Contacts of the helix formed by residues 216 - 233 (chain A) in PDB entry 5AJQ
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 TYR 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A HIS* 3.5 52.8 - + + +
152A ARG* 6.4 1.3 - - - -
154A ILE* 3.6 20.4 - - + -
213A PRO 3.4 25.5 + - - -
214A TYR* 4.5 0.7 - - - -
215A ASP* 1.3 86.5 + - - +
217A LYS* 1.3 98.5 + - + +
218A ALA 3.1 0.2 - - - -
219A ASP* 3.1 23.1 + - - +
220A ILE* 4.0 1.6 + - + -
284A SER* 4.3 20.7 - - - -
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Residues in contact with LYS 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A PRO 5.7 0.2 - - - -
214A TYR* 3.3 24.8 - - + +
215A ASP 3.1 0.8 - - - -
216A TYR* 1.3 110.6 - - + +
218A ALA* 1.3 64.4 + - - +
219A ASP 3.2 0.2 - - - -
220A ILE* 3.1 15.0 + - + -
221A TRP 3.4 0.3 + - - -
279A PRO* 3.2 24.3 + - + +
280A GLU* 3.1 21.8 + - - +
282A ARG* 2.6 63.6 + - - +
283A PRO 4.0 11.0 - - - +
284A SER* 4.4 8.3 - - - +
287A GLN* 5.6 1.0 + - - -
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A ILE* 5.5 4.3 - - + -
200A ALA* 4.0 16.5 + - + +
202A GLU* 3.9 7.2 + - - +
203A VAL* 4.3 15.7 - - + -
214A TYR 4.2 0.2 + - - -
215A ASP 3.1 16.0 + - - +
216A TYR 3.1 1.2 - - - -
217A LYS* 1.3 77.4 - - - +
219A ASP* 1.3 62.3 + - - +
220A ILE 3.4 0.2 + - - -
221A TRP* 3.4 5.0 + - - +
222A SER* 3.3 22.8 + - - -
282A ARG* 3.8 9.8 - - - +
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A LEU* 3.7 7.1 - - + +
149A HIS* 2.8 28.8 + - + +
154A ILE* 3.7 10.4 - - - +
155A HIS* 2.9 30.6 + - - +
156A ARG* 3.0 26.3 + - - -
158A LEU* 3.3 20.6 - - + +
216A TYR 3.1 11.1 + - - +
218A ALA* 1.3 78.7 - - - +
220A ILE* 1.3 57.9 + - - +
222A SER* 3.3 5.3 + - - -
223A LEU* 2.8 25.3 + - - +
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 4.9 2.5 - - + -
145A LEU* 4.6 8.5 - - + -
149A HIS* 4.2 12.8 - - + +
216A TYR* 4.5 3.1 - - + +
217A LYS* 3.1 20.8 + - + +
219A ASP* 1.3 75.8 - - - +
221A TRP* 1.3 65.5 + - - +
223A LEU* 3.3 8.0 + - + +
224A GLY* 3.1 17.3 + - - -
274A ALA* 4.2 11.4 - - + +
282A ARG* 3.9 13.7 - - + -
283A PRO 3.4 24.0 - - - +
284A SER* 4.0 2.5 - - - -
285A ALA* 3.5 39.0 - - + +
288A LEU* 3.6 22.7 - - + -
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Residues in contact with TRP 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A TYR 5.4 0.6 + - - -
198A TRP 3.6 11.9 - - - -
199A MET 3.4 11.1 + - - -
200A ALA* 3.5 25.8 - - + -
201A PRO* 3.5 23.8 - - + -
217A LYS 3.4 3.2 + - - -
218A ALA 3.7 8.3 - - - +
219A ASP 3.4 0.2 - - - -
220A ILE* 1.3 78.7 - - - +
222A SER* 1.3 62.6 + - - +
224A GLY 3.0 11.1 + - - -
225A ILE* 3.1 25.8 + - + +
249A ILE* 4.9 11.5 - - + +
252A SER 5.9 0.4 - - - -
254A PRO* 4.1 5.6 - - + -
