Contacts of the helix formed by residues 204 - 216 (chain K) in PDB entry 6LTJ
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 ALA 204 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202K THR* 3.0 20.5 - - + +
203K THR* 1.3 77.0 - - - +
205K GLU* 1.3 60.8 + - + +
207K GLU* 3.1 30.1 + - - +
208K ILE* 2.9 28.4 + - + +
243K PRO* 5.4 9.0 - - + -
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Residues in contact with GLU 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190K MET* 4.8 1.1 - - - -
198K TYR* 6.0 1.6 - - - +
199K SER 4.3 8.5 - - - +
200K PHE* 3.3 38.2 - - + -
202K THR* 3.2 12.0 + - - +
203K THR 3.1 0.4 - - - -
204K ALA* 1.3 79.6 - - + +
206K ARG* 1.3 57.3 + - - +
207K GLU 3.1 0.2 - - - -
208K ILE* 3.2 16.4 + - + +
209K VAL* 2.9 35.6 + - - +
212K ILE* 5.8 1.1 - - + +
242K LEU* 3.4 35.5 - - - +
243K PRO* 4.6 9.2 - - + -
244K ASP* 5.0 12.1 - - - +
246K GLN* 5.3 2.3 + - - +
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Residues in contact with ARG 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K ARG* 4.5 19.4 - - - +
186K THR* 3.5 32.7 - - - +
187K ASP* 4.1 13.1 + - - -
190K MET* 4.1 26.3 - - + +
200K PHE* 4.9 2.6 - - + +
202K THR 4.2 0.2 + - - -
203K THR* 3.0 37.7 + - + +
205K GLU* 1.3 78.4 - - - +
207K GLU* 1.3 56.3 + - - +
209K VAL* 3.2 12.6 - - + +
210K ARG* 3.8 13.2 + - - +
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Residues in contact with GLU 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K THR 2.9 8.3 + - - +
204K ALA* 3.1 34.2 + - - +
206K ARG* 1.3 78.4 - - - +
208K ILE* 1.3 62.8 + - + +
210K ARG* 2.7 50.5 + - - +
211K ASP* 4.8 0.5 + - - +
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Residues in contact with ILE 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204K ALA* 2.9 16.4 + - + +
205K GLU* 3.3 24.0 - - + +
207K GLU* 1.3 82.5 - - + +
209K VAL* 1.3 60.6 + - - +
210K ARG 3.1 2.7 - - - -
211K ASP* 3.0 10.8 + - + +
212K ILE* 2.9 35.2 + - + +
240K TYR* 4.1 20.5 + - + +
242K LEU* 3.7 22.0 - - + -
243K PRO* 3.6 38.8 - - + -
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Residues in contact with VAL 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186K THR* 3.9 24.2 - - + -
189K LEU* 4.1 14.1 - - + +
190K MET* 3.7 27.6 - - + -
193K LEU* 6.2 1.1 - - + -
200K PHE* 5.1 8.3 - - + -
205K GLU 2.9 15.2 + - - +
206K ARG* 3.2 29.2 - - - +
208K ILE* 1.3 74.3 - - - +
210K ARG* 1.3 61.8 + - - +
212K ILE* 3.4 22.0 - - + +
213K LYS* 2.9 33.7 + - - +
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Residues in contact with ARG 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186K THR* 5.3 6.7 - - - +
206K ARG* 3.9 24.5 - - - +
207K GLU* 2.7 52.5 + - - +
209K VAL* 1.3 78.2 - - - +
211K ASP* 1.3 56.8 + - - +
213K LYS* 3.3 12.0 - - - +
214K GLU* 2.9 30.0 + - + +
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Residues in contact with ASP 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207K GLU 4.8 0.6 + - - +
208K ILE* 3.0 11.9 + - + +
210K ARG* 1.3 77.4 - - - +
212K ILE* 1.3 60.0 + - - +
214K GLU* 3.9 16.9 - - - +
215K LYS* 2.8 48.9 + - - +
240K TYR* 2.5 33.2 + - - +
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Residues in contact with ILE 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189K LEU* 4.3 16.8 - - + -
193K LEU* 6.0 9.0 - - + -
200K PHE* 5.8 5.8 - - + -
205K GLU* 5.8 0.7 - - - +
208K ILE* 2.9 29.1 + - + +
209K VAL* 3.2 33.8 + - + +
211K ASP* 1.3 73.2 - - - +
213K LYS* 1.3 59.5 + - - +
216K LEU* 2.9 37.5 + - + +
217K CYS* 3.5 8.7 + - + +
240K TYR* 3.5 32.3 - - + -
242K LEU* 5.0 4.0 - - + -
248K ILE* 6.4 0.9 - - + -
250K ILE* 6.0 6.3 - - + -
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Residues in contact with LYS 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K GLY* 4.6 2.2 - - - -
185K LEU* 2.8 28.2 + - + +
186K THR* 3.7 25.1 - - - +
189K LEU* 3.4 18.1 - - + +
209K VAL 2.9 20.9 + - - +
210K ARG* 3.3 11.7 - - - +
212K ILE* 1.3 77.4 - - - +
214K GLU* 1.3 62.3 + - + +
215K LYS 3.2 1.0 + - - -
216K LEU 4.1 2.1 + - - -
217K CYS* 3.5 16.7 + - - +
257K CYS* 2.7 35.6 - - - -
306K TYR* 3.2 51.3 - - + +
307K PRO* 6.0 0.2 - - - +
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Residues in contact with GLU 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K ARG* 2.9 20.7 + - + +
211K ASP* 3.3 21.2 + - - +
213K LYS* 1.3 75.9 - - + +
215K LYS* 1.3 67.9 + - + +
305K MET* 5.9 10.4 - - + +
306K TYR* 4.9 4.3 - - + -
307K PRO* 5.8 3.5 - - - +
336K LYS* 4.2 23.9 + - - +
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Residues in contact with LYS 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211K ASP* 2.8 39.4 + - - +
213K LYS 4.4 0.2 - - - -
214K GLU* 1.3 90.6 - - - +
216K LEU* 1.3 79.6 + - + +
217K CYS 4.0 1.1 - - - -
218K TYR* 4.7 8.9 - - - -
240K TYR* 4.5 4.3 - - + -
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Residues in contact with LEU 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K ILE* 2.9 17.1 + - + +
215K LYS* 1.3 98.7 - - + +
217K CYS* 1.3 67.3 + - - +
218K TYR* 3.7 8.3 - - - -
238K LYS* 4.6 21.3 - - + +
239K SER 3.4 39.9 - - - +
240K TYR* 3.6 25.6 - - + +
250K ILE* 6.1 5.2 - - + -
254K ARG* 3.3 23.0 - - + +
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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