Contacts of the helix formed by residues 217 - 234 (chain B) in PDB entry 3AG9
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 LYS 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B HIS* 3.2 68.6 + - + +
161B ASP* 4.6 13.7 + - - +
163B ILE* 3.4 24.6 - - + +
191B VAL 5.7 3.6 - - - +
216B ASN* 1.3 86.4 - - + +
218B ALA* 1.3 57.9 + - - +
219B VAL 3.0 6.1 - - - -
220B ASP* 3.0 26.7 + - - +
221B TRP* 3.8 4.5 + - - +
283B ASN* 5.6 2.5 - - - +
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Residues in contact with ALA 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B GLU* 4.4 0.9 - - - +
216B ASN* 3.1 15.5 + - - +
217B LYS* 1.3 79.1 - - - +
219B VAL* 1.3 61.8 + - - +
221B TRP* 3.3 13.2 + - - +
222B TRP 3.2 12.8 + - - -
277B LEU* 3.7 27.1 - - + -
280B ARG* 3.0 21.7 + - - +
283B ASN* 3.7 26.5 - - + +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ILE* 4.0 15.7 - - + -
165B ARG* 4.4 8.3 - - + -
204B TYR 4.8 1.7 - - - +
206B ALA* 3.8 13.4 + - + +
208B GLU* 3.3 19.1 - - - +
209B ILE* 3.8 27.6 - - + -
215B TYR* 3.6 33.0 - - + -
216B ASN 3.2 19.5 - - - +
217B LYS 3.0 0.8 - - - -
218B ALA* 1.3 78.8 - - - +
220B ASP* 1.3 59.6 + - - +
222B TRP* 3.5 3.1 + - - +
223B ALA* 3.0 27.0 + - - +
280B ARG* 4.2 0.2 - - - +
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Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PHE* 3.2 35.2 - - + -
158B HIS* 2.7 29.8 + - + +
163B ILE* 3.2 11.4 - - - +
164B TYR* 3.0 24.1 + - - +
165B ARG* 3.0 28.6 + - - -
167B LEU* 5.6 0.7 + - - +
217B LYS 3.0 10.6 + - - +
219B VAL* 1.3 78.2 - - - +
221B TRP* 1.3 58.8 - - - +
223B ALA* 3.3 7.4 + - - +
224B LEU 2.9 22.5 + - - -
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Residues in contact with TRP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B VAL* 3.6 15.9 - - + -
154B PHE* 3.5 34.1 - + + -
155B GLU* 4.4 4.0 - - - -
158B HIS* 3.4 22.8 + + - -
217B LYS* 3.8 15.1 - - + +
218B ALA* 3.3 13.5 + - - +
220B ASP* 1.3 74.7 - - - +
222B TRP* 1.3 66.1 + - - +
224B LEU* 3.2 25.9 + - + +
225B GLY 3.1 16.8 + - - -
272B LEU* 3.7 13.2 - - + +
280B ARG* 4.6 2.5 - - - -
281B PHE 3.5 19.1 - - - +
282B GLY* 3.5 30.8 + - - -
283B ASN 4.6 0.2 - - - -
288B VAL* 3.6 34.3 - - + -
291B ILE* 3.5 22.7 - - + -
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Residues in contact with TRP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU 5.2 0.4 + - - -
204B TYR 3.8 8.2 - - - -
205B LEU 3.6 11.3 + - - -
206B ALA* 3.7 16.6 - - + -
207B PRO* 3.8 26.5 - - + -
218B ALA 3.2 6.3 + - - -
219B VAL 3.6 7.6 - - - +
220B ASP 3.3 0.2 - - - -
221B TRP* 1.3 76.8 - - - +
223B ALA* 1.3 63.4 + - - +
225B GLY 3.1 10.4 + - - -
226B VAL* 3.1 26.7 + - + +
238B PHE* 3.5 32.6 - + - -
250B ILE* 3.7 23.8 - - + +
253B GLY* 4.6 0.7 - - - -
272B LEU 3.6 9.9 - - - -
273B LEU* 3.3 47.1 - - + +
274B GLN 3.7 22.2 - - - -
275B VAL* 3.8 6.7 - - + -
280B ARG* 3.8 20.0 - - - +
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Residues in contact with ALA 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ARG* 6.4 1.3 - - - -
167B LEU* 3.6 30.2 - - + +
204B TYR* 3.7 26.4 - - + +
219B VAL 3.0 15.4 + - - +
220B ASP* 3.4 13.2 - - - +
222B TRP* 1.3 73.9 - - - +
224B LEU* 1.3 61.0 + - - +
226B VAL* 3.2 7.6 + - - +
227B LEU* 2.9 24.8 + - - +
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Residues in contact with LEU 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ALA* 4.2 8.1 - - + +
150B ILE* 3.9 29.2 - - + -
151B VAL* 3.6 24.9 - - + -
154B PHE* 4.5 2.5 - - + -
167B LEU* 3.7 10.9 - - + +
220B ASP 2.9 14.1 + - - +
221B TRP* 3.2 31.6 + - + +
223B ALA* 1.3 76.5 - - - +
225B GLY* 1.3 61.4 + - - +
227B LEU* 3.2 5.3 + - + +
228B ILE* 3.0 47.2 + - + +
272B LEU* 4.1 17.3 - - + -
291B ILE* 4.6 4.9 - - + -
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Residues in contact with GLY 225 (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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221B TRP 3.1 7.1 + - - -
222B TRP 3.1 8.8 + - - -
224B LEU* 1.3 75.3 - - - +
226B VAL* 1.3 62.3 + - - +
229B TYR* 3.0 22.3 + - - +
269B LEU* 3.4 14.1 - - - +
272B LEU* 3.7 27.7 - - - +
273B LEU* 3.8 12.1 - - - +
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Residues in contact with VAL 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B GLU 3.4 26.5 - - - +
