Contacts of the helix formed by residues 215 - 232 (chain A) in PDB entry 4BJI
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 SER 215 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A GLU 4.0 0.4 + - - -
214A PRO* 1.3 76.9 - - - +
216A LYS* 1.3 60.3 + - - +
217A THR* 3.5 11.7 + - - -
218A ILE* 3.1 30.6 + - - +
219A GLN* 2.9 27.0 + - - +
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Residues in contact with LYS 216 (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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215A SER* 1.3 73.4 - - - +
217A THR* 1.3 63.6 + - - +
219A GLN* 3.2 9.4 + - - +
220A GLU* 3.1 23.0 + - - +
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Residues in contact with THR 217 (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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215A SER* 3.1 10.2 + - - -
216A LYS* 1.3 79.9 - - - +
218A ILE* 1.3 61.8 + - + +
220A GLU* 3.6 20.2 + - - +
221A VAL* 3.7 10.0 - - - +
248A TYR* 5.6 0.5 - - - -
251A TYR* 3.6 41.7 - - + +
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Residues in contact with ILE 218 (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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214A PRO* 4.0 20.2 - - + -
215A SER* 3.1 18.6 + - - +
217A THR* 1.3 77.6 - - + +
219A GLN* 1.3 66.0 + - - +
220A GLU 3.2 0.7 - - - -
221A VAL* 2.9 13.9 + - + +
222A ILE* 2.9 15.6 + - + +
251A TYR* 3.5 50.3 - - + +
254A PHE* 4.1 18.4 - - + +
255A ALA* 3.9 27.1 - - + +
258A TYR* 4.6 2.2 - - + -
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Residues in contact with GLN 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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213A GLU* 5.4 0.5 - - - +
214A PRO* 3.2 28.2 - - + +
215A SER 2.9 17.3 + - - +
216A LYS* 3.2 10.5 + - - +
218A ILE* 1.3 75.8 - - - +
220A GLU* 1.3 62.9 + - - +
222A ILE* 3.1 22.8 + - - +
223A GLU* 2.8 55.8 + - + +
226A LYS* 4.5 2.8 - - - +
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Residues in contact with GLU 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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216A LYS 3.1 11.9 + - - +
217A THR* 3.6 16.0 - - - +
218A ILE 3.2 0.4 - - - -
219A GLN* 1.3 75.8 - - - +
221A VAL* 1.3 61.7 - - - +
223A GLU* 3.4 8.1 - - - +
224A ALA* 3.2 20.8 - - - -
248A TYR* 2.5 41.2 + - + +
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Residues in contact with VAL 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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217A THR 3.7 15.0 - - - +
218A ILE* 2.9 8.4 + - - +
220A GLU* 1.3 74.0 + - - +
222A ILE* 1.3 65.4 + - - +
224A ALA* 3.1 3.6 + - - +
225A LEU* 2.9 30.5 + - + +
244A LEU* 5.1 1.8 - - + -
248A TYR* 3.7 45.1 - - + -
251A TYR* 4.0 19.7 - - + -
252A LEU* 4.3 18.4 - - + -
255A ALA* 3.6 22.0 - - + -
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Residues in contact with ILE 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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214A PRO* 3.8 23.3 - - + -
218A ILE* 2.9 19.5 + - + +
219A GLN* 3.5 25.1 - - - +
221A VAL* 1.3 75.9 - - - +
223A GLU* 1.3 61.5 + - - +
225A LEU* 3.1 10.7 + - - +
226A LYS* 3.1 42.1 + - - +
255A ALA* 3.9 21.8 - - + +
258A TYR* 3.6 34.3 - - + -
259A LEU* 3.8 16.1 - - + +
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Residues in contact with GLU 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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219A GLN* 2.8 49.7 + - + +
220A GLU* 3.8 7.4 - - - +
222A ILE* 1.3 74.4 - - - +
224A ALA* 1.3 60.8 + - - +
226A LYS* 2.9 35.4 + - - +
227A PRO* 3.1 21.0 - - - +
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Residues in contact with ALA 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 GLU 3.2 11.6 - - - -
