Contacts of the helix formed by residues 210 - 226 (chain W) in PDB entry 6NE3
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 210 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184W GLN* 3.5 19.0 + - - +
208W GLY 3.5 0.4 - - - -
209W LEU* 1.3 79.0 - - - +
211W LYS* 1.3 53.6 + - - +
212W THR 3.4 1.1 - - - -
213W LEU* 3.1 6.8 + - - +
214W GLN* 2.5 36.3 + - - +
801W ADP 3.3 33.1 + - - -
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Residues in contact with LYS 211 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203W LEU* 4.9 4.7 - - + +
205W ASP* 4.2 12.8 - - + +
206W GLU 3.5 19.5 - - - +
207W MET* 3.5 15.0 - - - +
209W LEU* 4.2 9.9 - - + +
210W GLY* 1.3 72.2 - - - +
212W THR* 1.3 59.6 + - - +
214W GLN* 3.1 9.9 + - - +
215W THR* 3.0 28.6 + - - +
308W ASP* 5.4 1.1 + - - -
335W LEU* 3.4 34.0 - - + +
336W THR* 3.4 32.7 - - - +
337W GLY 4.8 0.8 - - - +
801W ADP 2.5 55.9 + - - +
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Residues in contact with THR 212 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211W LYS* 1.3 76.8 - - - +
213W LEU* 1.3 63.3 + - + +
215W THR* 3.3 2.1 - - - +
216W ILE* 3.0 41.1 + - - +
243W ASN* 5.5 5.6 - - - +
244W TRP* 3.4 49.8 - - - +
247W GLU* 3.7 28.8 - - + +
335W LEU* 4.0 0.2 - - - +
595W ARG* 4.5 0.4 - - - +
801W ADP 2.9 34.1 + - + +
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Residues in contact with LEU 213 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175W VAL* 5.0 4.0 - - + -
180W LEU* 5.1 12.4 - - + +
184W GLN* 5.1 3.6 - - - +
210W GLY* 3.1 17.1 + - - +
212W THR* 1.3 81.2 - - + +
214W GLN* 1.3 60.0 + - - +
216W ILE* 4.3 7.9 - - + -
217W SER* 2.9 32.5 + - - +
247W GLU* 3.4 39.9 - - + +
251W TRP* 3.5 49.4 - - + -
801W ADP 4.1 25.1 - - + +
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Residues in contact with GLN 214 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180W LEU* 5.0 1.1 - - - +
184W GLN* 2.6 48.0 + - - +
187W GLY* 3.9 8.2 - - - -
188W LEU* 3.2 28.4 - - - +
191W LEU* 3.8 8.3 - - + -
203W LEU* 3.6 25.7 - - + +
209W LEU 5.5 1.6 + - - -
210W GLY 2.5 18.0 + - - +
211W LYS* 3.1 15.5 + - - +
213W LEU* 1.3 74.7 - - - +
215W THR* 1.3 58.5 + - - +
217W SER* 2.4 25.7 + - - -
218W LEU* 2.9 13.2 + - - +
395W ARG* 5.0 5.3 - - - +
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Residues in contact with THR 215 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191W LEU* 5.3 1.8 - - - -
203W LEU* 6.4 0.9 - - - -
211W LYS 3.0 13.7 + - - +
212W THR 3.3 13.9 - - - +
214W GLN* 1.3 73.8 - - - +
216W ILE* 1.3 60.6 + - + +
218W LEU* 3.2 13.4 + - - +
219W LEU* 3.0 28.8 + - - +
234W VAL* 5.3 3.5 - - - +
244W TRP* 3.6 28.9 - - + -
248W PHE* 5.6 2.7 - - + -
304W TYR* 6.0 0.9 - - - -
306W VAL* 3.8 29.4 - - + +
335W LEU* 4.1 9.4 - - + -
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Residues in contact with ILE 216 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212W THR* 3.0 31.1 + - - +
213W LEU* 4.0 9.4 - - + +
215W THR* 1.3 75.9 - - - +
217W SER* 1.3 57.0 + - - +
219W LEU* 3.4 3.4 + - - +
220W GLY* 2.9 25.5 + - - -
244W TRP* 4.7 2.0 - - + -
247W GLU* 3.7 31.6 - - + +
248W PHE* 3.6 51.6 - - + +
251W TRP* 4.4 8.1 - - + -
252W VAL* 3.7 35.3 - - + +
255W LEU* 4.7 0.5 - - - +
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Residues in contact with SER 217 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174W TYR* 3.2 24.2 + - - -
175W VAL* 5.8 1.6 - - - -
180W LEU* 3.8 29.9 - - - +
188W LEU* 3.9 9.7 - - - +
213W LEU* 2.9 17.2 + - - +
214W GLN* 2.4 35.9 + - - -
216W ILE* 1.3 73.6 - - - +
218W LEU* 1.3 58.2 + - - +
221W TYR* 2.9 24.1 + - - +
252W VAL* 4.8 3.8 - - - -
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Residues in contact with LEU 218 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188W LEU* 3.7 13.2 - - + -
