Contacts of the helix formed by residues 219 - 238 (chain T) in PDB entry 1J0B
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 PHE 219 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215T ALA* 4.7 4.3 - - + -
218T ARG* 1.3 93.3 - - - +
220T GLY* 1.3 87.4 + - - +
222T VAL* 3.5 15.2 - - - +
223T MET* 3.8 21.6 - - + +
224T THR* 3.9 7.6 - - - -
248T LEU* 2.8 52.7 - - + -
249T TYR* 3.2 29.6 - - - -
250T ASP* 3.3 31.2 - - + +
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Residues in contact with GLY 220 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219T PHE* 1.3 100.0 - - - +
221T GLU* 1.3 72.1 + - - +
222T VAL* 3.7 0.9 - - - -
223T MET 3.3 1.4 + - - -
224T THR* 3.2 17.2 + - - -
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Residues in contact with GLU 221 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220T GLY* 1.3 73.5 - - - +
222T VAL* 1.3 69.7 + - + +
224T THR* 2.8 9.5 + - - +
225T SER* 2.6 39.6 + - - -
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Residues in contact with VAL 222 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218T ARG* 3.5 28.0 - - + +
219T PHE 3.5 20.9 - - - +
220T GLY 4.4 0.4 - - - -
221T GLU* 1.3 78.1 - - + +
223T MET* 1.3 68.8 + - + +
225T SER* 4.0 2.0 - - - -
226T LYS* 2.8 41.6 + - + +
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Residues in contact with MET 223 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189T ALA* 4.3 7.9 - - + +
190T GLY 4.3 20.6 - - - +
191T SER 5.7 3.1 - - - +
192T GLY* 5.6 4.9 - - - -
215T ALA* 4.3 13.0 - - + -
217T GLY 6.1 0.2 - - - -
218T ARG* 4.7 8.3 - - + -
219T PHE* 3.8 34.8 - - - +
220T GLY 3.9 4.9 - - - +
221T GLU 2.8 2.0 + - - -
222T VAL* 1.3 90.5 - - + +
224T THR* 1.3 51.7 + - - +
226T LYS* 2.8 9.4 + - - +
227T LEU* 2.8 39.5 + - + +
248T LEU* 3.1 39.0 - - + -
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Residues in contact with THR 224 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219T PHE* 3.9 6.0 - - - -
220T GLY* 3.2 16.5 + - - +
221T GLU* 2.8 16.9 + - - +
223T MET* 1.3 80.4 - - - +
225T SER* 1.3 67.3 + - - +
227T LEU* 3.5 18.3 + - - +
228T ASP* 3.6 13.3 + - - +
245T ARG* 3.6 28.8 + - - +
248T LEU* 3.1 29.4 - - - +
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Residues in contact with SER 225 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221T GLU* 2.6 44.0 + - - -
222T VAL* 4.0 2.0 - - - -
224T THR* 1.3 76.2 - - - +
226T LYS* 1.3 59.5 + - - +
228T ASP* 2.9 34.0 + - - +
229T ASN* 3.5 5.2 + - - +
245T ARG* 5.3 0.2 - - - +
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Residues in contact with LYS 226 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156T PRO* 6.2 3.8 - - - +
159T ALA* 6.0 5.3 - - - +
191T SER* 5.0 14.0 + - - +
222T VAL* 2.8 32.1 + - + +
223T MET* 2.8 6.9 + - - +
225T SER* 1.3 73.6 + - - +
227T LEU* 1.3 60.1 - - - +
229T ASN* 3.6 8.9 + - + +
230T LEU* 3.2 28.1 + - + +
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Residues in contact with LEU 227 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192T GLY* 5.5 12.6 - - - +
195T LEU* 4.4 10.3 - - + -
196T ALA* 4.5 14.4 - - + +
223T MET* 2.8 20.6 + - + +
224T THR* 3.5 14.1 - - - +
225T SER 3.1 0.2 - - - -
226T LYS* 1.3 70.2 - - - +
228T ASP* 1.3 69.2 + - - +
230T LEU* 3.3 11.2 - - - +
231T ILE* 3.0 35.7 + - + +
245T ARG* 6.2 1.3 - - - -
246T PRO* 4.2 30.1 - - + +
248T LEU* 3.9 29.8 - - + -
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Residues in contact with ASP 228 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224T THR 3.6 12.8 - - - +
225T SER* 2.9 13.5 + - - +
227T LEU* 1.3 79.7 - - - +
229T ASN* 1.3 62.4 + - - +
230T LEU 3.0 5.1 + - - -
231T ILE* 3.2 20.7 + - - +
232T LYS* 3.2 12.7 + - - +
245T ARG* 3.3 50.0 + - - +
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Residues in contact with ASN 229 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225T SER 3.5 6.4 + - - +
226T LYS* 4.0 10.3 - - + +
227T LEU 3.5 0.2 - - - -
228T ASP* 1.3 79.6 - - - +
230T LEU* 1.3 62.4 + - - +
