Contacts of the helix formed by residues 222 - 238 (chain A) in PDB entry 5K9S
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 ALA 222 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A GLU* 5.8 1.1 - - - +
220A THR 3.8 2.2 + - - -
221A LEU* 1.3 73.7 - - - +
223A CYS* 1.3 69.4 + - - +
224A GLY 4.4 1.8 - - - +
225A TYR* 3.1 21.8 + - + +
226A LEU* 2.9 21.3 + - - +
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Residues in contact with CYS 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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221A LEU 3.5 4.1 + - - -
222A ALA* 1.3 72.5 - - - +
224A GLY* 1.3 58.1 + - - +
226A LEU* 3.4 7.3 + - - +
227A ARG* 3.0 56.2 + - - +
262A HIS* 6.2 1.1 - - - -
264A ASP* 3.2 32.1 - - - -
267A VAL* 6.1 0.4 - - - -
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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
----------------------------------------------------------
180A GLU* 3.5 10.3 - - - -
222A ALA* 3.2 2.6 - - - +
223A CYS* 1.3 75.7 - - - +
225A TYR* 1.3 65.8 + - - +
227A ARG* 3.4 12.0 + - - +
228A ASN* 3.0 28.9 + - - -
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Residues in contact with TYR 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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176A ALA* 4.3 18.6 - - + -
179A SER* 2.6 29.9 + - - -
180A GLU* 3.4 52.9 + - + +
183A VAL* 4.5 7.0 - - + -
212A LEU* 3.4 23.9 - - + +
221A LEU* 3.9 29.8 - - + -
222A ALA* 3.1 24.2 + - + +
224A GLY* 1.3 76.1 - - - +
226A LEU* 1.3 63.4 + - - +
228A ASN* 3.1 3.7 + - + +
229A LEU* 3.0 35.2 + - + +
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Residues in contact with LEU 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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213A LEU* 3.4 31.4 - - + -
218A LEU* 3.8 25.4 - - + +
219A SER* 5.6 0.2 - - - -
221A LEU* 3.9 16.5 - - + +
222A ALA 2.9 15.9 + - - +
223A CYS* 3.8 7.0 - - - +
225A TYR* 1.3 75.1 - - - +
227A ARG* 1.3 61.1 + - - +
229A LEU* 3.4 6.0 + - - +
230A THR* 2.9 30.1 + - - +
259A LEU* 3.9 15.3 - - + -
262A HIS* 3.7 35.7 - - + +
267A VAL* 4.2 11.2 - - + -
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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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223A CYS* 3.0 37.4 + - - +
224A GLY* 3.6 8.1 - - - +
225A TYR 3.2 0.2 - - - -
226A LEU* 1.3 77.2 - - - +
228A ASN* 1.3 58.4 + - - +
230A THR* 3.2 3.8 + - - -
231A TRP* 2.8 29.6 + - - +
264A ASP* 2.6 45.1 + - - +
265A PRO* 5.0 3.4 - - - +
266A GLU* 3.5 44.7 + - + +
267A VAL* 4.0 14.4 - - + +
270A ASP* 4.3 4.5 - - - +
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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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180A GLU* 2.9 38.5 + - + +
183A VAL* 3.9 12.8 - - + -
184A TRP* 3.8 28.2 - - + +
224A GLY* 3.0 15.2 + - - +
225A TYR 3.1 4.2 + - - +
227A ARG* 1.3 76.6 - - - +
229A LEU* 1.3 57.4 + - - +
231A TRP* 3.2 8.1 + - + +
232A THR* 2.8 34.7 + - - -
17B MET* 3.5 27.2 - - - +
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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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183A VAL* 3.8 23.3 - - + -
209A LEU* 4.1 23.6 - - + +
212A LEU* 3.7 31.4 - - + -
213A LEU* 3.8 33.7 - - + -
221A LEU* 4.5 6.3 - - + -
225A TYR* 3.0 41.2 + - + +
226A LEU* 3.7 8.1 - - - +
227A ARG 3.3 0.2 - - - -
228A ASN* 1.3 77.3 - - - +
230A THR* 1.3 57.7 + - - +
232A THR* 4.0 0.5 - - - -
233A LEU* 2.9 36.6 + - + +
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Residues in contact with THR 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 LEU* 2.9 17.9 + - - +
227A ARG* 3.6 6.7 - - - -
229A LEU* 1.3 78.0 - - - +
231A TRP* 1.3 56.1 + - - +
233A LEU* 3.5 2.9 + - - +
234A SER* 2.9 28.1 + - - -
256A LEU* 5.7 2.5 - - + +
259A LEU* 3.7 33.0 - - + +
267A VAL* 3.6 24.1 - - - +
270A ASP* 3.6 15.0 - - + -
271A SER* 3.6 27.1 - - - +
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Residues in contact with TRP 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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184A TRP* 3.8 21.1 - + - -
187A GLY* 3.6 24.9 - - - -