221A VAL 3.1 9.0 + - - +
223A GLU* 1.3 76.9 - - - +
225A LEU* 1.3 61.7 + - - +
227A PRO* 3.6 15.0 - - - +
228A LEU* 3.7 15.1 - - - +
244A LEU* 3.8 21.7 - - + +
248A TYR* 3.9 14.8 - - + +
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Residues in contact with LEU 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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221A VAL* 2.9 20.8 + - + +
222A ILE* 3.1 6.9 + - - +
224A ALA* 1.3 76.8 - - - +
226A LYS* 1.3 65.1 + - - +
228A LEU* 3.0 6.3 + - - +
229A PHE* 3.0 28.8 + - + -
240A LEU* 3.9 31.2 - - + -
244A LEU* 4.0 12.3 - - + -
252A LEU* 3.9 27.4 - - + -
255A ALA* 3.8 27.1 - - + -
256A LEU* 4.0 16.6 - - + +
259A LEU* 3.6 17.0 - - + -
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Residues in contact with LYS 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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219A GLN* 4.5 2.8 - - - +
222A ILE* 3.1 28.7 + - - +
223A GLU* 2.9 40.0 + - - +
225A LEU* 1.3 78.0 - - - +
227A PRO* 1.3 72.2 - - + +
229A PHE* 3.2 5.4 + - - +
230A GLU* 3.1 25.5 + - + +
259A LEU* 4.0 23.3 - - + -
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Residues in contact with PRO 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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223A GLU 3.1 16.8 - - - +
224A ALA* 3.6 11.4 - - - +
226A LYS* 1.3 93.4 - - + +
228A LEU* 1.3 58.6 + - + +
230A GLU* 3.2 11.1 + - + +
231A LYS* 3.0 43.7 + - - +
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Residues in contact with LEU 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 ALA 3.7 17.5 - - - +
225A LEU* 3.0 10.3 + - - +
227A PRO* 1.3 80.0 - - + +
229A PHE* 1.3 56.4 + - + +
231A LYS* 3.3 26.0 + - + +
232A ARG 3.0 22.3 + - - -
235A TRP* 3.0 31.2 + - + -
240A LEU* 3.9 22.7 - - + -
243A HIS* 4.1 34.3 - - + +
244A LEU* 3.8 24.5 - - + -
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Residues in contact with PHE 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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225A LEU* 3.0 34.9 + - + -
226A LYS* 3.2 7.8 + - - +
228A LEU* 1.3 74.5 - - + +
230A GLU* 1.3 64.0 + - - +
231A LYS 3.3 0.2 - - - -
232A ARG 3.3 14.4 - - - +
233A PRO* 3.6 24.0 - - - +
235A TRP* 3.8 19.3 - + - -
240A LEU* 4.4 3.6 - - + -
256A LEU* 3.8 26.0 - - + -
259A LEU* 4.2 20.4 - - + -
260A SER* 3.7 20.6 - - - -
272A TYR* 3.6 25.6 - - + -
274A ARG* 3.6 39.3 + - + +
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Residues in contact with GLU 230 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A LYS* 3.1 16.2 + - + +
227A PRO* 3.2 13.0 + - + +
229A PHE* 1.3 78.8 - - - +
231A LYS* 1.3 61.9 + - + +
232A ARG 3.5 0.3 + - - -
233A PRO* 5.3 1.9 - - - +
274A ARG* 3.0 38.5 + - - +
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Residues in contact with LYS 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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227A PRO* 3.0 27.5 + - - +
228A LEU* 3.3 27.8 + - + +
230A GLU* 1.3 79.0 - - + +
232A ARG* 1.3 62.8 + - + +
233A PRO* 4.5 2.4 - - - +
235A TRP* 5.2 2.7 - - + -
288A TYR* 4.5 5.5 + - - -
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Residues in contact with ARG 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 LEU 3.0 6.0 + - - +
229A PHE* 3.3 6.5 - - - +
230A GLU 3.3 0.6 - - - -
231A LYS* 1.3 81.7 - - + +
233A PRO* 1.3 64.4 - - - +
234A VAL 3.3 22.4 + - - +
235A TRP* 2.8 66.7 + - + +
239A ALA* 3.7 9.5 - - - +
243A HIS* 5.1 4.4 - - - -
288A TYR* 3.8 20.0 - - + -
322A GLN* 2.7 28.5 + - - -
324A CYS* 3.5 16.4 - - - -
325A ASP* 2.8 38.4 + - - -
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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