255A PRO* 4.0 28.9 - - + -
274A ALA 4.2 4.3 - - - -
275A LEU* 3.3 44.4 - - + +
276A ASP 3.6 23.6 - - - -
277A LYS* 3.9 17.7 - - + -
282A ARG* 3.7 13.2 - - - +
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Residues in contact with SER 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A ARG 5.7 2.5 + - - -
158A LEU* 3.9 27.4 + - - -
198A TRP* 2.7 29.5 + - - +
199A MET* 4.4 3.6 - - - -
200A ALA 4.6 0.2 + - - -
218A ALA 3.3 12.8 + - - -
219A ASP* 3.5 11.3 + - - -
220A ILE 3.3 0.2 - - - -
221A TRP* 1.3 74.4 - - - +
223A LEU* 1.3 56.3 + - - +
225A ILE* 3.3 3.1 + - - +
226A THR* 2.8 38.4 + - - -
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A CYS* 4.6 3.4 - - - -
141A MET* 3.6 41.5 - - + -
142A LEU* 3.2 39.0 - - + +
145A LEU* 4.4 13.9 - - + -
158A LEU* 4.1 5.6 - - + +
219A ASP 2.8 13.9 + - - +
220A ILE* 3.4 11.9 - - + +
221A TRP 3.2 0.4 - - - -
222A SER* 1.3 74.8 - - - +
224A GLY* 1.3 59.5 + - - +
226A THR* 3.2 7.7 + - - -
227A LEU* 2.9 48.4 + - + +
270A PHE* 4.5 12.3 - - + -
274A ALA* 6.0 0.2 - - + -
288A LEU* 4.7 6.7 - - + -
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Residues in contact with GLY 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ILE 3.1 5.9 + - - -
221A TRP 3.0 8.7 + - - -
223A LEU* 1.3 80.3 - - - +
225A ILE* 1.3 59.6 + - - +
227A LEU* 3.2 13.3 + - - -
228A ILE* 3.2 11.4 + - - +
271A LEU* 3.3 24.9 - - - +
274A ALA* 4.7 7.2 - - - +
275A LEU* 3.7 18.2 - - - -
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Residues in contact with ILE 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A TYR 3.7 16.6 - - - +
198A TRP* 3.4 28.7 - - + +
221A TRP* 3.1 41.8 + - + +
222A SER 3.8 5.6 - - - +
223A LEU 3.3 0.2 - - - -
224A GLY* 1.3 72.8 - - - +
226A THR* 1.3 60.8 + - - +
228A ILE* 3.1 6.4 + - - +
229A GLU* 2.8 26.9 + - - +
235A PRO* 4.1 2.9 - - + -
236A PRO* 3.8 21.7 - - + +
255A PRO* 3.6 31.6 - - + -
275A LEU* 3.9 8.1 - - + -
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Residues in contact with THR 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A MET* 4.1 20.0 - - + -
158A LEU* 3.6 3.3 + - - +
159A LYS* 3.3 25.9 + - - +
160A ALA* 3.9 24.0 - - - +
163A VAL* 4.8 1.1 - - + -
198A TRP* 3.7 1.5 - - - -
222A SER 2.8 17.6 + - - -
223A LEU* 3.4 12.1 - - - -
225A ILE* 1.3 77.5 - - - +
227A LEU* 1.3 55.7 + - - +
229A GLU* 3.3 9.6 + - - +
230A MET* 2.9 43.1 + - + +
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Residues in contact with LEU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ILE* 3.9 8.9 - - + +
138A CYS* 3.7 28.9 - - + -
141A MET* 5.2 0.2 - - - -
223A LEU* 2.9 30.6 + - + +
224A GLY* 3.2 7.6 + - - +
226A THR* 1.3 76.4 - - - +
228A ILE* 1.3 56.3 + - - +
230A MET* 3.3 27.3 + - + +
