Contacts of the helix formed by residues 207 - 217 (chain H) in PDB entry 3LUE
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 GLU 207 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14H SER 5.7 0.7 - - - +
59H GLN* 4.9 13.9 - - + +
186H THR* 5.4 0.2 - - - +
203H THR 3.7 0.4 + - - +
204H ALA* 2.6 13.8 + - - +
206H ARG* 1.3 89.5 + - - +
208H ILE* 1.3 60.7 + - + +
209H VAL 3.4 1.6 - - - -
210H ARG* 3.1 53.5 + - - +
211H ASP* 3.4 12.8 - - - +
288J ASP* 3.9 6.3 - - - +
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Residues in contact with ILE 208 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H PHE* 3.7 24.2 - - + -
204H ALA* 3.5 6.7 + - + +
205H GLU* 3.1 35.2 + - + +
207H GLU* 1.3 78.3 - - + +
209H VAL* 1.3 64.8 + - - +
211H ASP* 3.6 14.2 + - - +
212H ILE* 3.2 29.0 + - + +
240H TYR* 4.8 13.0 - - + +
242H LEU* 4.2 11.9 - - + -
243H PRO* 4.3 28.7 - - + -
248H ILE* 5.1 1.6 - - + -
291J LYS* 5.0 4.0 - - - -
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Residues in contact with VAL 209 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H THR* 3.4 23.6 - - + +
189H LEU* 3.2 17.2 - - + +
190H MET* 3.8 37.2 - - + +
193H LEU* 4.6 3.1 - - + -
200H PHE* 4.0 32.8 - - + -
205H GLU 3.9 0.6 + - - +
206H ARG 2.9 24.2 - - - +
208H ILE* 1.3 76.2 - - - +
210H ARG* 1.4 64.9 + - - +
212H ILE* 3.0 9.8 + - + -
213H LYS* 2.9 21.5 + - - +
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Residues in contact with ARG 210 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H SER 5.1 2.5 - - - -
15H GLY* 3.9 34.4 + - - -
16H MET* 4.8 10.3 - - - +
186H THR* 4.0 22.0 - - + +
207H GLU* 3.1 45.9 + - - +
209H VAL* 1.4 79.6 - - - +
211H ASP* 1.3 80.2 + - - +
213H LYS* 3.5 5.5 - - - +
214H GLU* 3.0 71.9 + - - +
215H LYS* 4.7 3.4 - - - +
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Residues in contact with ASP 211 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H GLU* 3.4 16.3 - - - +
208H ILE* 3.6 13.8 + - - +
209H VAL 3.2 0.8 - - - -
210H ARG* 1.3 94.0 + - - +
212H ILE* 1.3 59.7 + - - +
214H GLU* 4.3 2.2 - - - +
215H LYS* 2.6 64.3 + - + +
240H TYR* 3.3 24.9 - - + +
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Residues in contact with ILE 212 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H LEU* 4.1 13.5 - - + -
193H LEU* 3.9 19.1 - - + -
200H PHE* 4.4 5.4 - - + -
208H ILE* 3.2 21.3 + - + +
209H VAL* 3.0 14.6 + - - +
211H ASP* 1.3 73.3 - - - +
213H LYS* 1.3 58.4 + - - +
215H LYS 2.8 0.9 + - - -
216H LEU* 2.7 60.8 + - + +
217H CYS* 3.7 2.2 + - - -
240H TYR* 3.8 25.6 - - + -
248H ILE* 3.9 22.0 - - + -
250H ILE* 3.8 18.2 - - + -
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Residues in contact with LYS 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H ASP* 5.9 0.2 + - - -
182H GLY* 3.2 19.3 + - - -
185H LEU* 3.6 5.4 - - + +
186H THR* 2.6 44.7 + - - +
189H LEU* 3.6 11.4 - - + +
209H VAL 2.9 16.5 + - - +
210H ARG* 3.5 7.5 - - - +
212H ILE* 1.3 76.8 - - - +
214H GLU* 1.3 88.7 + - - +
217H CYS* 3.2 31.0 + - - +
257H CYS* 4.0 17.0 - - - -
303H THR* 6.0 0.2 - - - -
306H TYR* 3.8 27.5 - - - +
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Residues in contact with GLU 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H GLY* 5.1 2.4 - - - -
210H ARG* 3.0 70.8 + - - +
211H ASP* 4.3 2.8 - - - +
213H LYS* 1.3 99.9 + - - +
215H LYS* 1.3 65.1 + - + +
217H CYS 4.8 2.9 + - - +
306H TYR* 5.4 6.0 - - + -
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Residues in contact with LYS 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H ARG* 4.7 4.8 - - - +
211H ASP* 2.6 65.9 + - + +
212H ILE* 2.8 2.9 + - - +
214H GLU* 1.3 82.2 + - + +
216H LEU* 1.3 70.6 + - + +
217H CYS 5.1 1.0 - - - +
218H TYR* 5.7 2.3 - - - -
240H TYR* 4.5 15.0 + - + -
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Residues in contact with LEU 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212H ILE* 2.7 43.5 + - + +
215H LYS* 1.3 84.5 - - + +
217H CYS* 1.4 65.8 + - - +
218H TYR* 3.1 10.7 - - - -
238H LYS* 3.9 30.3 - - + +
239H SER 5.2 5.6 - - - +
240H TYR* 4.3 13.9 - - + -
250H ILE* 3.7 21.5 - - + -
254H ARG* 2.8 44.3 + - + +
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Residues in contact with CYS 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189H LEU* 4.5 6.7 - - - -
212H ILE* 4.6 1.3 - - - -
213H LYS* 3.2 33.1 + - - +
214H GLU 5.1 2.3 - - - +
215H LYS 3.9 1.6 - - - +
216H LEU* 1.4 77.4 - - - +
218H TYR* 1.3 69.9 - - - +
253H GLU 4.4 0.2 - - - -
254H ARG* 3.0 27.8 - - - +
257H CYS* 3.7 23.6 - - - -
258H PRO* 3.8 3.8 - - + -
306H TYR* 3.8 23.1 - - + -
307H PRO* 3.8 13.7 - - - +
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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