Contacts of the helix formed by residues 225 - 237 (chain D) in PDB entry 4GKH
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 ARG 225 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D HIS* 3.6 23.2 + - + +
191D ASP* 2.7 50.7 + - + +
193D VAL* 3.6 48.9 - - + +
195D THR* 4.5 0.4 - - - -
223D ALA 3.6 0.4 + - - -
224D ASP* 1.3 76.2 + - - +
226D TYR* 1.3 79.8 + - + +
227D GLN 3.1 1.7 + - - -
228D ASP 3.2 10.3 + - - -
229D LEU* 3.2 16.5 + - + +
251D TYR* 2.9 36.0 + - - +
253D ILE* 4.6 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D ASP* 2.8 20.3 + - - +
225D ARG* 1.3 86.7 - - + +
227D GLN* 1.3 59.9 + - - +
228D ASP 3.1 0.2 - - - -
229D LEU* 4.1 17.3 - - + -
230D ALA* 2.8 35.6 + - - +
248D PHE* 3.6 28.3 - + - -
253D ILE* 4.0 16.1 - - + +
255D ASN 4.9 0.2 + - - -
256D PRO* 3.6 6.8 - - - +
257D ASP* 2.8 42.7 + - + +
260D LYS* 3.5 26.9 - - + +
261D LEU* 3.8 22.9 - - + -
264D HIS* 3.5 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D SER* 6.4 0.2 - - - -
148D ARG* 5.8 3.1 - - - +
195D THR* 4.2 14.4 - - + +
197D GLY* 3.0 40.8 + - - -
219D ARG* 3.8 12.1 - - - +
223D ALA* 4.3 9.6 - - + -
224D ASP 3.0 16.4 + - - +
226D TYR* 1.3 78.6 - - - +
228D ASP* 1.3 60.4 + - - +
230D ALA* 4.7 0.7 - - - +
231D ILE* 3.5 29.3 - - - +
264D HIS* 3.4 32.0 + - + +
267D LEU* 4.3 13.2 - - - +
268D ASP* 4.9 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU* 3.7 16.2 - - + -
131D LEU* 3.6 5.0 - - - +
132D HIS* 2.9 32.2 + - + +
195D THR* 3.2 9.1 - - - -
196D HIS* 3.0 21.7 + - - -
197D GLY* 3.1 26.0 + - - -
199D PHE* 3.7 22.7 + - + +
225D ARG 3.2 1.4 + - - -
226D TYR 3.1 0.4 - - - -
227D GLN* 1.3 79.2 - - - +
229D LEU* 1.3 66.8 - - - +
230D ALA 3.2 1.3 + - - -
231D ILE* 3.4 1.7 + - - -
232D LEU* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU* 3.7 24.2 - - + +
132D HIS* 4.9 0.2 - - + -
225D ARG* 3.2 29.2 + - + +
226D TYR* 4.1 12.1 - - + -
228D ASP* 1.3 79.1 - - - +
230D ALA* 1.3 56.8 + - - +
232D LEU* 4.0 2.0 - - - +
233D TRP* 2.9 33.1 + - - +
247D LEU* 4.2 13.8 - - + +
248D PHE* 3.9 26.9 - - + -
251D TYR* 3.8 33.7 - - + -
253D ILE* 3.7 25.4 - - + -
261D LEU* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D TYR* 2.8 25.3 + - + +
227D GLN 4.7 0.7 - - - +
229D LEU* 1.3 74.0 - - - +
231D ILE* 1.3 58.5 + - + +
233D TRP* 3.3 1.6 + - - +
234D ASN 2.9 25.3 + - - -
261D LEU* 3.6 31.4 - - + +
264D HIS* 3.7 21.1 - - + -
265D LEU* 3.3 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D GLY 3.7 12.3 - - - +
198D ASP* 4.1 11.4 - - - +
199D PHE 3.7 24.5 - - - +