231A ALA* 3.0 27.7 + - - +
267A PHE* 4.0 25.1 - - + -
270A PHE* 3.4 39.0 - - + -
271A LEU* 4.0 9.9 - - + -
293A PHE* 4.6 1.6 - - + -
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLY 3.2 9.0 + - - +
225A ILE* 3.1 9.9 + - - +
227A LEU* 1.3 75.5 - - - +
229A GLU* 1.3 58.9 + - - +
231A ALA* 3.1 7.0 + - - +
232A GLN* 2.9 56.1 + - - +
234A GLU 4.7 1.3 - - - +
236A PRO* 4.0 20.6 - - + -
255A PRO* 3.9 29.4 - - + +
256A THR 4.5 7.0 - - - +
257A LEU* 4.5 4.7 - - + -
271A LEU* 3.7 21.3 - - + -
275A LEU* 3.8 28.0 - - + -
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASP* 4.2 11.4 - - - +
122A MET* 3.6 2.6 - - + +
159A LYS 3.8 0.2 - - - -
160A ALA* 2.9 44.9 + - + +
161A GLY 4.6 0.9 + - - -
198A TRP* 2.9 35.4 + - - +
225A ILE 2.8 13.4 + - - +
226A THR* 3.4 8.1 - - - +
228A ILE* 1.3 77.7 - - - +
230A MET* 1.3 56.5 + - - +
233A ILE* 2.8 48.9 + - - +
234A GLU 3.8 10.5 - - - -
235A PRO* 4.0 16.7 - - + +
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Residues in contact with MET 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A VAL* 4.0 30.7 - - + -
122A MET* 3.5 7.6 - - - +
128A GLY* 3.4 5.0 - - - -
129A LEU* 2.9 34.6 - - + -
134A ILE* 3.9 19.7 - - + -
137A VAL* 3.7 37.9 - - + -
141A MET* 4.8 0.2 - - - -
160A ALA* 4.4 10.1 - - + -
163A VAL* 5.6 1.1 - - - -
226A THR* 2.9 29.7 + - + +
227A LEU* 3.4 36.8 - - + +
229A GLU* 1.3 74.6 - - - +
231A ALA* 1.3 61.2 - - - +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLY* 4.2 9.6 - - - -
129A LEU 4.4 1.1 - - - +
134A ILE* 3.6 13.4 - - + +
227A LEU 3.0 16.6 + - - +
228A ILE 3.5 4.9 - - - +
230A MET* 1.3 78.8 + - - +
232A GLN* 1.3 60.3 + - + +
233A ILE 3.7 0.2 - - - -
257A LEU* 3.8 20.0 - - + -
262A LYS* 4.9 5.7 + - - -
263A TRP* 3.6 37.7 - - + -
267A PHE* 4.2 2.2 - - + -
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Residues in contact with GLN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ILE* 2.9 32.8 + - - +
231A ALA* 1.3 84.5 - - + +
233A ILE* 1.3 67.7 + - - +
234A GLU* 3.0 20.8 + - - +
235A PRO 6.0 0.2 - - - -
236A PRO* 5.9 2.4 - - - +
256A THR 5.2 1.8 + - - -
257A LEU* 3.5 13.4 - - + +
258A LEU* 2.7 50.0 + - + +
259A THR 4.6 0.7 + - - -
263A TRP* 5.0 4.0 + - + +
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Residues in contact with ILE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASP* 5.7 1.4 - - - +
122A MET* 3.7 27.8 - - + +
123A LEU* 5.5 6.5 - - + +
126A ASP* 4.3 13.2 - - - +
127A ARG* 3.8 31.4 - - - +
128A GLY* 3.7 17.9 - - - +
229A GLU* 2.8 27.9 + - - +
231A ALA 3.7 1.0 - - - -
232A GLN* 1.3 79.3 - - - +
234A GLU* 1.3 72.2 - - + +
235A PRO* 4.7 0.2 - - - +
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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