Contacts of the helix formed by residues 210 - 231 (chain D) in PDB entry 7KHI
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 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208D THR* 3.9 4.8 + - - -
209D ASN* 1.3 82.5 + - - +
211D GLU* 1.3 58.6 + - - +
212D THR* 3.5 1.3 - - - -
213D LYS* 4.1 20.4 - - - -
214D ARG* 2.6 39.9 + - - +
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Residues in contact with GLU 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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210D SER* 1.3 72.3 - - - +
212D THR* 1.3 64.4 + - + +
214D ARG* 3.4 4.5 - - - +
215D LYS* 3.0 61.7 + - - +
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Residues in contact with THR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D SER* 3.5 0.9 - - - -
211D GLU* 1.3 76.9 - - + +
213D LYS* 1.3 69.5 + - - +
215D LYS* 3.2 23.6 + - - +
216D LYS* 3.0 45.8 + - - +
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Residues in contact with LYS 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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204D GLU* 4.1 15.7 + - - +
207D GLU* 4.8 1.2 + - - -
208D THR* 3.3 31.8 + - + +
210D SER* 3.5 18.3 + - - +
211D GLU 3.4 0.4 - - - -
212D THR* 1.3 83.1 + - - +
214D ARG* 1.3 59.8 + - - +
216D LYS* 3.3 8.6 + - + +
217D LEU* 2.9 59.7 + - - +
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Residues in contact with ARG 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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205D LEU* 2.2 58.2 + - + +
206D ASN 4.7 0.8 + - - -
208D THR* 2.3 37.2 + - - +
209D ASN* 3.4 13.3 + - - +
210D SER 2.6 29.7 + - - +
211D GLU* 3.4 5.8 - - - +
213D LYS* 1.3 79.5 - - - +
215D LYS* 1.3 56.7 + - + +
217D LEU* 3.3 6.7 + - - +
218D THR* 2.7 34.7 + - - +
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Residues in contact with LYS 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 GLU* 3.0 51.4 + - - +
212D THR* 3.6 26.2 - - - +
214D ARG* 1.3 76.9 - - + +
216D LYS* 1.3 75.1 + - + +
218D THR* 3.1 11.1 + - - -
219D LYS* 2.9 28.5 + - + +
1275D LEU* 4.9 20.0 - - + -
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Residues in contact with LYS 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 THR* 3.0 41.9 + - - +
213D LYS* 3.6 10.1 - - - +
215D LYS* 1.3 83.4 - - + +
217D LEU* 1.3 63.8 + - - +
219D LYS* 3.1 31.8 + - - +
220D ARG* 3.0 28.3 + - + +
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Residues in contact with LEU 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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201D LEU* 3.5 41.7 - - + +
204D GLU* 3.8 5.4 - - + +
205D LEU* 3.3 50.7 - - + +
208D THR* 3.6 5.2 - - + -
213D LYS* 2.9 38.3 + - - +
214D ARG 3.4 7.0 - - - +
216D LYS* 1.3 77.2 - - - +
218D THR* 1.3 64.4 + - - +
220D ARG* 3.2 5.7 + - - +
221D ILE* 2.9 32.1 + - + +
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Residues in contact with THR 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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202D ARG* 6.1 2.0 - - - +
205D LEU* 3.8 17.8 - - + +
214D ARG* 2.7 21.3 + - - +
215D LYS* 3.3 10.3 - - - -
217D LEU* 1.3 77.8 - - - +
219D LYS* 1.3 64.0 + - - +
221D ILE* 3.1 12.0 + - + +
222D LYS* 2.9 25.0 + - + +
1273D ASP* 5.9 7.4 - - + +
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Residues in contact with LYS 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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215D LYS* 2.9 17.9 + - + +
216D LYS* 3.2 48.6 - - - +
218D THR* 1.3 78.1 - - - +
220D ARG* 1.3 63.9 + - + +
222D LYS* 3.2 6.6 + - - +
223D LEU* 2.9 33.5 + - + +
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Residues in contact with ARG 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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126D LEU* 2.4 36.3 + - - -
127D LEU* 3.1 19.2 + - - +
129D ASP* 2.8 36.3 + - - +
192D MET* 5.3 0.2 - - - +
197D GLU* 2.8 28.3 + - - -
201D LEU* 4.5 17.4 - - + +
216D LYS* 3.0 17.0 + - + +
217D LEU* 3.6 9.0 - - - +
219D LYS* 1.3 76.4 - - + +
221D ILE* 1.3 63.2 + - - +
223D LEU* 3.2 17.5 + - + +
224D LEU* 3.0 45.2 + - - +
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Residues in contact with ILE 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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198D CYS* 4.6 4.6 - - - +
201D LEU* 3.3 55.4 - - + +
202D ARG* 3.6 38.4 - - - +
205D LEU* 4.4 10.1 - - + -
217D LEU* 2.9 26.0 + - + +
