Contacts of the helix formed by residues 196 - 208 (chain X) in PDB entry 6FF7
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 ASN 196 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176X GLY 4.9 0.6 + - - -
194X PHE* 3.5 10.1 - - - +
195X GLU* 1.4 82.0 - - + +
197X ASP* 1.4 63.8 + - - +
198X GLY* 4.3 5.4 - - - +
199X GLN* 3.3 17.1 + - + +
200X ALA 3.2 14.6 + - - -
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Residues in contact with ASP 197 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195X GLU 4.3 0.6 + - - -
196X ASN* 1.4 70.9 - - - +
198X GLY* 1.3 65.9 + - - +
200X ALA* 3.0 10.2 + - - +
201X GLY* 2.9 20.4 + - - -
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Residues in contact with GLY 198 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196X ASN* 3.3 4.5 - - - +
197X ASP* 1.3 77.4 - - - +
199X GLN* 1.3 61.2 + - - +
201X GLY* 3.2 2.7 + - - -
202X ALA* 3.2 20.4 + - - +
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Residues in contact with GLN 199 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174X PHE* 3.7 24.1 - - - +
175X PRO* 4.3 21.1 - - + +
176X GLY 5.4 0.2 - - - +
194X PHE* 4.5 5.8 - - + -
196X ASN* 3.3 22.5 + - + +
197X ASP 3.2 0.2 - - - -
198X GLY* 1.3 74.6 - - - +
200X ALA* 1.3 63.3 + - - +
202X ALA* 3.1 9.1 + - - +
203X ALA* 2.9 19.6 + - - +
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Residues in contact with ALA 200 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194X PHE* 4.2 15.3 - - + +
196X ASN 3.2 8.7 + - - +
197X ASP* 3.0 14.5 + - - +
199X GLN* 1.3 80.3 - - - +
201X GLY* 1.3 62.6 + - - +
203X ALA* 3.2 7.1 + - - +
204X ARG* 2.9 25.0 + - - +
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Residues in contact with GLY 201 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197X ASP 2.9 13.7 + - - -
198X GLY 3.2 3.6 + - - -
199X GLN 3.2 0.2 - - - -
200X ALA* 1.3 75.7 - - - +
202X ALA* 1.3 63.0 + - - +
204X ARG* 3.3 6.0 + - - +
205X ASP* 3.0 23.9 + - - +
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Residues in contact with ALA 202 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174X PHE* 4.5 9.2 - - + -
198X GLY 3.2 11.5 + - - +
199X GLN* 3.1 11.1 + - - +
201X GLY* 1.3 76.2 - - - +
203X ALA* 1.3 63.2 + - - +
205X ASP* 3.2 6.0 + - - +
206X ALA* 3.1 24.1 + - - +
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Residues in contact with ALA 203 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171X PHE* 5.0 9.2 - - + +
174X PHE* 3.9 18.8 - - + +
199X GLN 2.9 12.0 + - - +
200X ALA* 3.6 10.3 - - - +
202X ALA* 1.3 75.8 - - - +
204X ARG* 1.3 56.4 + - - +
206X ALA* 4.8 3.4 - - - -
207X LEU* 2.7 42.8 + - + +
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Residues in contact with ARG 204 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200X ALA 2.9 18.6 + - - +
201X GLY* 3.6 6.7 - - - +
203X ALA* 1.3 78.7 - - - +
205X ASP* 1.3 64.7 + - - +
207X LEU* 4.9 2.5 - - - -
208X GLN* 3.6 19.9 + - - +
220X ILE* 5.2 14.9 - - + +
221X THR* 6.0 0.9 - - - -
222X TYR* 5.9 8.7 - - + +
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Residues in contact with ASP 205 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201X GLY 3.0 13.9 + - - +
202X ALA* 3.2 9.2 + - - +
204X ARG* 1.3 80.3 - - - +
206X ALA* 1.3 61.3 + - - +
208X GLN* 4.2 7.8 + - - +
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Residues in contact with ALA 206 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202X ALA 3.1 13.3 + - - +
203X ALA* 4.0 3.6 - - - +
205X ASP* 1.3 81.3 - - - +
207X LEU* 1.3 62.2 + - - +
208X GLN 3.5 6.8 + - - +
210X PHE* 5.1 2.9 + - - +
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Residues in contact with LEU 207 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203X ALA* 2.7 26.6 + - + +
204X ARG 4.6 0.9 - - - +
206X ALA* 1.3 70.4 - - - +
208X GLN* 1.3 55.0 + - - +
210X PHE* 2.7 41.5 + - - +
218X MET 4.1 1.4 - - - +
220X ILE* 4.6 14.6 - - + -
975v LYS* 3.5 17.1 + - + +
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Residues in contact with GLN 208 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204X ARG 3.6 13.0 + - - +
205X ASP 4.7 5.4 - - - +
206X ALA 3.4 8.9 - - - +
207X LEU* 1.3 79.1 - - - +
209X GLY* 1.4 60.2 + - - +
210X PHE 3.4 0.2 + - - -
218X MET 4.0 4.0 - - - -
219X LYS* 5.3 0.9 - - - -
220X ILE* 4.3 24.8 - - - +
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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