
241M LEU* 3.7 24.0 - - + -
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Residues in contact with LEU 196 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184M MET* 3.6 21.5 - - + -
191M PHE* 4.1 14.6 - - + -
192M PRO 4.4 0.6 + - - -
193M LEU* 3.1 12.6 + - + +
195M LEU* 1.3 76.3 - - - +
197M LEU* 1.3 61.8 + - + +
199M VAL* 3.1 13.3 + - + +
200M LEU* 2.9 50.6 + - + +
238M LEU* 3.7 21.8 - - + -
257M VAL* 5.1 9.9 - - + -
261M ILE* 5.3 9.6 - - + -
303M PHE* 3.5 42.4 - - + -
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Residues in contact with LEU 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 LEU* 2.9 31.4 + - + +
194M VAL* 3.4 13.9 - - - +
196M LEU* 1.3 78.3 - - + +
198M ARG* 1.3 58.7 + - - +
200M LEU* 4.5 1.8 - - + -
201M GLY 3.6 2.1 + - - -
202M TYR* 3.0 53.9 + - + +
207M LEU* 3.9 27.1 - - + -
221M LEU* 3.6 32.8 - - + -
227M PHE* 6.3 0.4 - - + -
300M ASP* 4.8 0.9 - - - +
303M PHE* 4.8 18.4 - - + -
304M LEU* 5.3 5.8 - - + +
307M LEU* 4.0 13.7 - - + -
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Residues in contact with ARG 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 VAL 2.9 13.4 + - - +
195M LEU 3.0 9.1 + - - +
197M LEU* 1.3 75.8 - - - +
199M VAL* 1.3 64.7 + - - +
201M GLY* 3.0 15.6 + - - -
202M TYR 3.5 24.3 + - - -
203M ASP* 4.8 13.7 + - - +
226M VAL* 3.5 28.2 + - + +
227M PHE* 3.7 34.3 + - + +
229M MET 3.1 25.2 + - - +
230M ARG* 4.0 9.1 - - - +
231M PRO* 3.5 41.0 - - - +
234M ALA* 4.0 11.0 - - + -
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Residues in contact with VAL 199 (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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195M LEU 2.9 21.9 + - - +
196M LEU* 3.1 18.8 + - + +
198M ARG* 1.3 77.0 - - - +
200M LEU* 1.3 62.0 + - + +
201M GLY* 3.1 1.3 + - - -
231M PRO* 4.0 17.0 - - + +
234M ALA 3.6 31.9 - - - +
235M LEU* 3.6 32.3 - - + +
238M LEU* 4.4 8.3 - - + -
257M VAL* 5.0 3.4 - - + -
298M PHE* 4.1 27.8 + - + +
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Residues in contact with LEU 200 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196M LEU* 2.9 51.4 + - + +
197M LEU* 3.8 9.0 - - + +
198M ARG 3.2 0.2 - - - -
199M VAL* 1.3 77.3 - - + +
201M GLY* 1.3 57.9 + - - +
202M TYR* 3.5 16.9 - - + -
261M ILE* 6.1 1.1 - - + -
291M ALA* 3.9 12.8 - - + -
298M PHE* 2.9 29.2 - - + +
299M LYS* 3.6 18.9 - - - +
300M ASP* 3.5 45.5 + - - +
303M PHE* 4.7 9.9 - - + -
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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