218D THR* 3.4 12.6 - - + +
220D ARG* 1.3 77.3 - - - +
222D LYS* 1.3 63.2 + - - +
224D LEU* 3.4 2.0 + - - +
225D GLU* 2.9 47.0 + - + +
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Residues in contact with LYS 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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218D THR* 2.9 14.6 + - + +
219D LYS* 3.6 10.3 - - - +
221D ILE* 1.3 77.4 - - - +
223D LEU* 1.3 68.4 + - + +
225D GLU* 3.3 13.6 + - - +
226D ALA* 2.9 28.4 + - + +
1273D ASP* 3.9 18.3 + - - +
1276D GLU* 4.1 25.6 - - - +
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Residues in contact with LEU 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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126D LEU* 4.1 32.5 - - + +
219D LYS* 2.9 27.4 + - + +
220D ARG* 3.5 22.9 - - + +
222D LYS* 1.3 81.6 - - + +
224D LEU* 1.3 64.0 + - + +
226D ALA* 3.2 5.3 + - - +
227D PHE* 3.0 22.4 + - - +
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Residues in contact with LEU 224 (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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127D LEU* 4.0 18.8 - - + -
192D MET* 5.0 4.0 - - + -
194D LEU* 3.3 45.1 - - + +
197D GLU* 4.0 12.3 - - + +
198D CYS* 4.6 16.2 - - + +
201D LEU* 3.5 29.4 - - + -
220D ARG* 3.0 33.5 + - - +
221D ILE 3.9 2.9 - - - +
223D LEU* 1.3 76.2 - - + +
225D GLU* 1.3 64.9 + - - +
227D PHE* 3.1 5.8 + - + +
228D VAL* 2.9 27.3 + - - +
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Residues in contact with GLU 225 (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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198D CYS* 3.8 18.5 - - - -
202D ARG* 2.5 34.1 + - - -
221D ILE* 2.9 38.0 + - - +
222D LYS* 3.6 11.5 - - - +
224D LEU* 1.3 76.7 - - - +
226D ALA* 1.3 61.9 + - - +
228D VAL* 3.1 12.7 - - + +
229D GLN* 2.9 30.5 + - + +
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Residues in contact with ALA 226 (chain D).
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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222D LYS* 2.9 22.3 + - + +
223D LEU* 3.6 6.1 - - - +
225D GLU* 1.3 75.3 - - - +
227D PHE* 1.3 64.0 + - - +
229D GLN* 3.2 6.4 + - - +
230D SER* 2.9 24.8 + - - -
1337D VAL 5.9 0.4 - - - -
1338D ALA* 5.0 8.1 - - + +
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Residues in contact with PHE 227 (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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24D LEU* 4.8 4.7 - - + -
127D LEU* 4.6 9.6 - - + -
194D LEU* 4.4 12.6 - - + -
223D LEU 3.0 15.0 + - - +
224D LEU* 3.6 13.5 - - + +
226D ALA* 1.3 77.9 - - - +
228D VAL* 1.3 61.7 + - - +
230D SER* 3.3 12.8 + - - -
231D GLY 3.4 8.1 + - - -
232D ASN* 3.2 42.0 + - + +
233D LYS 4.6 0.7 - - - -
234D PRO* 3.6 30.5 - - + -
237D MET* 3.4 30.5 - - + -
1337D VAL* 4.2 34.5 - - + -
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Residues in contact with VAL 228 (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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194D LEU* 4.7 28.9 - - + -
195D GLU* 5.3 16.2 - - + +
198D CYS* 6.0 4.7 - - + -
224D LEU 2.9 16.5 + - - +
225D GLU* 3.1 21.3 - - + +
227D PHE* 1.3 78.5 - - - +
229D GLN* 1.3 65.9 + - + +
231D GLY* 3.7 10.0 + - - +
232D ASN 5.4 1.1 - - - -
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Residues in contact with GLN 229 (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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225D GLU* 2.9 24.0 + - + +
226D ALA* 3.6 7.2 - - - +
228D VAL* 1.3 81.0 - - + +
230D SER* 1.3 64.8 + - - +
231D GLY* 3.1 2.0 + - - -
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Residues in contact with SER 230 (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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23D ALA* 5.6 0.2 - - - +
226D ALA 2.9 15.1 + - - -
227D PHE 3.3 4.9 + - - -
229D GLN* 1.3 77.5 - - - +
231D GLY* 1.3 58.0 + - - +
232D ASN* 2.3 32.8 + - - +
1337D VAL 3.9 3.4 - - - -
1338D ALA 3.2 24.2 - - - -
1339D GLY* 3.4 16.1 - - - -
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Residues in contact with GLY 231 (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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227D PHE 3.4 4.4 + - - -
228D VAL* 3.7 10.0 + - - -
229D GLN 3.1 4.9 - - - -
230D SER* 1.3 78.7 - - - +
232D ASN* 1.3 63.3 + - - +
233D LYS* 3.8 5.6 + - - +
236D TRP* 4.4 10.0 - - - -
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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