Contacts of the helix formed by residues 210 - 224 (chain X) in PDB entry 1JJ2
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 210 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13130 A 2.8 19.2 + - - -
13140 U 4.0 7.4 - - - -
13160 G 3.7 23.8 - - - -
208X LYS 3.2 3.2 + - - -
209X VAL* 1.3 75.3 - - - +
211X ALA* 1.3 61.5 + - - -
212X ARG 3.3 2.7 - - - -
213X LYS 3.3 4.1 + - - -
214X ARG* 2.9 26.9 + - - +
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Residues in contact with ALA 211 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13150 G 3.4 31.3 + - - +
13160 G 3.1 15.5 + - - +
100X ARG* 5.3 0.9 + - - -
210X GLY* 1.3 71.0 - - - -
212X ARG* 1.3 61.8 + - - +
214X ARG* 3.7 11.8 - - - +
215X GLU* 3.1 24.6 + - - +
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Residues in contact with ARG 212 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3120 U 5.5 2.2 + - - -
3130 U 5.7 1.4 - - - -
3190 A 4.6 16.2 + - - -
3200 G 3.2 51.4 + - - -
13140 U 4.6 13.3 + - - +
13150 G 3.1 93.2 + - + +
210X GLY 3.3 0.2 - - - -
211X ALA* 1.3 77.7 - - - +
213X LYS* 1.3 61.7 + - - +
215X GLU* 3.6 14.4 + - - +
216X ARG* 3.7 35.5 + - - +
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Residues in contact with LYS 213 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13120 G 2.7 35.1 + - - +
13130 A 2.9 40.8 + - - +
188X HIS 4.0 15.7 - - - +
189X ASN* 4.3 6.5 - - + -
190X VAL* 5.4 4.5 - - + +
209X VAL* 3.7 5.2 - - + -
210X GLY 3.3 2.2 + - - -
212X ARG* 1.3 79.3 - - + +
214X ARG* 1.3 65.3 + - - +
216X ARG* 3.3 17.7 + - + +
217X ILE* 3.0 35.9 + - + +
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Residues in contact with ARG 214 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13350 C 4.0 11.0 + - - -
100X ARG* 5.4 0.2 - - - +
205X ILE* 3.5 36.3 + - + +
206X ALA 5.0 1.0 + - - -
207X SER* 5.9 0.4 - - - +
209X VAL* 3.6 29.6 - - + +
210X GLY 2.9 19.5 + - - +
211X ALA* 3.7 10.1 - - - +
213X LYS* 1.3 77.0 - - - +
215X GLU* 1.3 55.3 + - - +
217X ILE* 3.2 5.9 + - - +
218X GLU* 2.7 48.2 + - - +
230X ASN* 2.8 36.4 + - - +
231X PRO* 3.6 2.6 + - - +
232X THR* 3.1 33.6 + - - +
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Residues in contact with GLU 215 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13150 G 3.4 25.9 + - - +
100X ARG* 3.5 36.1 + - - +
211X ALA 3.1 16.6 + - - +
212X ARG* 3.7 7.7 - - - +
213X LYS 3.2 0.2 - - - -
214X ARG* 1.3 77.3 - - - +
216X ARG* 1.3 65.1 + - + +
218X GLU* 3.5 1.2 + - - +
219X GLU* 3.2 31.5 + - + +
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Residues in contact with ARG 216 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3200 G 4.3 13.1 + - - -
3210 A 5.1 13.5 + - - -
190X VAL* 4.2 16.1 - - + +
212X ARG* 3.7 38.2 + - - +
213X LYS* 3.3 19.7 + - + +
214X ARG 3.2 0.4 - - - -
215X GLU* 1.3 79.5 - - + +
217X ILE* 1.3 65.3 + - - +
219X GLU* 3.2 20.6 - - - +
220X GLU* 3.2 26.6 + - - +
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Residues in contact with ILE 217 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187X VAL* 4.4 9.2 - - + -
