Contacts of the helix formed by residues 197 - 215 (chain B) in PDB entry 1J1J
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 GLY 197 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B LYS 3.6 3.0 + - - -
194B ARG 2.9 12.6 + - - -
196B ASP* 1.3 77.8 - - - +
198B LEU* 1.3 61.5 + - - +
199B LYS* 3.2 4.2 + - - -
200B TYR* 3.4 20.1 + - - +
201B ASP* 3.4 13.1 - - - +
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LEU* 4.5 15.7 - - + +
148B ALA* 3.5 32.5 - - + -
174B ILE* 4.4 9.4 - - + +
177B LEU* 4.6 2.9 - - + -
178B ASP* 3.7 42.4 - - + +
181B PHE* 4.5 4.3 - - + -
194B ARG 3.8 1.4 + - - -
195B TYR* 3.0 33.9 + - + +
197B GLY* 1.3 76.9 - - - +
199B LYS* 1.3 60.9 + - - +
201B ASP* 3.1 14.0 + - + +
202B VAL* 2.9 32.3 + - + +
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Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ASP* 5.4 2.7 + - - -
195B TYR 4.4 2.0 + - - -
196B ASP* 3.1 49.9 + - - +
197B GLY* 4.5 0.7 - - - -
198B LEU* 1.3 78.3 - - - +
200B TYR* 1.3 61.9 + - + +
202B VAL* 3.2 8.1 + - - +
203B LYS* 2.9 30.4 + - - +
153C ARG* 6.4 2.0 - - - -
201C ASP* 6.1 1.3 - - - -
204C LYS* 6.2 4.0 - - + -
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Residues in contact with TYR 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TYR* 5.2 16.6 - + - -
203A LYS* 3.2 42.0 - - - +
207A GLU* 4.7 2.9 + - - -
197B GLY* 3.4 11.6 + - - +
198B LEU 3.2 0.2 - - - -
199B LYS* 1.3 85.0 - - + +
201B ASP* 1.3 69.5 + - - +
203B LYS* 3.3 10.3 + - + +
204B LYS* 3.0 49.3 + - + +
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Residues in contact with ASP 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LYS* 4.5 1.4 + - - -
145B LEU 4.7 0.3 - - - +
148B ALA* 4.3 2.7 - - + +
149B SER* 3.1 42.5 + - - +
152B SER* 2.9 31.6 + - - +
174B ILE* 4.9 2.9 - - + -
197B GLY 3.4 15.4 - - - +
198B LEU* 3.1 25.4 + - + +
200B TYR* 1.3 92.6 - - - +
202B VAL* 1.3 60.8 + - - +
204B LYS* 3.4 2.4 + - - +
205B VAL* 3.2 22.0 + - - +
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Residues in contact with VAL 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B ILE* 3.7 27.4 - - + +
175B ASN* 3.8 18.6 - - - +
178B ASP* 4.2 21.5 - - + +
198B LEU* 2.9 28.6 + - + +
199B LYS* 3.2 7.6 + - - +
201B ASP* 1.3 76.3 - - - +
203B LYS* 1.3 61.4 + - - +
205B VAL* 3.6 4.1 + - + +
206B GLU* 3.2 21.3 + - - +
153C ARG* 6.1 3.8 - - + -
156C VAL* 4.2 15.2 - - + +
157C ASN* 4.4 9.0 - - - +
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Residues in contact with LYS 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LYS 2.9 16.1 + - - +
200B TYR* 3.4 12.8 - - + +
202B VAL* 1.3 76.2 - - - +
204B LYS* 1.3 65.3 - - - +
206B GLU* 3.1 29.6 + - + +
207B GLU* 2.9 40.9 + - - +
156C VAL* 4.1 15.7 - - + -
204C LYS* 3.1 43.5 - - - +
207C GLU* 5.0 3.0 + - - +
208C VAL* 4.2 9.4 - - - +
211C ASP* 2.8 29.5 + - - -
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Residues in contact with LYS 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A LYS* 3.3 36.8 + - - +
207A GLU* 2.9 32.9 + - - +
152B SER* 3.5 35.2 - - - +
153B ARG* 4.2 2.0 - - - +
156B VAL* 3.9 21.5 - - + +
200B TYR* 3.0 39.2 + - + +
201B ASP* 3.7 6.1 - - - +
203B LYS* 1.3 78.6 - - - +
205B VAL* 1.3 60.7 + - - +
207B GLU* 3.5 18.0 + - - +
208B VAL* 3.5 19.9 + - - +
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Residues in contact with VAL 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B SER* 3.7 16.4 - - - -
155B SER* 3.9 14.1 - - - +
167B PRO 4.4 3.6 - - - +
170B ILE* 4.3 3.8 - - + -
171B SER* 3.3 43.1 - - - +
174B ILE* 3.7 24.9 - - + -
201B ASP 3.2 16.8 + - - +
202B VAL* 4.0 6.5 - - - +
203B LYS 3.2 0.2 - - - -
204B LYS* 1.3 76.8 - - - +
206B GLU* 1.3 63.4 + - - +