188A ASN* 3.1 25.8 - - - -
227A ARG 2.8 21.7 + - - +
228A ASN* 3.7 10.3 - - - +
230A THR* 1.3 72.6 - - - +
232A THR* 1.3 75.8 + - - +
234A SER* 2.7 28.2 + - - -
235A ASN* 3.1 17.7 + - - +
238A ARG* 5.4 0.2 - - - +
270A ASP* 3.5 22.9 + - - +
13B THR* 4.9 8.1 - - - -
14B ASN* 3.1 21.7 + - - +
15B LYS 3.3 22.9 - - - -
16B LYS* 4.1 2.5 - - - -
17B MET* 3.7 36.5 - - + -
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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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183A VAL* 2.7 38.2 + - + +
184A TRP* 4.3 0.2 - - - -
186A LEU* 4.3 8.7 - - + +
187A GLY* 3.4 25.8 - - - +
190A ALA* 5.8 0.2 - - + -
209A LEU* 4.5 20.6 - - + -
228A ASN 2.8 21.4 + - - -
229A LEU 4.0 1.1 - - - -
231A TRP* 1.3 75.6 - - - +
233A LEU* 1.3 68.0 + - - +
235A ASN* 3.1 13.5 + - - +
236A LEU* 3.1 18.4 + - + +
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Residues in contact with LEU 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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206A ILE* 5.5 1.6 - - + -
209A LEU* 4.7 15.0 - - + -
210A LEU* 3.9 25.8 - - + -
213A LEU* 3.6 31.2 - - + -
229A LEU* 2.9 19.3 + - + +
230A THR* 3.8 4.0 - - - +
232A THR* 1.3 75.4 - - - +
234A SER* 1.3 62.6 + - - +
236A LEU* 3.0 33.5 + - + +
237A CYS* 3.3 15.9 + - - -
252A ILE* 4.2 25.3 - - + +
255A THR* 4.1 8.1 - - + -
256A LEU* 5.0 8.5 - - + -
259A LEU* 4.3 9.6 - - + -
274A ALA* 5.4 0.7 - - - -
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Residues in contact with SER 234 (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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230A THR* 2.9 15.7 + - - -
231A TRP* 2.7 29.3 + - - -
232A THR 3.1 0.2 - - - -
233A LEU* 1.3 76.5 - - - +
235A ASN* 1.3 63.8 + - - +
237A CYS* 3.1 14.2 + - - +
238A ARG 3.3 8.1 + - - -
256A LEU* 5.6 0.6 - - - +
270A ASP* 3.7 26.1 - - - +
273A TRP* 5.1 1.9 - - - +
274A ALA* 3.9 19.7 - - - -
277A TYR* 3.5 17.0 + - - -
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Residues in contact with ASN 235 (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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187A GLY 2.9 27.6 + - - +
190A ALA* 4.3 10.1 - - + +
191A GLY* 3.3 16.1 - - - +
197A ARG* 3.9 10.6 - - - +
231A TRP* 3.1 26.3 + - - +
232A THR* 3.1 9.8 + - - +
234A SER* 1.3 83.2 + - - +
236A LEU* 1.3 60.1 + - - +
238A ARG* 3.4 44.5 + - - +
239A ASN* 5.3 0.3 - - - +
277A TYR* 5.2 0.2 - - - -
14B ASN 4.3 1.2 - - - +
15B LYS 3.0 22.0 + - - -
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Residues in contact with LEU 236 (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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190A ALA* 3.7 24.2 - - + -
197A ARG* 3.6 23.9 - - + -
200A VAL* 3.9 21.8 - - + -
201A ILE* 4.2 16.1 - - + +
205A ALA* 5.2 0.2 - - + -
206A ILE* 4.0 23.8 - - + -
209A LEU* 3.9 27.6 - - + -
232A THR* 3.1 14.9 + - + +
233A LEU* 3.0 21.9 + - + +
235A ASN* 1.3 76.3 - - - +
237A CYS* 1.3 58.6 + - - +
238A ARG 3.4 0.2 - - - -
244A PRO* 3.7 9.9 - - - +
252A ILE* 4.3 12.4 - - + +
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Residues in contact with CYS 237 (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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233A LEU 3.6 14.4 - - - -
234A SER 3.1 10.1 + - - +
236A LEU* 1.3 76.2 - - - +
238A ARG* 1.3 63.0 + - - +
239A ASN 4.4 0.3 - - - +
244A PRO* 3.4 19.8 - - - +
249A VAL* 6.0 1.6 - - - -
252A ILE* 4.3 24.2 - - - -
256A LEU* 4.4 1.3 - - - -
274A ALA* 4.1 21.5 - - + +
277A TYR* 3.5 13.6 - - + +
278A LEU* 3.6 41.0 - - + +
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Residues in contact with ARG 238 (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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191A GLY* 5.6 3.1 - - - -
197A ARG* 3.2 19.4 + - - +
231A TRP* 5.4 0.2 - - - +
234A SER 3.3 9.2 + - - +
235A ASN* 3.4 39.9 + - - +
236A LEU 3.4 0.2 - - - -
237A CYS* 1.3 76.5 - - - +
239A ASN* 1.3 101.7 + - - +
277A TYR* 3.3 42.9 + - + -
13B THR* 2.6 37.3 + - - +
14B ASN 3.5 14.1 + - - -
15B LYS* 3.6 13.9 - - - +
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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