Contacts of the helix formed by residues 193 - 202 (chain A) in PDB entry 6PAU
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 SER 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A TYR* 4.1 3.4 - - - -
191A ASP* 3.3 5.6 + - - -
192A TYR* 1.3 75.7 - - - +
194A PRO* 1.3 76.2 - - - +
195A GLU* 3.5 17.6 + - - +
196A PHE* 3.0 29.6 + - - +
197A LEU* 2.9 22.6 + - - +
380A HIS 4.8 7.6 + - - -
381A ILE* 4.8 0.2 - - - +
404A PRO* 5.4 5.0 - - - +
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Residues in contact with PRO 194 (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* 3.9 33.8 - - + +
170A LYS* 5.7 4.3 - - + -
173A TYR* 3.7 31.4 - - + -
193A SER* 1.3 83.6 - - - +
195A GLU* 1.3 78.5 + - + +
197A LEU* 3.2 9.6 + - + +
198A LEU* 3.0 24.3 + - - +
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Residues in contact with GLU 195 (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 SER* 3.5 13.9 + - - -
194A PRO* 1.3 97.9 - - + +
196A PHE* 1.3 62.9 + - - +
198A LEU* 3.2 14.4 + - + +
199A TRP* 3.0 18.0 + - - +
378A ARG* 5.3 0.7 + - - -
379A GLU 5.4 0.7 - - - +
380A HIS* 4.7 16.5 + - - +
381A ILE* 3.3 27.3 - - + +
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Residues in contact with PHE 196 (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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192A TYR* 3.5 37.2 - + - -
193A SER* 3.0 30.8 + - - +
195A GLU* 1.3 77.7 - - - +
197A LEU* 1.3 57.5 + - + +
199A TRP* 3.1 23.9 + + - +
200A ALA* 2.9 33.5 + - + -
380A HIS 5.0 0.9 - - - +
381A ILE* 3.8 27.9 - - + +
401A TYR* 3.7 20.9 - + - -
402A THR 3.0 29.6 - - - -
403A LEU* 4.6 2.7 - - + -
496A GLN* 3.7 24.2 - - + -
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Residues in contact with LEU 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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163A LEU* 5.1 0.4 - - - -
169A LEU* 4.3 12.6 - - + -
172A LEU* 4.1 13.2 - - + -
173A TYR* 4.0 26.5 - - + +
176A LEU* 3.7 34.1 - - + -
192A TYR* 3.8 16.4 - - + +
193A SER 2.9 18.1 + - - +
194A PRO* 3.2 6.7 + - + +
196A PHE* 1.3 76.1 - - - +
198A LEU* 1.3 58.2 + - - +
200A ALA* 4.5 1.3 - - - +
201A LEU* 2.9 48.5 + - + +
247A PHE* 3.8 27.8 - - + -
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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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163A LEU* 3.8 38.6 - - + +
164A SER* 5.5 0.7 - - - -
169A LEU* 3.9 16.2 - - + -
194A PRO 3.0 14.8 + - - +
195A GLU* 3.2 14.6 + - + +
197A LEU* 1.3 77.5 - - - +
199A TRP* 1.3 60.6 + - - +
201A LEU* 5.1 1.6 - - - -
202A ARG* 3.2 47.9 + - - +
373A HIS* 4.7 1.0 - - - -
378A ARG* 5.0 3.9 + - - +
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Residues in contact with TRP 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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195A GLU 3.0 12.7 + - - +
196A PHE* 3.1 28.2 + + - +
198A LEU* 1.3 78.2 - - - +
200A ALA* 1.3 68.3 + - - +
201A LEU 3.5 0.2 + - - -
202A ARG 4.0 0.3 + - - -
373A HIS* 2.6 54.3 + - - -
374A TRP* 3.4 39.3 - + - +
378A ARG* 3.6 41.5 - - - +
381A ILE* 3.5 24.2 - - + -
382A ILE* 3.8 16.5 - - + +
401A TYR* 4.1 18.4 - - + -
422A PHE* 4.2 7.2 - + - -
496A GLN* 3.4 38.1 - - + -
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Residues in contact with ALA 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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196A PHE* 2.9 35.2 + - + +
197A LEU 4.1 2.7 - - - +
199A TRP* 1.3 79.3 - - + +
201A LEU* 1.3 61.3 + - - +
202A ARG 3.5 0.4 + - - -
203A PRO* 3.9 0.5 - - - +
229A ILE* 3.7 23.7 - - - +
247A PHE* 4.1 22.1 - - + -
374A TRP* 3.8 14.0 - - - -
496A GLN* 4.4 13.6 - - + +
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Residues in contact with LEU 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 LEU* 3.6 26.0 - - + -
172A LEU* 4.0 17.7 - - + -
197A LEU* 2.9 30.7 + - + +
200A ALA* 1.3 77.9 - - - +
202A ARG* 1.3 60.0 + - + +
203A PRO* 3.4 6.2 - - - +
206A TRP* 3.7 3.1 - - - +
211A HIS* 2.8 38.2 + - + +
225A PHE* 4.3 7.6 - - + -
227A SER* 3.1 38.6 - - - +
229A ILE* 3.6 14.1 - - + +
247A PHE* 3.8 19.1 - - + -
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Residues in contact with ARG 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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162A ASP* 2.9 28.3 + - - -
163A LEU* 3.4 18.0 - - + +
164A SER* 2.6 34.1 + - - +
198A LEU* 3.2 32.9 + - + +
200A ALA 3.5 0.2 - - - -
201A LEU* 1.3 86.5 - - + +
203A PRO* 1.3 64.5 - - - +
206A TRP* 3.2 66.0 + - + +
208A LEU* 4.1 3.2 - - - +
211A HIS* 3.9 6.6 - - + -
373A HIS* 3.0 19.3 + - - -
508A GOL 4.6 1.6 + - - -
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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