Contacts of the helix formed by residues 205 - 217 (chain L) in PDB entry 5IJO
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 GLN 205 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201L GLU 3.9 4.7 + - - +
202L ILE 3.6 3.9 + - - -
203L ARG 3.5 0.2 - - - -
204L SER* 1.3 80.0 - - - +
206L GLN* 1.4 53.3 + - - +
207L GLN* 2.6 19.0 + - - -
208L GLN* 3.0 17.1 + - + +
209L LEU* 3.1 11.2 + - + +
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Residues in contact with GLN 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L ILE 3.0 17.5 + - - +
203L ARG* 3.3 15.6 + - - +
204L SER 3.6 0.6 + - - -
205L GLN* 1.4 70.5 - - - +
207L GLN* 1.4 58.5 + - - +
208L GLN 3.3 0.2 - - - -
209L LEU* 3.4 13.4 + - - +
210L VAL* 3.4 12.3 + - - +
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Residues in contact with GLN 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205L GLN* 2.6 9.8 + - + +
206L GLN* 1.4 62.9 - - - +
208L GLN* 1.3 76.7 - - + +
209L LEU 2.9 0.8 + - - -
210L VAL* 3.2 3.1 + - - -
211L GLU* 3.1 23.6 + - - +
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Residues in contact with GLN 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205L GLN* 3.0 12.1 + - + +
207L GLN* 1.3 87.0 - - + +
209L LEU* 1.3 66.1 - - - +
211L GLU* 4.6 3.4 - - + +
212L SER* 2.6 37.0 + - - +
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Residues in contact with LEU 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202L ILE* 5.2 7.2 - - + +
205L GLN* 3.1 15.7 + - + +
206L GLN* 3.7 10.1 - - - +
207L GLN 2.9 0.6 - - - -
208L GLN* 1.3 85.6 - - - +
210L VAL* 1.3 61.9 + - + +
212L SER* 3.2 7.8 - - - -
213L LEU* 3.1 15.4 + - - +
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Residues in contact with VAL 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L GLN 3.4 6.9 + - - +
207L GLN 3.2 4.9 + - - -
208L GLN 3.0 0.4 - - - -
209L LEU* 1.3 76.5 - - + +
211L GLU* 1.4 50.4 + - - +
212L SER 2.9 4.9 - - - -
213L LEU* 2.9 10.3 + - + +
214L HIS* 2.6 31.2 + - - +
225L VAL* 3.9 27.5 - - + +
226L ASN 6.0 2.5 - - - +
227L VAL* 6.4 2.0 - - + -
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Residues in contact with GLU 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207L GLN 3.1 15.9 + - - +
208L GLN* 3.7 2.9 - - - +
210L VAL* 1.4 69.0 - - - +
212L SER* 1.3 44.2 + - - +
213L LEU 3.1 0.2 - - - -
214L HIS* 2.8 14.2 - - + +
215L LYS* 2.7 35.3 + - - +
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Residues in contact with SER 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208L GLN* 2.6 22.0 + - - -
209L LEU* 3.2 9.9 - - - -
211L GLU* 1.3 81.2 - - - +
213L LEU* 1.4 61.1 + - - +
215L LYS* 3.2 7.0 + - - +
216L VAL* 3.2 18.5 + - - +
277L LEU* 5.7 9.2 - - - -
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Residues in contact with LEU 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209L LEU 3.1 6.9 + - - +
210L VAL* 2.9 21.9 + - + +
212L SER* 1.4 82.5 - - - +
214L HIS* 1.3 57.3 + - - -
216L VAL* 3.3 9.7 + - - +
217L LEU* 3.2 19.6 + - - +
225L VAL* 4.8 6.7 - - + -
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Residues in contact with HIS 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L VAL 2.6 14.9 + - - +
211L GLU* 2.8 26.2 - - + +
213L LEU* 1.3 71.4 - - - +
215L LYS* 1.3 56.8 + - - +
217L LEU* 3.1 19.7 - - - +
219L GLY* 2.9 24.3 + - - -
223L LEU* 6.0 0.3 - - - +
225L VAL* 5.1 11.0 - - + +
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Residues in contact with LYS 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211L GLU 2.7 10.0 + - - +
212L SER* 3.4 11.9 - - - +
213L LEU 3.2 0.2 - - - -
214L HIS* 1.3 74.5 - - - +
216L VAL* 1.4 61.3 + - - +
217L LEU 2.9 1.6 - - - -
218L GLY* 2.6 25.4 + - - -
219L GLY* 3.8 12.3 - - - +
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Residues in contact with VAL 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212L SER 3.2 8.7 + - - +
213L LEU* 3.3 13.0 + - - +
215L LYS* 1.4 80.4 - - - +
217L LEU* 1.4 58.1 + - - +
270L ILE* 5.2 15.9 - - + +
273L GLN* 5.2 15.0 - - + -
274L LEU* 6.2 0.7 - - - +
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Residues in contact with LEU 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213L LEU 3.2 9.5 + - - +
214L HIS* 3.1 17.3 - - - +
215L LYS 2.9 0.2 - - - -
216L VAL* 1.4 77.7 - - - +
218L GLY* 1.4 55.8 + - - +
219L GLY 3.8 1.3 + - - +
223L LEU* 5.3 13.0 - - + -
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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