Contacts of the helix formed by residues 215 - 229 (chain A) in PDB entry 3A3K
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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190A GLU* 2.6 35.1 + - - -
214A SER* 1.3 81.9 + - - +
216A PRO* 1.3 76.4 - - - +
217A ASP* 3.7 6.9 + - - +
218A ALA 3.0 21.1 + - - -
219A PHE* 3.1 2.9 + - - +
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Residues in contact with PRO 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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214A SER 3.8 1.5 - - - +
215A SER* 1.3 86.7 - - - +
217A ASP* 1.3 56.7 + - - +
219A PHE* 3.3 5.0 + - - +
220A ARG* 3.1 27.2 + - - +
240A HIS* 4.0 14.4 - - + -
242A ASP* 5.9 0.2 - - - +
246A GLN* 3.8 21.1 - - + +
247A SER* 3.7 39.9 - - - +
262A ARG* 3.9 15.6 + - - +
274A PHE* 5.6 0.7 - - - -
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Residues in contact with ASP 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* 3.2 7.0 + - - +
216A PRO* 1.3 77.4 - - - +
218A ALA* 1.3 59.6 + - - +
220A ARG* 3.7 4.3 - - - +
221A ASN* 3.0 34.3 + - - +
262A ARG* 2.7 42.1 + - - +
194B ASP* 5.0 14.6 - - - +
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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
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188A PHE* 4.5 10.3 - - + -
190A GLU* 3.7 22.7 - - + +
196A TYR* 4.6 9.5 + - - +
214A SER* 3.5 17.3 - - - +
215A SER* 3.0 16.0 + - - +
217A ASP* 1.3 77.7 - - - +
219A PHE* 1.3 63.0 + - - +
221A ASN* 3.5 7.7 + - - +
222A LEU* 3.0 30.4 + - + +
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Residues in contact with PHE 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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212A ILE* 3.8 37.7 - - + -
214A SER* 3.4 6.4 + - - +
215A SER 3.1 11.2 + - - +
216A PRO 3.6 8.5 - - - +
217A ASP 3.2 0.2 - - - -
218A ALA* 1.3 75.7 - - - +
220A ARG* 1.3 64.5 + - - +
222A LEU* 3.2 6.8 + - - +
223A MET* 2.9 49.3 + - + +
238A PHE* 4.0 8.5 - - + -
239A PHE 4.2 2.0 - - - -
240A HIS* 3.5 54.3 - + + -
274A PHE* 3.8 22.4 - + - -
277A ALA* 3.7 27.6 - - + -
278A LYS 4.7 0.4 - - - -
279A ILE* 5.5 2.9 - - + -
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Residues in contact with ARG 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 PRO 3.1 16.5 + - - +
217A ASP* 3.7 7.4 - - - +
219A PHE* 1.3 75.1 - - - +
221A ASN* 1.3 69.8 + - - +
223A MET* 3.2 3.8 + - - +
224A LEU* 2.9 44.1 + - + +
259A PRO 4.6 0.7 - - - +
260A TRP* 2.8 23.1 + - - +
262A ARG* 3.4 40.2 - - - +
264A ASP* 2.9 41.6 + - - -
266A GLN* 3.9 7.1 - - - +
267A ASP* 3.0 19.2 + - - -
270A ALA* 3.8 14.7 - - + +
274A PHE* 4.0 24.9 - - + -
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Residues in contact with ASN 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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196A TYR* 4.5 15.8 + - + -
217A ASP* 3.0 20.9 + - - +
218A ALA* 3.7 7.0 - - - +
220A ARG* 1.3 83.6 + - - +
222A LEU* 1.3 61.8 + - - +
224A LEU* 3.2 14.2 + - - +
225A LEU* 3.0 28.6 + - + +
266A GLN* 5.4 1.6 + - - -
193B PRO* 3.8 14.5 + - - +
194B ASP* 2.7 48.1 + - - +
197B PRO* 4.0 12.0 - - + +
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Residues in contact with LEU 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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153A LEU* 5.1 6.7 - - + -
188A PHE* 4.1 26.2 - - + -
196A TYR* 4.1 15.7 - - + -
199A LEU* 3.8 26.0 - - + -
200A LEU* 3.9 25.4 - - + +
203A VAL* 6.2 1.8 - - + -