204B TYR* 3.5 27.8 - - + +
222B TRP* 3.1 39.0 + - + +
223B ALA* 3.2 8.3 + - - +
225B GLY* 1.3 74.5 - - - +
227B LEU* 1.3 55.6 + - - +
229B TYR* 3.3 3.6 + - - +
230B GLU* 2.9 28.2 + - - +
236B PRO* 4.3 3.6 - - + -
237B PRO* 3.7 26.9 - - + +
238B PHE* 4.9 1.8 - - + -
273B LEU* 3.6 6.7 - - + +
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Residues in contact with LEU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B MET* 4.4 0.9 - - - -
147B ALA* 5.6 0.2 - - - -
150B ILE* 3.9 20.9 - - + -
167B LEU* 3.9 14.4 - - + -
168B LYS* 4.3 2.9 - - - -
169B PRO* 3.9 38.8 - - + -
172B LEU* 3.7 28.0 - - + -
180B ILE* 5.8 0.4 - - + -
204B TYR* 3.5 11.8 - - + -
223B ALA 2.9 13.3 + - - +
224B LEU* 3.2 11.4 + - + +
226B VAL* 1.3 76.8 - - - +
228B ILE* 1.3 57.1 + - - +
230B GLU* 3.2 1.7 + - - +
231B MET* 2.8 60.6 + - + +
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Residues in contact with ILE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 4.9 2.0 - - + +
147B ALA* 3.6 31.4 - - + -
224B LEU* 3.0 41.9 + - + +
227B LEU* 1.3 70.6 - - + +
229B TYR* 1.3 68.2 + - - +
231B MET* 3.4 12.3 + - + +
232B ALA* 3.0 23.6 + - - +
265B LEU* 3.6 29.8 - - + -
268B LEU* 4.2 13.0 - - + -
269B LEU* 3.8 9.4 - - + -
272B LEU* 4.2 14.1 - - + -
296B TRP* 3.9 16.2 - - + -
297B PHE* 4.6 1.8 - - + -
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Residues in contact with TYR 229 (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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225B GLY 3.0 18.3 + - - +
226B VAL 3.6 4.3 - - - +
228B ILE* 1.3 78.5 - - - +
230B GLU* 1.3 57.0 + - - +
232B ALA 3.7 0.2 - - - -
233B ALA* 2.8 39.0 + - + +
235B TYR* 3.2 32.2 + + - -
236B PRO 3.8 2.7 - - - -
237B PRO* 3.5 38.3 + - + +
255B VAL* 3.8 8.5 - - + -
256B ARG 2.6 30.1 + - - -
257B PHE* 3.6 31.6 - + - -
258B PRO* 3.5 13.9 - - + +
261B PHE* 3.8 10.2 - + - -
269B LEU* 4.0 12.7 - - + +
273B LEU* 4.9 2.5 - - + -
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Residues in contact with GLU 230 (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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129B PHE* 4.9 1.2 - - - -
132B LEU* 3.8 11.7 - - + +
133B ARG* 3.2 20.6 + - - -
169B PRO* 3.7 14.1 - - + +
204B TYR* 2.3 35.2 + - - +
226B VAL 2.9 17.3 + - - +
227B LEU 3.2 2.0 + - - +
229B TYR* 1.3 76.1 - - - +
231B MET* 1.3 57.1 + - - +
234B GLY* 2.7 33.3 + - - -
235B TYR* 3.3 26.7 - - - +
236B PRO* 3.9 10.6 - - + +
351B A02 2.7 35.6 + - - -
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Residues in contact with MET 231 (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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128B MET* 3.6 40.6 - - - +
132B LEU* 3.7 15.0 - - + +
137B ARG* 3.7 1.7 - - - -
138B PHE* 2.8 37.9 + - + +
143B ALA* 3.3 33.9 - - + +
146B TYR* 3.8 15.7 - - - -
147B ALA 4.1 9.6 - - - +
227B LEU* 2.8 34.6 + - + +
228B ILE* 3.7 26.9 - - + +
230B GLU* 1.3 77.9 - - + +
232B ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 232 (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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137B ARG* 3.2 22.6 + - - +
138B PHE 3.7 13.6 - - - +
140B GLU* 5.0 6.5 - - + -
143B ALA* 4.6 10.8 - - + -
228B ILE 3.0 17.3 + - - +
231B MET* 1.3 77.7 - - - +
233B ALA* 1.3 58.1 + - - +
260B HIS* 3.2 10.2 - - + -
261B PHE* 3.6 20.4 - - + -
265B LEU* 3.8 17.7 - - + -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLY 5.3 0.2 - - - -
137B ARG* 3.6 16.1 - - - +
229B TYR* 2.8 42.1 + - + +
232B ALA* 1.3 80.0 - - - +
234B GLY* 1.3 54.5 + - - +
235B TYR* 3.4 27.6 - - + +
258B PRO* 3.9 20.6 - - + -
260B HIS* 4.6 1.5 + - - -
261B PHE* 3.9 4.9 - - + -
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Residues in contact with GLY 234 (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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132B LEU* 4.4 4.7 - - - +
133B ARG* 2.9 25.4 + - - -
136B GLY 3.1 27.3 - - - +
137B ARG* 3.7 5.0 - - - +
230B GLU* 2.7 19.4 + - - -
233B ALA* 1.3 73.2 - - - +
235B TYR* 1.3 63.1 + - - +
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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
------------------------------------------------------------
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