Contacts of the helix formed by residues 200 - 211 (chain D) in PDB entry 6APL
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 THR 200 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ASN* 4.7 2.2 + - - -
199D PHE* 1.3 76.2 - - - +
201D VAL* 1.3 65.7 + - - +
202D ASN* 3.6 7.5 + - - +
203D THR* 3.0 29.2 + - - +
204D MSE 2.9 24.4 + - - +
230D ILE* 3.8 23.1 - - + -
232D SER* 3.6 29.6 - - - +
236D ASP* 3.6 4.5 - - - -
302D MSE 5.4 4.9 - - - -
305D THR* 4.2 14.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 201 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D PHE* 3.9 8.2 - - + -
200D THR* 1.3 70.3 - - - +
202D ASN* 1.3 62.0 + - - +
204D MSE 3.8 4.6 - - - +
205D LYS* 3.1 29.2 + - + +
229D PHE* 4.3 8.1 - - + -
235D ARG* 3.8 9.6 - - + +
236D ASP* 2.7 33.5 + - - +
239D MSE 3.6 42.0 - - + -
254D ASP* 3.2 35.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 202 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D THR* 3.1 7.5 + - - +
201D VAL* 1.3 81.1 - - - +
203D THR* 1.3 65.3 + - - +
205D LYS* 4.0 1.4 - - - +
206D ASN* 2.9 59.9 + - - +
233D ASP* 6.5 1.1 - - + -
235D ARG* 3.3 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ASN* 3.5 42.7 + - + +
200D THR* 3.0 22.8 + - - +
202D ASN* 1.3 85.6 + - - +
204D MSE 1.3 56.8 + - - +
206D ASN* 3.7 6.9 - - + +
207D SER* 2.8 40.0 + - - +
305D THR* 5.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ASN* 5.5 1.8 + - - +
197D TYR* 3.2 39.0 - - + +
199D PHE* 3.4 36.0 - - + +
200D THR 2.9 17.7 + - - +
201D VAL* 3.8 6.3 - - - +
203D THR* 1.3 75.5 - - - +
205D LYS* 1.3 61.6 + - + +
207D SER* 3.2 6.7 + - - -
208D LEU* 3.0 33.8 + - + +
216D PHE* 4.2 0.5 - - - -
219D VAL* 3.5 24.7 - - + -
239D MSE 6.4 0.2 - - - -
262D TYR* 4.4 18.2 - - - -
263D PHE* 3.5 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D VAL* 3.1 21.6 + - + +
202D ASN 4.1 1.6 - - - +
204D MSE 1.3 79.9 - - + +
206D ASN* 1.3 65.7 + - - +
208D LEU* 3.6 9.6 + - + +
209D VAL* 3.2 27.7 + - + +
235D ARG* 4.3 6.4 - - - +
253D LEU* 4.8 5.1 + - - +
254D ASP* 3.0 37.6 + - + +
257D ASP* 2.9 24.3 + - - +
262D TYR* 3.5 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ASN* 2.9 49.6 + - - +
203D THR* 3.7 7.7 - - + +
205D LYS* 1.3 76.5 - - - +
207D SER* 1.3 64.2 + - - +
209D VAL* 3.1 8.0 + - - +
210D SER* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ASN* 4.0 2.5 - - - +
180D GLY* 3.7 19.1 + - - -
203D THR* 2.8 29.8 + - - +
204D MSE 3.5 5.8 - - - -
206D ASN* 1.3 76.6 - - - +
208D LEU* 1.3 64.4 + - - +
211D TYR* 2.9 51.8 + - - +
216D PHE* 3.7 21.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D MSE 3.0 25.6 + - + +
205D LYS* 3.8 10.5 - - + +
207D SER* 1.3 75.4 - - - +
209D VAL* 1.3 61.6 + - + +
212D TRP* 3.3 37.8 + - + +
216D PHE* 3.6 34.1 - - + +
217D THR* 3.7 6.7 - - - +
218D SER* 3.6 26.0 - - - +
219D VAL* 4.7 2.5 - - + +
262D TYR* 3.6 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D LYS* 3.2 15.9 + - + +
206D ASN* 3.1 11.3 + - - +
207D SER 3.0 1.0 - - - -
208D LEU* 1.3 81.4 - - + +
210D SER* 1.3 69.3 + - - +
212D TRP* 3.8 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ASN* 3.0 17.7 + - - +
209D VAL* 1.3 81.9 - - - +
211D TYR* 1.3 84.1 + - - +
212D TRP 3.4 1.8 + - - -
213D ASN 5.0 1.7 + - - -
214D LEU* 4.6 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D GLY* 4.5 8.1 - - - -
207D SER* 2.9 41.3 + - - +
210D SER* 1.3 93.0 - - - +
212D TRP* 1.3 65.2 + - - +
213D ASN 3.4 1.8 - - - -
214D LEU* 3.2 25.0 + - + -
215D GLY 3.2 0.5 + - - -
216D PHE* 3.0 30.5 + - + +
336D HIS* 3.1 31.0 - + - -
338D PHE* 3.5 39.3 - + + -
339D GLU* 4.6 5.6 - - - -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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