212A ILE* 4.2 27.6 - - + -
218A ALA* 3.0 23.4 + - + +
219A PHE* 3.2 4.5 + - - +
221A ASN* 1.3 74.3 - - - +
223A MET* 1.3 68.3 + - + +
225A LEU* 3.3 5.5 + - - +
226A ALA* 2.8 29.3 + - - +
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Residues in contact with MET 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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212A ILE* 3.7 18.4 - - + -
219A PHE* 2.9 40.2 + - + +
220A ARG 3.2 7.6 + - - +
222A LEU* 1.3 81.6 - - + +
224A LEU* 1.3 65.5 + - - +
226A ALA* 3.2 3.9 + - - +
227A LEU 2.9 19.8 + - - -
238A PHE* 3.4 59.0 - - + -
273A ALA* 3.5 28.1 - - + +
274A PHE* 3.9 16.6 - - + -
277A ALA* 4.1 8.1 - - + -
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Residues in contact with LEU 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 ARG* 2.9 41.8 + - + +
221A ASN* 3.5 11.9 - - - +
223A MET* 1.3 75.9 - - - +
225A LEU* 1.3 61.8 + - - +
227A LEU* 3.4 5.4 + - + +
228A ASN* 3.1 23.8 + - - +
266A GLN* 3.7 36.1 - - - +
269A SER* 3.8 18.2 - - - +
270A ALA* 3.6 35.0 - - + +
273A ALA* 4.4 3.1 - - + -
274A PHE* 6.3 0.2 - - + -
197B PRO* 3.7 18.5 - - + +
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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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196A TYR* 3.7 36.6 - - + -
200A LEU* 3.9 26.3 - - + +
221A ASN* 3.0 17.0 + - + +
222A LEU* 3.6 7.2 - - - +
224A LEU* 1.3 75.4 - - - +
226A ALA* 1.3 65.0 + - - +
228A ASN* 3.3 5.4 + - + +
229A ALA* 3.0 24.4 + - - +
193B PRO 5.8 0.4 - - - +
196B TYR* 4.1 9.6 - - + +
197B PRO* 3.8 35.2 - - + -
200B LEU* 4.5 16.4 - - + -
225B LEU* 4.6 16.4 - - + -
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Residues in contact with ALA 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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200A LEU* 4.0 12.9 - - + +
203A VAL* 5.7 0.4 - - + -
222A LEU 2.8 20.2 + - - +
223A MET* 3.2 9.2 + - + +
225A LEU* 1.3 72.7 - - - +
227A LEU* 1.3 55.7 + - - +
229A ALA 3.3 5.5 + - - -
231A LEU* 2.8 46.5 + - + +
238A PHE* 3.9 33.7 - - + -
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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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223A MET 2.9 13.4 + - - +
224A LEU* 3.5 9.9 - - + +
226A ALA* 1.3 74.3 - - - +
228A ASN* 1.3 61.4 + - - +
230A GLY* 2.9 20.6 + - - -
231A LEU 4.2 6.9 + - - +
232A THR* 4.8 15.4 - - + +
269A SER* 3.5 37.5 - - - +
272A GLN* 4.1 41.1 - - + +
273A ALA* 4.0 11.4 - - + +
204B ARG* 5.9 0.9 + - - -
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Residues in contact with ASN 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 LEU 3.1 16.7 + - - +
225A LEU* 3.3 8.0 + - + +
227A LEU* 1.3 79.0 - - - +
229A ALA* 1.3 56.7 + - - +
230A GLY 3.2 3.2 + - - -
197B PRO* 5.3 3.6 - - + +
200B LEU* 3.2 38.2 + - + +
201B ARG* 3.4 29.2 - - + +
204B ARG* 3.2 47.9 + - - +
229B ALA* 4.1 9.5 - - - +
231B LEU* 5.3 0.2 - - - +
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Residues in contact with ALA 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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200A LEU* 4.5 2.7 - - + -
204A ARG* 5.8 0.5 + - - -
225A LEU 3.0 16.9 + - - +
226A ALA 3.7 5.4 - - - +
227A LEU 3.1 0.6 - - - -
228A ASN* 1.3 75.3 + - - +
230A GLY* 1.3 62.1 + - - +
231A LEU* 3.5 22.5 + - + +
204B ARG* 6.1 0.4 - - - -
228B ASN* 4.1 15.2 - - - +
229B ALA* 3.7 37.3 - - + +
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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