200D SER* 3.8 13.9 - - - +
227D GLN* 3.5 38.3 + - - +
228D ASP 3.4 3.2 + - - +
229D LEU 3.4 0.2 - - - -
230D ALA* 1.3 78.6 - - + +
232D LEU* 1.3 62.4 + - - +
234D ASN* 3.5 6.8 + - - +
235D CYS* 3.2 25.3 + - - -
264D HIS* 5.2 2.7 - - + +
265D LEU* 4.6 3.1 - - + -
268D ASP* 3.6 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D LEU* 4.1 22.2 - - + +
128D LEU* 5.0 3.4 - - + -
199D PHE* 3.4 43.2 + - + +
200D SER 4.6 1.3 - - - -
201D LEU* 3.7 36.1 - - + +
204D LEU* 5.0 2.2 - - + -
228D ASP 3.2 14.6 + - - +
229D LEU* 4.0 2.7 - - - +
231D ILE* 1.3 77.6 - - - +
233D TRP* 1.3 65.7 + - - +
235D CYS* 3.1 4.4 + - - +
236D LEU* 3.1 25.4 + - + +
247D LEU* 3.7 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D GLU* 6.0 0.7 - - - -
229D LEU 2.9 20.9 + - - +
230D ALA* 3.5 4.5 - - - +
232D LEU* 1.3 76.1 - - - +
234D ASN* 1.3 74.3 + - - +
236D LEU* 3.3 5.2 + - - -
237D GLY 3.3 6.6 + - - -
244D GLN* 2.9 79.8 + - + +
245D LYS* 4.8 0.8 - - - +
247D LEU* 3.8 11.4 - - + +
248D PHE* 3.2 35.9 - + + -
258D MSE 5.5 6.1 - - + +
261D LEU* 3.9 30.7 - - + -
262D GLN* 5.6 2.5 - - - -
265D LEU* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ASP* 3.0 35.2 + - - +
230D ALA 2.9 17.1 + - - +
231D ILE* 3.5 7.4 - - - +
233D TRP* 1.3 87.5 - - - +
235D CYS* 1.3 63.9 + - - +
237D GLY* 3.1 14.4 + - - -
238D GLU* 4.2 5.0 + - - +
244D GLN* 4.4 1.2 + - - +
265D LEU* 3.6 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 235 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D SER* 3.7 30.1 - - - -
201D LEU* 3.6 30.2 - - + +
231D ILE* 3.2 24.7 + - - -
232D LEU* 3.1 9.3 + - - +
234D ASN* 1.3 76.5 - - - +
236D LEU* 1.3 61.5 + - - +
237D GLY 3.3 0.9 + - - -
238D GLU* 3.4 18.5 + - - +
239D PHE* 3.6 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU* 3.8 28.5 - - + -
121D VAL* 3.9 22.7 - - + -
124D LEU* 4.8 3.1 - - + -
201D LEU* 4.4 8.7 - - + -
232D LEU* 3.1 27.0 + - + +
233D TRP* 3.6 7.6 - - - +
234D ASN 3.2 0.4 - - - -
235D CYS* 1.3 74.6 - - - +
237D GLY* 1.3 66.2 + - - +
238D GLU 3.1 0.2 - - - -
239D PHE* 2.9 16.9 + - + +
240D SER 3.0 15.8 + - - +
243D LEU* 3.9 26.4 - - + +
244D GLN* 3.9 13.5 - - + +
247D LEU* 4.0 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233D TRP 3.3 4.9 + - - -
234D ASN 3.1 11.1 + - - -
236D LEU* 1.3 78.6 - - - +
238D GLU* 1.3 61.1 + - - +
239D PHE 3.4 1.0 + - - -
240D SER* 4.0 9.6 + - - -
241D PRO* 4.8 5.6 - - - +
244D GLN* 3.3 25.5 - - - +
----------------------------------------------------------
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