Contacts of the helix formed by residues 202 - 214 (chain D) in PDB entry 4L28
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 202 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D THR* 4.0 0.9 - - - -
192D PRO 5.5 0.2 - - - -
195D ALA* 4.2 10.8 - - - -
196D ARG 3.2 25.1 - - - -
197D PHE* 3.0 26.8 + - - -
199D SER* 3.2 7.0 + - - -
200D PRO 3.3 0.8 - - - -
201D GLU* 1.3 80.5 - - - +
203D HIS* 1.3 63.2 + - - +
204D VAL* 3.7 4.1 + - - +
205D GLY 3.0 16.8 + - - -
206D VAL* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 203 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D PRO* 3.6 24.3 - - + +
146D THR 3.7 20.6 - - - -
168D VAL* 3.6 21.4 - - + +
170D PRO* 4.2 16.5 - - + +
191D THR* 3.4 30.1 + - - +
197D PHE* 5.8 2.9 - - + -
202D SER* 1.3 76.2 - - - +
204D VAL* 1.3 71.3 + - + +
207D ALA* 3.0 29.1 + - - +
223D TYR* 3.0 24.5 + + - -
308D TYR* 4.2 16.8 + + - -
309D ASP* 6.2 0.2 - - - -
310D PHE* 5.0 5.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D TRP* 3.9 13.5 - - + +
46D PRO* 4.0 31.6 - - + -
145D PRO* 4.0 10.1 - - + -
197D PHE* 5.0 4.9 - - + +
202D SER* 3.2 6.5 + - - +
203D HIS* 1.3 102.1 + - + +
205D GLY* 1.3 64.5 + - - +
207D ALA* 3.2 3.3 + - - +
208D TRP* 3.0 45.3 + - + +
221D ASP* 6.1 1.1 - - - +
223D TYR* 4.2 20.6 - - + -
310D PHE* 4.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D TRP* 4.3 16.2 - - - -
197D PHE 5.3 0.4 - - - -
199D SER 4.5 4.3 - - - -
200D PRO* 4.0 11.9 - - - -
202D SER* 3.0 15.8 + - - -
204D VAL* 1.3 78.3 - - - +
206D VAL* 1.3 63.4 + - - +
208D TRP* 3.2 3.9 + - - +
209D ARG* 2.9 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B HIS* 4.3 10.3 - - + +
536B ALA* 6.0 0.2 - - + -
537B ILE* 4.1 14.1 - - + -
168D VAL* 4.0 13.9 - - + -
189D VAL* 4.0 17.9 - - + -
191D THR* 3.8 17.7 - - + -
200D PRO 3.5 15.5 - - - +
201D GLU* 3.8 6.7 - - - +
202D SER 2.8 23.5 + - - +
203D HIS 4.1 2.7 - - - +
205D GLY* 1.3 72.5 - - - -
207D ALA* 1.3 65.1 + - - +
209D ARG* 3.2 15.8 + - - +
210D LEU* 2.9 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ILE* 3.9 14.6 - - + +
145D PRO* 3.8 29.6 - - + -
168D VAL* 4.2 12.8 - - + +
203D HIS 3.0 20.1 + - - +
204D VAL 3.4 5.8 - - - +
205D GLY 3.1 0.2 - - - -
206D VAL* 1.3 78.8 - - - +
208D TRP* 1.3 63.9 + - + +
210D LEU* 3.3 3.6 + - - +
211D LYS* 3.0 22.0 + - - +
219D ILE* 3.7 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 208 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D TRP* 3.5 38.1 - + + -
44D ILE* 3.6 58.2 + - + -
204D VAL* 3.0 34.9 + - + +
205D GLY 3.2 6.0 + - - +
207D ALA* 1.3 78.5 - - + +
209D ARG* 1.3 63.4 + - + +
211D LYS* 2.9 38.3 + - + +
212D ASN* 3.0 28.4 + - - +
219D ILE* 3.6 32.1 - - + +
221D ASP* 4.1 20.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 209 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B HIS* 4.8 6.9 + - - -
535B THR* 5.7 3.0 + - - +
537B ILE* 3.3 44.9 - - + +
200D PRO* 3.0 48.1 + - - +
201D GLU* 4.4 6.5 + - - +
205D GLY 2.9 16.5 + - - +
206D VAL* 3.8 6.6 - - - +
208D TRP* 1.3 77.8 - - + +
210D LEU* 1.3 62.2 + - - +
212D ASN* 3.5 17.0 + - - +
213D GLU* 3.6 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B ALA* 5.0 5.6 - - + -
537B ILE* 3.8 27.1 - - + +
540B LEU* 3.7 25.1 - - + -
143D ILE* 4.0 11.9 - - + -
166D ILE* 4.1 13.5 - - + -
168D VAL* 3.8 28.9 - - + -
189D VAL* 4.1 18.6 - - + -
206D VAL* 2.9 25.0 + - + +
207D ALA* 3.6 4.0 - - - +
209D ARG* 1.3 74.0 - - - +
211D LYS* 1.3 66.5 + - - +
213D GLU* 3.2 10.0 + - - +
214D ILE* 3.3 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D ILE* 3.7 11.4 - - + +
207D ALA 3.0 13.1 + - - +
208D TRP* 2.9 30.9 + - + +
210D LEU* 1.3 78.4 - - - +
212D ASN* 1.3 76.4 + - - +
213D GLU 3.3 0.2 + - - -
214D ILE 3.2 9.2 - - - +
217D SER* 3.1 44.0 + - - +
218D HIS* 4.8 5.9 + - - +
219D ILE* 3.7 25.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 212 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D TRP* 5.5 6.3 - - - +
208D TRP* 3.0 29.9 + - - +
209D ARG* 3.9 11.0 - - - +
210D LEU 3.2 0.4 - - - -
211D LYS* 1.3 93.1 - - - +
213D GLU* 1.3 67.8 + - - +
214D ILE 3.8 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 213 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B ILE* 5.4 5.2 - - + -
540B LEU* 3.9 25.2 - - + +
541B ASN* 3.2 27.4 - - - +
544B ALA* 4.8 17.0 - - + +
548B ARG* 5.3 11.1 + - - -
209D ARG 3.6 13.4 + - - +
210D LEU 3.2 2.9 + - - +
212D ASN* 1.3 84.2 - - + +
214D ILE* 1.3 60.8 + - - +
215D PRO* 3.5 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 214 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 3.9 29.4 - - + -
141D THR* 4.7 6.1 - - - +
143D ILE* 4.1 8.5 - - + -
164D ARG* 4.1 20.4 - - - +
166D ILE* 3.7 29.6 - - + -
210D LEU* 3.3 22.7 + - + +
211D LYS 3.2 5.0 + - - +
212D ASN 3.4 0.9 - - - -
213D GLU* 1.3 82.0 - - - +
215D PRO* 1.3 77.5 - - + +
216D ASN 3.8 0.2 + - - -
217D SER* 2.6 36.6 + - - +
----------------------------------------------------------
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