Contacts of the helix formed by residues 215 - 232 (chain A) in PDB entry 2G19
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 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A ASP* 4.2 6.0 + - - -
213A PHE 3.6 1.4 - - - -
214A LEU* 1.3 79.5 - - - +
216A LYS* 1.3 66.9 + - - -
217A GLU 3.4 2.5 - - - -
218A THR 3.6 0.4 + - - -
219A GLY* 3.0 22.9 + - - -
361A ASP* 2.9 18.3 + - - +
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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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212A ASP* 3.9 20.1 + - - -
215A GLY* 1.3 72.5 - - - -
217A GLU* 1.3 59.3 + - + +
220A GLN* 2.8 34.2 + - - +
332A LYS* 4.2 16.3 - - - +
360A PHE* 3.3 41.2 + - + -
361A ASP* 4.8 2.5 - - - +
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Residues in contact with GLU 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 GLY 3.4 0.6 - - - -
216A LYS* 1.3 80.7 - - + +
218A THR* 1.3 64.8 + - - +
220A GLN* 3.7 7.4 - - - +
221A GLN* 3.1 40.3 + - - +
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Residues in contact with THR 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 LEU* 3.8 44.8 + - + -
215A GLY 3.6 1.8 + - - -
217A GLU* 1.3 77.5 - - - +
219A GLY* 1.3 66.4 + - - +
221A GLN* 3.1 14.1 + - - +
222A ILE* 2.9 22.6 + - + +
268A THR* 3.8 20.6 - - + -
271A LEU* 4.5 16.2 - - + +
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Residues in contact with GLY 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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214A LEU* 4.7 0.4 - - - +
215A GLY 3.0 17.4 + - - -
218A THR* 1.3 78.0 - - - +
220A GLN* 1.3 57.9 + - - +
222A ILE* 3.3 6.3 + - - +
223A GLY* 3.0 24.3 + - - -
328A TYR* 3.5 25.2 + - - -
330A LEU* 4.8 3.3 - - - +
360A PHE* 3.5 19.6 - - - -
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Residues in contact with GLN 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 2.8 19.2 + - - +
217A GLU* 3.7 8.5 - - - +
219A GLY* 1.3 75.5 - - - +
221A GLN* 1.3 58.3 + - + +
223A GLY* 3.2 2.3 + - - +
224A ASP* 2.7 45.8 + - - +
227A ARG* 3.4 17.3 + - - +
332A LYS* 5.5 9.9 - - + -
360A PHE* 3.6 11.5 - - + -
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Residues in contact with GLN 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 GLU* 3.1 31.6 + - - +
218A THR* 3.1 16.7 + - - +
220A GLN* 1.3 73.8 - - + +
222A ILE* 1.3 65.9 + - - +
224A ASP* 3.2 11.2 + - - +
225A GLU* 3.0 29.6 + - - +
268A THR* 3.8 29.2 + - + +
271A LEU* 6.0 1.4 - - - +
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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 LEU* 3.4 33.0 - - + -
218A THR* 2.9 18.1 + - + +
219A GLY* 3.5 7.0 - - - +
221A GLN* 1.3 74.0 - - - +
223A GLY* 1.3 67.1 + - - +
225A GLU* 3.1 7.7 + - - +
226A VAL* 2.9 24.4 + - + +
268A THR* 3.6 26.5 - - + +
269A ILE* 4.3 6.1 - - + -
272A LEU* 3.9 14.1 - - + -
328A TYR* 3.8 23.1 - - + +
330A LEU* 4.4 5.8 - - + -
386A ILE* 3.8 28.5 - - + -
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Residues in contact with GLY 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 GLY 3.0 14.3 + - - -
220A GLN* 3.2 4.7 + - - -
222A ILE* 1.3 77.5 - - - +
224A ASP* 1.3 56.0 + - - +
226A VAL* 3.3 1.2 + - - +
227A ARG* 2.9 47.0 + - - +
330A LEU* 3.5 23.7 - - - +
360A PHE* 6.2 0.7 - - - -
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Residues in contact with ASP 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 GLN* 2.7 35.8 + - - +
221A GLN* 3.6 12.1 - - - +
