Contacts of the helix formed by residues 196 - 208 (chain A) in PDB entry 1PTH
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 196 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ASN* 1.3 73.2 - - - +
197A MET* 1.3 65.6 + - - +
198A PHE 3.1 2.2 - - - -
199A ALA* 2.9 8.7 + - + +
200A PHE* 2.8 42.0 + - + -
391A MET* 5.2 0.4 - - + -
392A PRO* 3.8 36.1 - - + -
395A PHE* 3.9 17.5 - - + -
426A PHE* 2.9 27.5 + - + +
429A GLN* 2.8 26.9 + - + +
430A PRO 3.8 20.0 - - - +
431A ALA* 3.8 15.3 - - + -
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Residues in contact with MET 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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195A ASN* 2.9 11.1 + - - +
196A LEU* 1.3 73.9 - - - +
198A PHE* 1.3 58.1 + - - +
200A PHE* 5.1 0.7 - - - -
201A PHE 2.9 16.6 + - - -
300A LEU* 4.6 7.9 - - + -
301A TYR* 2.8 56.3 + - + +
304A ILE* 5.0 0.4 - - + -
423A VAL* 3.3 46.9 - - + -
426A PHE* 3.0 17.8 + - - -
427A SER* 3.8 16.4 - - - +
564A LEU* 4.5 10.3 - - + -
568A VAL* 4.3 14.6 - - + -
578A VAL* 4.7 0.2 - - + -
579A SER 3.6 14.6 - - - +
580A PHE* 4.1 8.1 - - + -
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Residues in contact with PHE 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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194A THR* 3.2 35.0 - - + -
195A ASN* 3.1 8.3 + - - +
197A MET* 1.3 75.1 - - - +
199A ALA* 1.3 72.4 + - - +
201A PHE* 3.1 0.9 + - - -
202A ALA* 2.8 26.9 + - + +
348A TYR* 3.6 45.3 - + - -
351A GLN* 4.2 10.3 - - + -
352A LEU* 3.6 38.4 - - + -
387A TRP* 4.0 15.0 - + - -
390A LEU* 4.3 14.4 - - + -
517A ILE* 5.2 0.4 - - + -
580A PHE* 3.6 32.0 - + + +
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Residues in contact with ALA 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 ASN 3.3 9.9 + - - +
196A LEU* 2.9 13.3 + - + +
198A PHE* 1.3 86.2 - - - +
200A PHE* 1.3 63.1 + - - +
202A ALA* 3.5 2.8 + - - +
203A GLN* 3.0 22.9 + - - +
390A LEU* 4.0 23.1 - - + -
391A MET* 3.4 27.1 - - + -
431A ALA* 4.4 4.3 - - + -
601A HEM 3.7 7.7 - - - +
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Residues in contact with PHE 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 LEU* 2.8 38.7 + - + +
197A MET 4.8 0.2 - - - -
199A ALA* 1.3 72.9 - - + +
201A PHE* 1.3 69.7 + - - +
203A GLN* 3.0 25.2 + - - +
204A HIS* 2.9 23.0 + - - +
295A LEU* 4.3 9.4 - - + -
297A GLY* 3.8 28.5 - - - -
298A LEU* 4.3 2.2 - - + +
300A LEU* 6.4 0.2 - - + -
301A TYR* 3.8 18.6 - - + -
391A MET* 4.2 15.5 - - + -
395A PHE* 4.0 12.3 - + - -
407A PHE* 3.5 25.8 - + - -
426A PHE* 3.8 39.3 - + + -
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Residues in contact with PHE 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 MET 2.9 11.9 + - - +
198A PHE* 3.4 4.3 - - - +
200A PHE* 1.3 77.0 - - - +
202A ALA* 1.3 54.2 + - - +
204A HIS* 3.6 5.6 - + - +
205A PHE* 2.7 49.4 + + + +
301A TYR* 3.2 48.1 - + - +
305A TRP* 4.7 19.7 - + - -
340A THR* 5.3 2.7 - - + -
343A ILE* 3.8 24.9 - - + -
344A VAL* 3.8 26.7 - - + -
348A TYR* 3.5 24.7 - + + -
564A LEU* 4.4 5.2 - - + -
567A LEU* 4.9 3.8 - - + -
580A PHE* 3.6 21.1 - + + -
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Residues in contact with ALA 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 PHE* 2.8 30.3 + - + +
199A ALA* 3.6 4.9 - - - +
201A PHE* 1.3 73.7 - - - +
203A GLN* 1.3 53.2 + - - +
205A PHE* 4.5 2.2 - - - -
