Contacts of the helix formed by residues 207 - 223 (chain D) in PDB entry 4K71
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 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202D SER 3.0 14.7 + - - +
203D LEU* 3.3 17.6 + - - +
204D GLN 4.8 0.2 - - - -
205D LYS 3.8 0.8 - - - -
206D PHE* 1.3 79.1 - - - +
208D GLU* 1.3 65.7 + - - +
209D ARG* 3.3 3.1 - - - -
210D ALA* 3.4 10.2 + - - +
211D PHE 3.8 1.0 + - - -
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Residues in contact with GLU 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D LEU* 4.1 17.0 + - + -
207D GLY* 1.3 70.0 - - - -
209D ARG* 1.3 68.9 + - + +
211D PHE* 3.1 6.9 + - - +
212D LYS* 3.0 42.5 + - + +
239D THR* 3.6 23.0 - - + +
243D THR* 4.8 4.3 + - - +
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Residues in contact with ARG 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206D PHE 6.0 0.4 - - - +
207D GLY* 3.3 1.0 - - - -
208D GLU* 1.3 82.4 - - - +
210D ALA* 1.3 59.1 + - - +
212D LYS* 3.3 11.3 + - + +
213D ALA* 2.9 39.0 + - + +
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D SER* 4.0 12.5 - - - +
206D PHE* 3.8 29.5 + - + +
207D GLY 3.4 13.6 + - - +
208D GLU 3.2 0.6 - - - -
209D ARG* 1.3 81.9 - - - +
211D PHE* 1.3 60.5 + - - +
213D ALA* 3.5 7.1 + - - +
214D TRP* 3.2 20.8 + - - +
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Residues in contact with PHE 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LYS* 4.0 33.0 - - + -
202D SER* 3.8 17.6 + - - +
203D LEU* 3.5 34.3 - - + -
207D GLY 3.8 2.0 + - - +
208D GLU 3.1 3.4 + - - +
210D ALA* 1.3 75.3 - - - +
212D LYS* 1.3 67.2 + - - +
214D TRP* 3.3 25.6 + + + +
215D ALA* 2.9 28.0 + - + +
238D LEU* 4.1 5.8 - - + -
239D THR* 3.3 46.0 - - + -
242D HIS* 3.8 31.4 - + + -
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Residues in contact with LYS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D GLU* 3.0 38.8 + - + +
209D ARG* 3.6 14.4 - - + +
211D PHE* 1.3 76.6 - - - +
213D ALA* 1.3 54.8 + - - +
215D ALA* 3.0 3.3 + - - +
216D VAL* 2.8 40.3 + - + +
235D VAL* 3.8 18.3 - - + +
236D THR* 3.6 27.1 + - - +
239D THR* 3.5 21.5 - - + +
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Residues in contact with ALA 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ARG* 2.9 29.4 + - + +
210D ALA* 3.6 8.1 - - - +
211D PHE 3.2 0.2 - - - -
212D LYS* 1.3 76.1 - - - +
214D TRP* 1.3 63.8 + - - +
216D VAL* 3.5 5.8 + - - +
217D ALA* 3.2 22.9 + - - +
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Residues in contact with TRP 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195D LYS* 6.4 1.1 - - + -
198D LEU* 6.2 4.8 - - + +
199D LYS* 3.3 41.5 - - + -
202D SER* 6.0 1.6 - - - +
210D ALA 3.2 11.2 + - - +
211D PHE* 3.5 28.5 - + + +
213D ALA* 1.3 79.8 - - - +
215D ALA* 1.3 85.1 + - + +
217D ALA* 3.3 6.1 + - + +
218D ARG* 3.1 56.6 + - + +
219D LEU* 6.5 0.2 - - + -
222D ARG* 5.2 7.4 - - - -
238D LEU* 5.1 8.5 - - + -
242D HIS* 6.1 0.2 - - - -
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Residues in contact with ALA 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D PHE* 2.9 26.7 + - + +
212D LYS* 3.0 8.0 + - - +
214D TRP* 1.3 91.9 - - + +
216D VAL* 1.3 66.7 + - - +
217D ALA 3.2 0.2 + - - -
218D ARG* 4.9 0.4 - - - -
219D LEU* 2.9 31.2 + - - +
235D VAL* 3.7 24.0 - - + -
