Contacts of the helix formed by residues 206 - 218 (chain D) in PDB entry 2CEA
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 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163D VAL* 6.2 0.4 - - - -
204D GLY 3.3 0.4 - - - -
205D THR* 1.3 80.3 - - - +
207D LYS* 1.3 67.7 + - - +
208D THR 3.3 2.2 - - - -
209D LEU* 3.4 5.6 - - - +
210D LEU* 2.9 34.7 + - - +
328D VAL* 4.7 1.6 - - - -
1608D ADP 2.8 33.8 + - - -
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Residues in contact with LYS 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D LEU* 3.0 41.3 - - + +
201D GLY 3.2 26.8 + - - +
202D PRO 3.1 22.4 + - - -
203D PRO* 3.8 4.8 - - - +
205D THR* 3.8 6.7 - - - +
206D GLY* 1.3 79.0 - - - +
208D THR* 1.3 64.2 + - - +
210D LEU* 3.4 6.6 + - - -
211D ALA* 3.4 2.4 + - - +
258D PHE* 4.5 1.3 - - - -
260D ASP* 5.4 3.2 + - - -
305D ALA* 3.8 28.3 - - + +
306D THR* 4.2 7.6 - - - +
307D ASN* 4.1 15.6 + - - +
328D VAL* 4.5 12.5 - - + +
1608D ADP 2.8 39.9 + - - +
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Residues in contact with THR 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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207D LYS* 1.3 72.4 - - - +
209D LEU* 1.3 64.9 + - - +
211D ALA* 3.0 4.5 + - - +
212D ARG* 2.9 35.7 + - + +
222D PHE* 4.6 0.2 - - + -
224D HIS* 3.3 33.3 - - + +
258D PHE* 3.5 28.6 - - + -
260D ASP* 4.2 8.3 + - - -
1608D ADP 2.8 36.2 + - - -
1609D MG 4.0 2.1 - - - -
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Residues in contact with LEU 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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158D VAL* 4.2 17.2 - - + +
162D ASP* 3.8 13.0 - - + +
163D VAL* 4.0 13.9 - - + -
206D GLY* 3.2 9.4 + - - +
208D THR* 1.3 80.3 - - - +
210D LEU* 1.3 51.7 + - + +
212D ARG* 3.2 28.7 + - - +
213D ALA* 2.6 37.0 + - - +
343D HIS* 5.9 0.2 - - + -
1608D ADP 3.2 76.1 + - + +
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D PHE* 4.6 4.0 - - + -
163D VAL* 4.0 27.6 - - + +
166D ALA* 4.8 4.0 - - + -
169D ALA* 4.0 19.1 - - + -
170D ILE* 4.3 16.8 - - + -
173D LEU* 3.9 24.5 - - + -
199D LEU* 4.3 10.8 - - + -
206D GLY* 2.9 22.6 + - - +
207D LYS 3.7 4.3 - - - +
208D THR 3.2 0.2 - - - -
209D LEU* 1.3 73.7 - - - +
211D ALA* 1.3 58.9 + - - +
213D ALA* 3.2 4.3 + - - +
214D VAL* 2.9 34.3 + - - +
328D VAL* 4.0 33.0 - - + -
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Residues in contact with ALA 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D LEU* 4.5 0.9 - - + +
207D LYS 3.4 6.0 + - - +
208D THR 3.0 9.2 + - - +
210D LEU* 1.3 75.2 - - - +
212D ARG* 1.3 68.0 + - - +
214D VAL* 2.9 14.6 + - - +
215D ALA* 3.0 10.4 + - - +
222D PHE* 3.5 21.6 - - + -
256D ILE* 4.2 2.3 - - - +
258D PHE* 3.7 24.5 - - + -
303D MET* 3.8 28.0 - - + -
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Residues in contact with ARG 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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155D ASN* 4.1 20.5 - - - +
156D LYS* 2.8 32.3 + - - +
158D VAL* 3.5 31.2 + - + +
208D THR* 2.9 30.3 + - - +
209D LEU* 3.5 24.5 - - - +