206A THR* 2.6 40.2 + - - +
348A TYR* 3.0 33.1 - - + +
385A TYR* 4.8 0.7 - - + -
387A TRP* 4.5 11.7 - - + -
390A LEU* 4.9 0.2 - - + -
601A HEM 4.1 7.9 - - + -
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Residues in contact with GLN 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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199A ALA 3.0 14.7 + - - +
200A PHE* 3.3 18.5 - - - +
201A PHE 3.0 0.2 + - - -
202A ALA* 1.3 73.0 - - - +
204A HIS* 1.3 66.9 - - - +
206A THR* 3.0 2.4 + - - -
207A HIS* 2.7 42.0 + - + +
295A LEU* 3.3 29.3 - - - +
298A LEU* 3.2 26.3 - - + +
601A HEM 3.0 64.6 + - + +
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Residues in contact with HIS 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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200A PHE 2.9 19.5 + - - +
201A PHE* 3.6 7.9 - + - +
203A GLN* 1.3 73.2 - - - +
205A PHE* 1.3 66.5 + - + +
207A HIS 3.2 6.9 + - - -
232A HIS* 3.2 38.2 + + - -
233A ILE* 5.2 4.9 - - + +
292A PHE* 3.0 46.2 - + - -
298A LEU* 3.7 22.7 + - + +
301A TYR* 4.0 18.1 - + + +
302A ALA* 3.9 24.5 - - + -
305A TRP* 3.7 27.2 - + - +
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Residues in contact with PHE 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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201A PHE* 2.7 38.5 + + + +
202A ALA 4.0 1.8 - - - +
204A HIS* 1.3 73.5 - - + +
206A THR* 1.3 73.5 + - + +
207A HIS 3.0 6.0 + - - -
208A GLN* 3.3 46.7 + - - +
209A PHE* 3.8 23.8 - + - -
228A VAL* 4.0 17.0 - - + -
232A HIS* 4.3 6.7 - - - -
340A THR* 3.7 27.4 - - + -
344A VAL* 3.7 32.1 - - + -
348A TYR* 5.0 9.2 - + - -
385A TYR* 5.1 4.7 - - - -
530A 0AH 5.5 3.8 - - - -
534A LEU* 4.4 6.7 - - + -
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Residues in contact with THR 206 (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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202A ALA 2.6 23.1 + - - +
203A GLN* 3.0 10.4 + - - -
205A PHE* 1.3 83.7 - - + +
207A HIS* 1.3 66.4 + - - +
208A GLN 3.1 3.9 + - - -
209A PHE* 3.4 15.1 + - + -
210A PHE* 3.1 47.6 + - + +
385A TYR* 3.4 46.4 - - + +
601A HEM 4.1 7.4 - - - +
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Residues in contact with HIS 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 GLN* 2.7 44.0 + - + +
204A HIS 3.2 3.6 + - - +
205A PHE 3.0 1.8 - - - -
206A THR* 1.3 82.0 + - - +
208A GLN* 1.3 56.7 + - - +
209A PHE 3.5 0.7 - - - -
210A PHE 3.7 13.3 - - - +
211A LYS* 4.7 2.3 - - - +
289A GLN* 2.7 37.1 + - - +
291A VAL* 4.6 16.4 - - + -
292A PHE* 3.4 28.5 - + + -
298A LEU* 5.9 1.3 - - + -
601A HEM 3.5 63.0 + + + +
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Residues in contact with GLN 208 (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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205A PHE* 3.3 32.1 + - - +
206A THR 3.1 1.2 - - - -
207A HIS* 1.3 79.6 - - - +
209A PHE* 1.3 71.7 + - + +
210A PHE 3.8 0.4 - - - -
211A LYS* 5.4 2.7 - - - -
223A ALA* 3.6 17.1 - - - +
225A GLY* 6.1 0.2 - - - -
226A HIS 5.6 0.5 + - - -
227A GLY 3.7 7.7 + - - +
228A VAL* 3.4 12.7 - - - +
229A ASP* 3.2 20.8 + - - +
230A LEU* 2.7 38.4 - - - +
231A GLY* 5.6 1.1 - - - -
232A HIS* 3.1 46.6 + - + +
289A GLN* 5.4 0.2 - - - -
340A THR* 4.8 0.2 - - - +
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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