188X HIS 3.8 8.1 - - - +
189X ASN* 3.3 46.4 - - - +
190X VAL* 3.7 12.3 - - + +
193X LEU* 3.7 19.2 - - + +
203X VAL* 5.4 1.1 - - + -
205X ILE* 3.6 31.2 - - + -
209X VAL* 4.3 9.0 - - + -
213X LYS* 3.0 28.0 + - + +
214X ARG 3.6 3.1 - - - +
216X ARG* 1.3 76.0 - - - +
218X GLU* 1.3 58.3 + - - +
221X ALA* 3.0 30.4 + - + +
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Residues in contact with GLU 218 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X ARG* 2.7 45.8 + - + +
101X GLY* 5.2 3.6 + - - -
205X ILE* 4.0 16.2 - - + -
214X ARG* 2.7 30.2 + - - +
215X GLU 3.9 3.6 - - - +
217X ILE* 1.3 75.8 - - - +
219X GLU* 1.3 59.8 + - - +
221X ALA* 4.1 4.4 - - - +
222X GLU* 3.4 23.9 + - - +
228X VAL* 4.6 13.7 - - + +
231X PRO* 3.3 9.0 - - - +
232X THR* 2.6 49.3 + - - -
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Residues in contact with GLU 219 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X ARG* 6.5 0.2 - - - +
215X GLU* 3.2 17.0 + - + +
216X ARG* 3.2 30.2 + - - +
218X GLU* 1.3 76.7 - - - +
220X GLU* 1.3 68.9 + - + +
222X GLU* 3.7 7.4 + - - +
223X ASP* 2.7 36.0 + - - +
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Residues in contact with GLU 220 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X VAL* 4.0 25.6 - - + +
193X LEU* 4.1 12.0 - - + +
216X ARG* 3.2 13.5 + - - +
217X ILE 4.4 1.3 - - - +
219X GLU* 1.3 82.5 - - + +
221X ALA* 1.3 64.2 + - - +
223X ASP* 3.6 10.8 + - + +
224X ALA* 3.2 22.3 + - - +
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Residues in contact with ALA 221 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193X LEU* 3.8 24.7 - - + +
203X VAL* 4.9 0.2 - - + -
217X ILE* 3.0 19.4 + - + +
218X GLU 4.1 1.3 - - - +
219X GLU 3.3 0.2 - - - -
220X GLU* 1.3 75.5 - - - +
222X GLU* 1.3 65.2 + - - +
224X ALA* 3.0 8.9 + - - -
226X ILE* 2.8 39.4 + - + +
228X VAL* 4.0 24.5 - - + -
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Residues in contact with GLU 222 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100X ARG* 5.0 1.6 - - - +
101X GLY* 3.3 36.5 + - - -
102X LEU* 4.0 24.7 - - + +
218X GLU 3.4 16.1 + - - +
219X GLU* 3.9 7.5 - - - +
221X ALA* 1.3 80.7 - - - +
223X ASP* 1.3 61.8 + - - +
225X GLY* 3.0 18.9 + - - -
226X ILE 3.9 8.9 + - - +
228X VAL* 5.7 0.2 - - - +
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Residues in contact with ASP 223 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219X GLU* 2.7 25.1 + - - +
220X GLU* 3.9 13.0 - - + +
221X ALA 3.2 0.4 - - - -
222X GLU* 1.3 81.3 - - - +
224X ALA* 1.3 58.1 + - - +
225X GLY 3.2 1.4 + - - -
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Residues in contact with ALA 224 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193X LEU* 5.9 2.9 - - + +
196X VAL 5.4 1.3 - - - +
198X GLY* 5.0 3.6 + - - -
220X GLU 3.2 16.1 + - - +
221X ALA* 3.0 7.1 + - - +
223X ASP* 1.3 77.3 - - - +
225X GLY* 1.3 61.4 + - - +
226X ILE* 3.5 21.9 + - + +
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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