Contacts of the helix formed by residues 190 - 197 (chain N) in PDB entry 6CET
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 ASP 190 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340D VAL* 5.0 10.7 - - - +
371D GLU* 4.3 2.6 - - - +
373D PRO* 4.9 13.9 - - - +
375D HIS* 5.6 4.5 - - + -
419D PHE* 2.9 36.1 - - - +
420D THR* 3.3 2.9 + - + +
421D PRO* 3.4 22.5 - - + +
189N TRP* 1.3 83.1 - - - +
191N LEU* 1.3 63.2 + - - +
192N THR* 4.3 11.4 - - - +
193N THR* 2.4 31.7 + - + +
194N GLN* 2.9 12.4 + - - +
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Residues in contact with LEU 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D SER* 5.6 5.2 - - - +
342D VAL* 4.7 20.2 - - + -
375D HIS* 4.7 19.9 - - + +
379D LEU* 6.4 1.1 - - + -
381D LYS* 4.0 31.2 - - - +
397D TYR* 5.5 2.2 - - - +
732D VAL* 5.6 3.6 - - + -
189N TRP 4.5 7.2 - - - +
190N ASP* 1.3 76.0 - - - +
192N THR* 1.3 61.2 + - + +
194N GLN* 3.2 27.4 + - + +
195N GLN* 2.9 45.5 + - + +
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Residues in contact with THR 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D LEU* 3.3 46.9 + - + +
375D HIS* 4.2 11.8 + - + +
419D PHE 5.6 1.0 + - - -
732D VAL* 5.2 0.9 - - + -
733D VAL* 4.2 17.0 - - + -
190N ASP* 4.3 7.3 - - - +
191N LEU* 1.3 75.3 - - - +
193N THR* 1.3 68.7 + - - +
195N GLN* 3.1 11.8 + - - +
196N ILE* 3.0 35.1 + - - +
215N VAL* 5.7 4.4 - - - +
219N LEU* 6.2 0.9 - - + -
223N ALA* 4.9 7.2 - - - +
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Residues in contact with THR 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D PHE 5.4 0.7 - - - +
420D THR* 3.7 25.8 - - + -
189N TRP* 3.2 15.5 - - + +
190N ASP* 2.4 40.2 + - + -
192N THR* 1.3 84.2 + - - +
194N GLN* 1.3 55.6 + - - -
196N ILE* 3.7 15.0 - - + -
197N LEU* 2.8 46.0 + - + +
223N ALA* 5.1 10.3 - - + +
227N LEU* 5.3 10.1 - - + -
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Residues in contact with GLN 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186N ASN 2.4 34.6 + - - +
187N SER* 3.8 16.6 + - - +
188N GLN 4.3 0.4 - - - +
189N TRP* 4.1 18.7 + - + +
190N ASP 2.9 17.6 + - - +
191N LEU* 3.2 31.6 + - + +
193N THR* 1.3 76.7 + - - +
195N GLN* 1.3 58.6 + - + +
197N LEU* 4.7 3.6 - - - -
198N PRO* 3.3 22.9 - - - +
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Residues in contact with GLN 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D LYS* 6.1 0.2 - - - +
397D TYR* 4.1 24.7 + - - +
731D PRO* 5.9 2.4 - - - +
732D VAL* 3.4 32.8 - - - +
733D VAL* 4.1 13.0 - - - +
191N LEU* 2.9 29.1 + - + +
192N THR* 3.1 10.6 + - - +
194N GLN* 1.3 78.4 - - + +
196N ILE* 1.3 63.6 + - + +
198N PRO* 4.6 2.3 - - - +
212N GLU* 4.1 9.4 - - - +
213N ALA* 4.0 22.6 - - - +
215N VAL* 4.2 7.5 - - + +
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Residues in contact with ILE 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192N THR* 3.0 20.8 + - - +
193N THR* 3.5 16.2 - - + +
195N GLN* 1.3 82.9 - - + +
197N LEU* 1.3 63.7 + - + +
198N PRO* 3.4 2.9 - - - -
199N TYR* 2.7 43.6 + - - +
200N ILE* 4.1 15.7 - - + -
208N LYS* 6.1 4.0 - - + -
212N GLU* 5.2 1.1 - - - +
213N ALA* 3.8 24.0 - - + -
215N VAL* 5.0 5.8 - - + -
220N VAL* 4.6 23.6 - - + -
223N ALA* 5.2 9.0 - - + -
224N ILE* 5.7 3.6 - - + +
227N LEU* 4.6 13.5 - - + -
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Residues in contact with LEU 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N PHE* 6.1 7.6 - - + -
181N LYS* 3.3 34.0 + - + +
189N TRP* 5.2 23.8 - - + +
193N THR* 2.8 38.2 + - - +
194N GLN* 4.7 2.2 - - - -
196N ILE* 1.3 83.4 - - + +
198N PRO* 1.3 67.7 - - + +
199N TYR 3.1 0.8 + - - -
200N ILE* 3.7 23.9 - - + +
227N LEU* 4.6 15.7 - - + -
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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