Contacts of the helix formed by residues 207 - 217 (chain L) in PDB entry 3J0S
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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L MET* 5.6 3.5 - - - +
32L PRO* 5.1 10.6 - - - +
56L ASP* 5.9 1.7 - - - +
59L GLN* 3.5 46.2 + - + +
183L ARG* 5.9 3.1 - - - +
186L THR* 5.7 0.4 - - - -
204L ALA 4.1 9.4 + - - +
205L GLU 3.2 0.4 - - - -
206L ARG* 1.3 80.1 + - - +
208L ILE* 1.3 65.7 + - + +
210L ARG* 3.0 49.2 + - - +
211L ASP* 4.0 3.1 + - - -
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Residues in contact with ILE 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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200L PHE* 5.5 4.0 - - + -
204L ALA 4.8 2.9 - - - +
205L GLU* 3.2 31.4 - - + +
206L ARG 3.2 0.6 - - - -
207L GLU* 1.3 80.5 - - + +
209L VAL* 1.3 63.5 + - + +
210L ARG 3.2 0.9 + - - -
211L ASP* 3.2 27.8 + - - +
212L ILE* 3.9 4.8 - - + +
240L TYR* 3.6 9.7 + - - +
242L LEU* 3.8 29.8 - - + -
243L PRO* 4.1 27.8 - - + -
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Residues in contact with VAL 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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186L THR* 3.3 34.0 - - + +
189L LEU* 4.1 9.6 - - + +
190L MET* 4.0 22.4 - - + +
193L LEU* 4.6 2.5 - - + -
200L PHE* 3.9 27.8 - - + -
205L GLU 4.5 1.1 - - - +
206L ARG* 2.9 25.3 + - + +
208L ILE* 1.3 75.0 - - + +
210L ARG* 1.3 60.1 + - - +
211L ASP 3.2 0.2 - - - -
212L ILE* 3.0 28.7 + - + +
213L LYS* 2.9 27.0 + - - +
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Residues in contact with ARG 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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16L MET* 3.9 37.0 - - + +
32L PRO* 5.8 5.1 - - - +
186L THR* 3.9 16.7 - - + +
207L GLU* 3.0 36.9 + - - +
209L VAL* 1.3 80.2 - - - +
211L ASP* 1.3 82.6 + - - +
213L LYS* 3.1 33.6 + - - +
214L GLU* 3.5 11.2 + - + +
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Residues in contact with ASP 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 GLU 4.8 3.8 - - - +
208L ILE* 3.2 15.9 + - - +
210L ARG* 1.3 104.0 + - - +
212L ILE* 1.3 59.8 + - - +
213L LYS 3.4 0.2 + - - -
214L GLU* 3.7 0.7 + - - -
215L LYS* 3.0 46.4 + - + +
240L TYR* 2.8 22.4 + - + +
243L PRO* 6.1 1.0 - - - +
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Residues in contact with ILE 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189L LEU* 3.6 19.7 - - + -
193L LEU* 4.4 15.5 - - + -
200L PHE* 5.4 0.9 - - + -
208L ILE* 3.9 5.6 - - + +
209L VAL* 3.0 39.7 + - + +
211L ASP* 1.3 79.2 - - - +
213L LYS* 1.3 53.1 + - - +
216L LEU* 2.7 53.7 + - + +
217L CYS 3.9 0.2 + - - -
240L TYR* 3.2 39.7 - - + +
242L LEU* 5.5 0.7 - - + -
248L ILE* 5.3 8.5 - - + -
250L ILE* 4.1 12.6 - - + -
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Residues in contact with LYS 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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16L MET* 6.4 1.3 - - - -
182L GLY 4.4 5.8 - - - +
185L LEU* 5.1 0.4 - - + -
186L THR* 3.5 28.7 - - - +
189L LEU* 4.2 6.7 - - + -
209L VAL 2.9 11.2 + - - +
210L ARG* 3.1 24.2 + - - +
212L ILE* 1.3 76.5 - - - +
214L GLU* 1.3 89.8 + - - +
217L CYS* 3.1 40.1 + - - +
302L GLY 4.5 5.9 + - - -
303L THR* 3.7 23.1 - - + +
306L TYR* 3.6 30.9 - - + +
336L LYS* 4.8 2.0 - - - +
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Residues in contact with GLU 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 ARG* 3.5 9.9 + - - +
211L ASP 3.7 1.3 + - - +
212L ILE 3.5 0.4 - - - -
213L LYS* 1.3 101.6 + - - +
215L LYS* 1.3 80.5 + - + +
217L CYS 4.5 4.9 + - - +
302L GLY 5.8 0.2 - - - +
305L MET* 4.9 17.9 - - + +
306L TYR* 5.5 5.2 - - + -
307L PRO* 5.2 6.4 - - - +
336L LYS* 3.0 28.4 + - - +
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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 ASP* 3.0 39.1 + - + +
212L ILE 4.3 0.9 - - - +
213L LYS 3.4 0.2 - - - -
214L GLU* 1.3 95.7 + - + +
216L LEU* 1.3 64.8 + - + +
217L CYS 3.8 0.2 - - - -
218L TYR* 3.6 20.3 + - - -
240L TYR* 4.5 14.4 - - + -
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Residues in contact with LEU 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 ILE* 2.7 26.0 + - + +
215L LYS* 1.3 81.3 - - + +
217L CYS* 1.3 63.1 + - - +
218L TYR* 3.4 21.3 + - + +
238L LYS* 4.1 24.0 - - + +
239L SER 3.7 18.6 - - - +
240L TYR* 3.3 42.2 - - + -
250L ILE* 3.4 37.0 - - + +
254L ARG* 4.1 12.5 - - + +
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Residues in contact with CYS 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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189L LEU* 4.2 15.9 - - - -
213L LYS* 3.1 49.3 + - - +
214L GLU 4.5 0.9 + - - +
215L LYS 3.8 1.2 - - - -
216L LEU* 1.3 77.5 - - - +
218L TYR* 1.3 59.6 + - - +
254L ARG 4.3 1.8 - - - -
257L CYS* 4.8 15.3 - - - -
258L PRO* 5.4 2.5 - - + -
306L TYR* 3.4 36.5 - - + +
307L PRO* 3.0 26.5 - - - +
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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