232T LYS* 3.7 25.8 - - - +
233T GLU* 3.1 45.7 + - - +
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Residues in contact with LEU 230 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159T ALA* 4.4 15.5 - - + +
160T SER 4.5 2.9 - - - -
161T PRO* 4.2 32.5 - - + -
164T THR* 4.5 13.5 - - - +
191T SER 4.8 4.5 - - - +
192T GLY 4.5 2.0 - - - -
193T GLY* 4.1 20.4 - - - +
196T ALA* 4.0 17.7 - - + -
226T LYS* 3.2 21.4 + - + +
227T LEU* 3.3 16.4 - - - +
228T ASP 3.0 0.4 - - - -
229T ASN* 1.3 75.9 - - - +
231T ILE* 1.3 59.3 + - + +
232T LYS 2.9 9.8 + - - -
233T GLU* 3.2 4.5 + - - +
234T ALA* 3.1 19.9 + - - +
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Residues in contact with ILE 231 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196T ALA* 3.4 40.4 - - + +
199T SER* 4.0 17.7 - - - -
200T LEU* 4.4 11.1 - - + +
227T LEU* 3.0 23.1 - - + +
228T ASP* 3.2 13.9 + - - +
230T LEU* 1.3 72.2 - - - +
232T LYS* 1.3 56.9 + - + +
234T ALA* 4.3 7.9 - - - -
235T ALA* 3.4 20.8 + - - +
242T VAL* 3.6 32.3 - - + +
244T VAL 5.3 0.4 - - - -
245T ARG* 4.4 19.1 - - + -
246T PRO* 4.5 2.9 - - + -
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Residues in contact with LYS 232 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228T ASP 3.2 10.6 + - - +
229T ASN* 3.6 28.3 - - - +
230T LEU 3.0 0.4 - - - -
231T ILE* 1.3 77.7 - - - +
233T GLU* 1.3 62.9 + - - +
234T ALA 3.1 1.1 - - - -
235T ALA* 3.1 7.1 + - + +
236T GLU* 2.9 49.6 + - + +
242T VAL* 5.5 11.7 - - + -
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Residues in contact with GLU 233 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161T PRO* 3.1 28.3 - - + +
229T ASN* 3.1 41.0 + - - +
230T LEU* 3.7 5.6 - - - +
232T LYS* 1.3 81.2 - - - +
234T ALA* 1.3 60.4 + - - +
236T GLU* 3.4 18.7 + - - +
237T LEU* 3.1 26.2 + - - +
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Residues in contact with ALA 234 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161T PRO* 4.4 2.4 - - + +
164T THR* 3.2 35.2 - - + +
165T LEU* 5.7 1.1 - - + -
200T LEU* 3.2 19.1 - - + +
230T LEU 3.1 15.3 + - - +
231T ILE* 4.3 4.3 - - - -
233T GLU* 1.3 75.1 - - - +
235T ALA* 1.3 60.9 + - - +
237T LEU* 2.9 36.5 + - - +
238T LEU* 3.2 7.4 + - - +
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Residues in contact with ALA 235 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200T LEU* 3.1 15.0 - - + +
231T ILE 3.4 18.8 + - - +
232T LYS* 3.1 9.7 + - + +
234T ALA* 1.3 78.7 - - - +
236T GLU* 1.3 55.7 + - - +
238T LEU 3.3 0.7 + - - -
239T GLY 2.9 6.1 + - - -
240T VAL* 2.7 57.2 + - + +
242T VAL* 4.8 12.6 - - + +
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Residues in contact with GLU 236 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232T LYS* 2.9 35.0 + - + +
233T GLU* 3.5 23.0 - - - +
235T ALA* 1.3 72.7 - - + +
237T LEU* 1.3 61.8 + - + +
238T LEU 2.9 1.6 - - - -
239T GLY* 2.5 26.9 + - - +
240T VAL 5.0 0.9 - - - -
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Residues in contact with LEU 237 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11T LYS* 4.1 11.3 + - - -
12T PHE* 3.1 40.7 - - + -
161T PRO* 3.3 46.4 - - + +
162T ILE* 3.7 10.5 - - + +
165T LEU* 4.4 7.6 - - + -
233T GLU 3.1 10.3 - - - +
234T ALA* 2.9 17.7 + - + +
236T GLU* 1.3 80.7 - - + +
238T LEU* 1.3 57.7 + - + +
239T GLY 3.8 0.3 + - - -
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Residues in contact with LEU 238 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8T LEU* 3.3 50.8 - - + +
9T LEU* 4.0 7.6 - - + -
12T PHE* 4.0 8.7 - - + -
165T LEU* 3.2 34.5 - - + -
168T VAL* 4.3 9.4 - - + -
200T LEU* 3.3 37.7 - - + -
204T ILE* 3.5 13.0 - - + -
234T ALA 3.2 5.9 + - - +
235T ALA 3.9 4.5 - - - +
236T GLU 2.9 0.6 - - - -
237T LEU* 1.3 74.4 - - - +
239T GLY* 1.3 64.8 + - - +
240T VAL* 3.0 6.1 + - + -
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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
------------------------------------------------------------
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