191W LEU* 3.8 20.6 - - + -
192W ILE* 3.9 21.3 - - + +
195W TYR* 6.1 0.2 - - + -
214W GLN 2.9 14.4 + - - +
215W THR* 3.2 16.6 + - - +
217W SER* 1.3 76.8 + - - +
219W LEU* 1.3 58.3 + - - +
221W TYR* 3.2 3.6 + - - +
222W MET* 2.9 52.4 + - + +
304W TYR* 3.6 31.4 - - + +
306W VAL* 5.9 0.4 - - + -
333W LEU* 3.7 24.2 - - + -
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Residues in contact with LEU 219 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215W THR* 3.0 16.0 + - - +
216W ILE* 4.1 2.5 - - - +
218W LEU* 1.3 76.3 - - - +
220W GLY* 1.3 57.7 + - - +
222W MET* 3.8 17.3 - - + -
223W LYS* 2.9 31.6 + - - +
228W ILE 5.4 0.2 - - - +
232W HIS* 3.5 60.6 - - + +
234W VAL* 6.5 0.2 - - + -
248W PHE* 4.9 4.0 - - + -
255W LEU* 3.7 32.6 - - + +
282W VAL* 3.9 19.1 - - + -
304W TYR* 4.3 9.6 - - + -
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Residues in contact with GLY 220 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174W TYR* 3.2 26.5 - - - -
216W ILE 2.9 16.7 + - - -
217W SER 3.8 0.2 - - - -
218W LEU 3.3 0.2 - - - -
219W LEU* 1.3 76.8 - - - +
221W TYR* 1.3 60.1 + - - +
223W LYS* 5.2 0.7 - - - -
224W HIS* 3.2 29.9 + - - +
252W VAL* 3.9 18.4 - - - -
255W LEU* 4.2 1.5 - - - +
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Residues in contact with TYR 221 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167W ARG* 3.2 40.0 + - + +
168W PHE* 3.5 23.0 + + + -
174W TYR* 3.4 32.9 - + - +
188W LEU* 5.2 0.7 - - + -
192W ILE* 3.7 15.7 - - + -
217W SER 2.9 9.6 + - - +
218W LEU* 3.2 10.1 + - - +
220W GLY* 1.3 75.8 - - - +
222W MET* 1.3 76.0 + - + +
225W TYR* 2.9 56.5 + + + +
226W ARG* 3.7 24.0 + - + -
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Residues in contact with MET 222 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192W ILE* 4.4 5.6 - - + -
195W TYR* 4.4 9.0 - - + -
218W LEU* 2.9 35.2 + - + +
219W LEU* 3.2 20.6 + - + +
221W TYR* 1.3 98.7 - - + +
223W LYS* 1.3 58.5 + - - +
226W ARG* 2.9 63.8 + - + +
227W ASN 3.0 7.4 + - - -
228W ILE* 3.4 28.9 + - + -
232W HIS* 5.5 0.4 - - + -
304W TYR* 3.5 30.5 - - + +
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Residues in contact with LYS 223 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219W LEU* 2.9 15.4 + - + +
220W GLY* 5.2 0.4 - - - -
222W MET* 1.3 78.0 - - - +
224W HIS* 1.3 71.0 + - + +
227W ASN* 3.7 13.5 - - - +
228W ILE 3.4 21.5 + - - +
229W PRO* 4.8 7.4 - - + -
254W THR* 2.5 48.8 + - + +
255W LEU* 3.7 28.0 - - + -
256W ARG* 3.6 21.7 - - - +
281W ASP* 3.8 6.3 - - - +
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Residues in contact with HIS 224 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174W TYR* 3.5 29.4 + - + +
220W GLY* 3.2 25.5 + - - +
221W TYR 3.5 0.8 + - - -
222W MET 3.3 0.4 - - - -
223W LYS* 1.3 88.2 + - + +
225W TYR* 1.3 85.3 + - + +
226W ARG 3.8 0.3 + - - -
227W ASN* 4.2 10.4 + - - +
254W THR* 3.4 35.8 + - + +
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Residues in contact with TYR 225 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168W PHE* 3.5 27.1 - + - -
173W SER* 3.5 19.8 + - - -
174W TYR* 3.5 15.2 + + - -
221W TYR* 2.9 49.0 + + + +
224W HIS* 1.3 91.8 + + + +
226W ARG* 1.3 66.7 + - - +
227W ASN* 3.6 8.2 + - - -
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Residues in contact with ARG 226 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167W ARG* 4.5 5.5 - - - +
192W ILE* 3.4 28.9 - - - +
195W TYR* 3.7 16.7 - - + -
196W GLU* 2.4 33.5 + - - -
221W TYR* 3.7 20.5 - - + +
222W MET* 2.9 37.9 + - + +
225W TYR* 1.3 86.4 - - - +
227W ASN* 1.3 75.1 + - - +
228W ILE* 3.3 22.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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