208B VAL* 3.5 4.1 + - + +
209B VAL* 3.1 21.6 + - + +
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B SER* 5.6 0.2 - - - -
202B VAL* 3.2 14.7 + - + +
203B LYS* 3.1 27.8 + - + +
205B VAL* 1.3 73.9 - - - +
207B GLU* 1.3 71.5 + - + +
209B VAL* 3.3 8.3 + - - +
210B TYR* 2.8 30.3 + - - +
156C VAL* 3.7 33.3 - - + +
159C VAL* 3.0 42.1 - - - +
160C THR* 4.4 13.7 - - - -
208C VAL* 4.7 5.7 - - - +
211C ASP* 4.5 7.5 - - - +
212C LEU* 5.2 1.9 - - - +
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 3.9 21.0 - - - +
210A TYR* 4.6 0.9 - - + -
203B LYS* 2.9 44.9 + - - +
204B LYS* 3.6 17.3 - - - +
205B VAL 3.3 0.2 - - - -
206B GLU* 1.3 84.5 - - + +
208B VAL* 1.3 57.7 + - + +
210B TYR* 3.2 5.5 + - - +
211B ASP* 2.8 39.7 + - - +
211C ASP* 3.9 13.3 - - - +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A TYR* 3.4 21.8 - - + +
155B SER* 3.9 20.0 - - - +
156B VAL* 3.9 19.1 - - + -
159B VAL* 3.7 28.9 - - + -
167B PRO* 3.8 21.5 - - + -
204B LYS 3.5 15.1 + - - +
205B VAL* 3.8 6.1 - - + +
206B GLU 3.3 0.6 - - - -
207B GLU* 1.3 73.9 - - + +
209B VAL* 1.3 68.6 + - + +
211B ASP* 3.0 2.4 + - - +
212B LEU* 2.9 25.7 + - + +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO 4.4 4.3 - - - +
168B LEU* 3.9 27.8 - - + -
171B SER* 3.3 33.2 - - - +
205B VAL* 3.1 16.5 + - + +
206B GLU 3.6 7.2 - - - +
208B VAL* 1.3 78.7 - - + +
210B TYR* 1.3 58.2 + - - +
212B LEU* 3.3 3.9 + - - +
213B SER* 2.9 40.7 + - - +
217B PHE* 4.7 3.8 - - + -
159C VAL 5.5 0.9 - - - +
160C THR* 4.3 24.9 - - - +
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Residues in contact with TYR 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU* 2.8 25.9 + - - +
207B GLU* 3.4 6.3 - - - +
209B VAL* 1.3 78.2 - - - +
211B ASP* 1.3 72.8 + - - +
212B LEU 3.2 0.2 + - - -
213B SER* 3.2 4.1 + - - -
214B ILE* 3.0 39.8 + - + +
159C VAL* 3.4 23.3 - - + -
160C THR* 6.2 0.2 - - - +
164C TYR* 3.1 41.7 - + - -
211C ASP* 4.4 18.6 - - + -
212C LEU* 4.4 12.1 + - + +
214C ILE* 5.6 1.6 - - + -
215C ARG* 2.4 51.4 + - + -
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Residues in contact with ASP 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A TYR* 2.7 42.6 + - - +
211A ASP* 4.8 2.4 - - - +
214A ILE* 3.6 13.4 - - + +
215A ARG* 5.1 3.3 + - - -
207B GLU* 2.8 25.5 + - - +
208B VAL 3.6 0.9 - - - +
210B TYR* 1.3 81.6 - - - +
212B LEU* 1.3 62.3 + - - +
214B ILE* 3.7 5.5 + - - +
215B ARG* 3.3 43.5 + - - +
215D ARG* 5.1 10.7 + - - -
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 4.1 16.4 - - + -
159B VAL* 4.1 13.2 - - + -
164B TYR* 3.7 37.0 - - + +
167B PRO* 3.9 21.1 - - + -
168B LEU* 3.6 31.9 - - + -
208B VAL* 2.9 22.4 + - + +
209B VAL* 3.6 4.3 - - - +
211B ASP* 1.3 75.8 - - - +
213B SER* 1.3 59.9 + - - +
215B ARG* 3.1 12.9 + - - +
216B GLY 3.2 0.3 + - - -
217B PHE* 2.4 46.3 + - + +
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B VAL* 2.9 26.5 + - - +
210B TYR* 3.7 5.1 - - - -
212B LEU* 1.3 71.9 - - - +
214B ILE* 1.3 56.7 + - - +
216B GLY* 2.7 26.5 + - - -
217B PHE* 2.9 44.1 + - - +
164C TYR* 4.0 19.4 + - - -
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Residues in contact with ILE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B TYR* 3.0 52.2 + - + +
211B ASP* 3.8 4.5 - - - +
213B SER* 1.3 80.0 - - - +
215B ARG* 1.3 88.0 + - + +
216B GLY 3.5 0.7 + - - -
164C TYR* 4.2 13.0 - - + +
215C ARG* 3.7 28.3 - - - +
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ILE* 3.3 48.7 + - - +
215A ARG* 2.6 42.5 - - - +
211B ASP* 3.3 23.1 + - - +
212B LEU* 3.1 8.9 + - - +
214B ILE* 1.3 91.9 - - + +
216B GLY* 1.3 60.4 + - - +
217B PHE 4.1 5.5 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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