222A ILE 3.2 0.2 - - - -
223A GLY* 1.3 76.7 - - - +
225A GLU* 1.3 58.1 + - + +
227A ARG* 2.5 42.6 + - - +
228A ALA* 2.9 29.7 + - - +
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Residues in contact with GLU 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 GLN 3.0 12.7 + - - +
222A ILE* 3.1 6.9 + - - +
224A ASP* 1.3 75.0 - - + +
226A VAL* 1.3 65.3 + - - +
228A ALA* 3.3 6.6 + - - +
229A LEU* 3.1 28.1 + - - +
265A GLY* 3.3 29.3 - - - +
266A CYS* 3.3 6.6 - - - -
267A GLU* 3.6 5.4 + - - +
268A THR* 2.8 47.2 + - - +
269A ILE* 3.0 22.0 + - + +
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Residues in contact with VAL 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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222A ILE 2.9 20.0 + - - +
223A GLY 3.9 3.1 - - - +
225A GLU* 1.3 72.8 - - - +
227A ARG* 1.3 67.3 + - - +
229A LEU* 3.1 10.6 + - - +
230A HIS* 3.0 19.6 + - - +
235A PHE* 3.9 2.3 - - + -
269A ILE* 4.0 11.4 - - + -
300A VAL* 3.8 22.0 - - + -
330A LEU* 3.8 15.5 - - + -
384A TYR* 3.4 38.4 - - + -
386A ILE* 4.0 24.0 - - + -
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Residues in contact with ARG 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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220A GLN* 3.4 17.8 + - - -
223A GLY* 2.9 25.0 + - - +
224A ASP* 2.5 50.4 + - - +
226A VAL* 1.3 76.2 - - - +
228A ALA* 1.3 57.6 + - - +
230A HIS* 3.1 2.6 + - - +
231A ASP* 2.9 40.7 + - - +
384A TYR* 3.9 32.0 - - + +
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Residues in contact with ALA 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 ASP 2.9 17.6 + - - +
225A GLU* 3.6 8.1 - - - +
226A VAL 3.2 0.2 - - - -
227A ARG* 1.3 72.9 - - - +
229A LEU* 1.3 58.7 + - - +
231A ASP* 3.8 6.2 - - - +
232A THR* 2.7 42.9 + - + +
265A GLY 5.8 1.6 - - - +
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Residues in contact with LEU 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 GLU 3.1 19.8 + - - +
226A VAL* 3.1 12.5 + - - +
228A ALA* 1.3 78.6 - - - +
230A HIS* 1.3 60.2 + - - +
232A THR* 3.4 7.3 + - - +
233A GLY 3.4 0.2 + - - -
234A LYS* 2.9 53.3 + - + +
235A PHE* 4.0 10.7 - - + -
257A THR* 4.4 8.7 - - + -
259A ILE* 3.9 29.8 - - + -
265A GLY 5.6 0.4 - - - +
266A CYS* 4.0 20.0 - - - -
269A ILE* 4.0 20.0 - - + -
300A VAL* 4.8 4.5 - - + -
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Residues in contact with HIS 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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226A VAL 3.0 10.1 + - - +
227A ARG* 3.1 8.2 + - - +
229A LEU* 1.3 77.0 - - - +
231A ASP* 1.3 68.6 + - - +
233A GLY* 3.1 14.4 + - - -
235A PHE* 3.5 27.5 + + + -
255A LYS* 3.5 26.7 + - + +
302A CYS* 3.8 21.3 - - - -
304A PRO* 5.9 2.0 - - + -
382A THR* 4.8 5.2 - - + -
384A TYR* 2.9 29.2 + - - +
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Residues in contact with ASP 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 ARG* 2.9 26.8 + - - +
228A ALA* 4.0 7.1 - - - +
230A HIS* 1.3 82.3 + - - +
232A THR* 1.3 63.1 + - + +
233A GLY 3.3 1.9 + - - -
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Residues in contact with THR 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 ALA* 2.7 27.7 + - + +
229A LEU* 3.4 7.8 + - - +
230A HIS 3.2 0.6 - - - -
231A ASP* 1.3 80.2 - - + +
233A GLY* 1.3 62.2 + - - +
234A LYS* 3.5 23.7 + - - +
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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