211D ALA* 1.3 77.5 - - - +
213D ALA* 1.3 61.1 + - - +
215D ALA* 3.2 3.1 + - - +
216D GLY* 2.9 19.8 + - - -
222D PHE* 3.3 38.4 - - + -
224D HIS* 5.1 3.6 - - - -
1608D ADP 4.5 8.7 + - - -
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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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158D VAL* 3.7 13.2 - - + +
159D THR* 3.9 14.3 - - - +
160D PHE* 3.6 27.1 - - + -
163D VAL* 4.0 5.8 - - + -
209D LEU 2.6 21.2 + - - +
210D LEU* 3.3 9.4 - - - +
211D ALA 3.1 0.2 - - - -
212D ARG* 1.3 73.5 - - - +
214D VAL* 1.3 64.4 + - - +
216D GLY* 3.2 0.7 + - - -
217D GLU* 2.8 27.9 + - - +
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Residues in contact with VAL 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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160D PHE* 4.3 6.5 - - + -
173D LEU* 4.0 36.6 - - + -
176D VAL* 4.1 22.7 - - + -
177D VAL* 3.6 23.5 - - + +
180D LEU* 4.2 4.0 - - + -
210D LEU 2.9 21.8 + - - +
211D ALA* 2.9 9.6 + - - +
213D ALA* 1.3 76.6 - - - +
215D ALA* 1.3 62.2 + - - +
217D GLU* 3.5 2.3 + - - +
218D ALA* 3.1 22.3 + - - +
256D ILE* 3.8 14.4 - - + -
303D MET* 4.4 6.3 - - - -
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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
----------------------------------------------------------
157D ARG* 4.8 0.9 - - - +
211D ALA 3.0 5.1 + - - -
212D ARG 3.5 8.1 - - - +
213D ALA 3.1 0.2 - - - -
214D VAL* 1.3 75.5 - - - +
216D GLY* 1.3 60.9 + - - +
218D ALA* 3.2 2.5 + - - +
219D ASN 2.9 22.2 + - - -
220D VAL* 2.9 30.5 + - - +
221D PRO 4.4 0.7 - - - +
222D PHE* 3.7 27.8 - - + -
256D ILE* 3.2 23.1 - - + +
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Residues in contact with GLY 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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157D ARG* 3.4 25.3 - - - +
158D VAL 3.3 19.5 - - - -
159D THR* 4.3 6.3 - - - +
212D ARG 2.9 11.1 + - - -
215D ALA* 1.3 72.9 - - - +
217D GLU* 1.3 61.1 + - - +
219D ASN* 2.9 28.9 + - - +
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Residues in contact with GLU 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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158D VAL 4.0 1.4 + - - -
159D THR* 3.2 14.4 + - - +
160D PHE* 2.7 58.6 + - + +
161D LYS 5.6 0.2 + - - -
174D LYS* 5.5 3.6 + - - +
177D VAL* 4.0 18.4 - - + -
181D LYS* 3.9 19.0 + - - +
213D ALA 2.8 15.1 + - - +
214D VAL 3.8 4.3 - - - +
216D GLY* 1.3 76.4 - - - +
218D ALA* 1.3 57.6 + - - +
219D ASN* 3.7 6.9 + - - -
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Residues in contact with ALA 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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177D VAL* 4.1 11.9 - - + +
180D LEU* 3.7 34.9 - - + +
181D LYS* 4.0 20.3 + - + +
214D VAL 3.1 17.4 + - - +
215D ALA 3.2 2.9 + - - +
216D GLY 3.0 0.4 - - - -
217D GLU* 1.3 77.5 - - - +
219D ASN* 1.3 70.7 + - - +
220D VAL* 3.1 9.6 + - + +
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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