238D LEU* 4.6 11.0 - - + -
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Residues in contact with VAL 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D LYS* 2.8 23.9 + - + +
213D ALA* 4.0 6.3 - - - +
215D ALA* 1.3 72.1 - - - +
217D ALA* 1.3 61.6 + - - +
220D SER* 2.6 41.1 + - - +
228D PHE* 4.7 24.2 - - + -
231D VAL* 4.1 8.4 - - + +
232D SER* 5.5 5.2 - - - +
235D VAL* 3.6 25.6 - - + -
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Residues in contact with ALA 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D ALA 3.2 12.4 + - - +
214D TRP* 3.6 10.3 - - + +
215D ALA 3.1 1.0 - - - -
216D VAL* 1.3 81.1 - - - +
218D ARG* 1.3 63.4 + - - +
220D SER* 3.3 4.6 + - - -
221D GLN* 3.1 30.4 + - - +
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Residues in contact with ARG 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TRP* 3.1 43.5 + - + +
215D ALA 4.2 1.6 - - - +
217D ALA* 1.3 78.6 - - - +
219D LEU* 1.3 59.9 + - + +
221D GLN* 3.3 25.9 + - - +
222D ARG* 2.9 66.4 + - - +
293D VAL 5.7 1.2 + - - -
295D ASN* 3.8 18.2 + - - +
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Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TRP* 6.5 0.4 - - + -
215D ALA* 2.9 18.2 + - - +
218D ARG* 1.3 77.9 - - + +
220D SER* 1.3 56.1 + - - +
222D ARG* 3.5 31.4 - - - +
223D PHE* 2.7 59.3 + - + +
231D VAL* 4.0 15.3 - - + +
234D LEU* 3.6 34.5 - - + -
235D VAL* 4.1 16.6 - - + -
238D LEU* 4.1 25.4 - - + -
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Residues in contact with SER 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216D VAL* 2.6 30.3 + - - +
217D ALA* 3.7 5.6 - - - -
219D LEU* 1.3 73.3 - - - +
221D GLN* 1.3 63.4 + - - +
223D PHE 4.5 5.2 - - - +
224D PRO* 3.2 27.6 - - - +
228D PHE* 6.1 1.0 - - - -
231D VAL* 3.9 17.4 - - - +
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Residues in contact with GLN 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217D ALA* 3.1 18.6 + - - +
218D ARG* 3.4 36.3 + - - +
220D SER* 1.3 77.0 - - - +
222D ARG* 1.3 61.2 + - - +
224D PRO* 3.4 12.2 - - - +
295D ASN* 3.4 25.2 + - - +
296D ASP 4.6 0.2 - - - +
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Residues in contact with ARG 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D TRP* 5.2 7.5 - - - -
218D ARG* 2.9 59.1 + - - +
219D LEU* 3.5 30.0 - - - +
221D GLN* 1.3 75.4 - - - +
223D PHE* 1.3 89.1 + - + +
224D PRO* 3.1 0.8 - - - +
238D LEU* 6.0 1.0 - - - +
272D SER* 4.7 0.2 + - - -
290D ILE* 4.3 14.0 + - - +
291D ALA* 3.4 31.5 + - - +
292D GLU* 5.4 0.4 - - - +
293D VAL 4.0 18.2 - - - +
294D GLU 4.5 1.8 - - - +
295D ASN* 3.4 14.8 - - - +
296D ASP* 2.9 28.8 + - - +
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Residues in contact with PHE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D LEU* 2.7 49.9 + - + +
220D SER* 3.6 6.5 - - - +
222D ARG* 1.3 103.6 - - + +
224D PRO* 1.4 57.9 - - - +
225D LYS 3.3 2.7 - - - -
226D ALA* 3.0 30.2 + - + +
231D VAL* 4.8 4.0 - - + +
234D LEU* 4.1 15.3 - - + -
264D ILE* 5.1 6.7 - - + -
271D ILE* 3.5 36.1 - - + +
272D SER* 3.7 22.4 - - - -
275D LEU* 4.8 9.2 - - + -
290D ILE* 4.8 10.5 - - + -
293D VAL* 4.3 19.5 - - + -
296D ASP* 4.8 1.8 - - - -
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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