Contacts of the strand formed by residues 225 - 234 (chain D) in PDB entry 2Q41
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 LEU 225 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D GLY* 3.2 5.6 - - - -
195D TYR* 3.4 13.9 - - + +
196D ASP 3.9 3.1 - - - +
197D ALA 3.7 12.6 - - - +
198D VAL* 3.4 24.2 - - + -
221D VAL* 3.0 27.3 + - + +
222D ALA 3.8 4.9 - - - +
223D ARG 3.0 14.5 + - - +
224D ALA* 1.3 77.2 - - - +
226D ARG* 1.3 63.8 + - - +
227D PRO* 4.7 0.5 - - - +
229D GLY* 3.9 5.2 - - - +
230D VAL* 3.2 40.4 - - - +
231D VAL* 3.5 18.2 - - + -
256D PHE* 4.6 0.4 - - + -
282D THR* 3.8 19.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ILE* 3.9 23.4 - - - +
119D PRO* 4.7 15.4 + - - +
121D PRO* 5.5 0.8 - - - +
193D GLY* 3.3 23.5 - - - +
195D TYR 2.6 12.4 + - - +
196D ASP* 2.7 55.9 + - - +
225D LEU* 1.3 75.8 - - - +
227D PRO* 1.3 86.5 + - + +
228D GLY* 3.9 18.8 + - - -
229D GLY* 2.8 10.4 + - - +
282D THR* 2.7 18.1 + - - -
285D PRO* 5.3 8.9 - - - +
287D VAL* 6.0 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193D GLY* 5.2 3.8 - - - +
225D LEU 4.7 0.7 - - - +
226D ARG* 1.3 109.8 + - + +
228D GLY* 1.3 57.7 + - - +
229D GLY 3.1 0.2 - - - -
282D THR* 3.5 2.9 - - - +
283D GLU* 3.0 17.7 - - + +
284D GLY* 4.6 4.7 - - - -
285D PRO* 4.0 11.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D ILE* 4.2 1.2 - - - +
226D ARG* 3.9 13.1 + - - -
227D PRO* 1.3 73.1 - - - +
229D GLY* 1.3 63.8 + - - +
230D VAL* 3.9 2.8 - - - +
281D SER* 4.7 1.3 - - - -
282D THR* 2.5 18.1 + - - -
283D GLU 2.7 11.0 + - - -
285D PRO* 4.0 26.9 - - - -
287D VAL* 3.8 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D ASP 3.5 14.6 - - - -
225D LEU* 3.9 10.7 - - - +
226D ARG* 2.8 24.7 + - - -
227D PRO 3.1 1.4 + - - -
228D GLY* 1.3 80.0 - - - +
230D VAL* 1.3 59.1 + - - -
281D SER* 3.0 3.5 - - - -
282D THR* 2.7 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D PRO* 4.3 22.7 - - + +
118D ILE* 3.4 32.8 - - + -
196D ASP 3.2 10.7 + - - +
197D ALA* 3.4 12.6 - - + -
198D VAL 3.1 24.3 + - - -
225D LEU* 3.2 13.1 - - - +
228D GLY 3.9 4.3 - - - +
229D GLY* 1.3 79.9 - - - +
231D VAL* 1.3 60.0 + - - +
280D CYS 3.0 7.2 - - - +
281D SER* 3.9 6.5 - - - -
287D VAL* 4.4 3.8 - - + -
289D PHE* 3.4 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D PRO* 5.1 0.7 - - - -
198D VAL* 3.5 9.0 - - + +
200D VAL* 4.6 6.7 - - + -
218D PHE* 4.9 7.6 - - + -
221D VAL* 3.3 30.1 - - + -
225D LEU* 3.5 2.0 - - + -
230D VAL* 1.3 79.3 - - - +
232D CYS* 1.3 64.4 - - - +
233D THR* 3.7 19.1 - - - +
256D PHE* 3.2 41.5 - - + -
278D MSE 3.2 5.7 - - + +
279D LEU* 3.2 6.9 - - - +
280D CYS* 2.7 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ILE* 3.5 32.2 - - - +
113D LEU* 4.9 1.8 - - - -
114D PRO* 3.5 28.7 - - + -
198D VAL 3.1 9.2 + - - +
199D ILE* 3.4 8.5 - - + +
200D VAL 2.9 23.2 + - - -
231D VAL* 1.3 75.7 - - - +
233D THR* 1.3 62.1 + - - +
277D PHE* 4.3 11.2 - - - -
278D MSE 3.1 2.7 - - - -
279D LEU* 3.6 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D VAL* 3.0 45.5 - - + +
202D SER* 4.9 3.6 - - - +
212D LEU 4.5 12.6 - - - +
213D PHE* 5.1 4.7 - - + -
218D PHE* 4.0 17.3 - - + -
231D VAL* 3.7 11.6 - - - +
232D CYS* 1.3 75.0 - - - +
234D GLN* 1.3 77.1 + - + +
235D ALA* 4.0 1.0 - - + +
248D ILE* 6.4 0.9 - - + -
277D PHE* 3.2 9.0 - - - -
278D MSE 2.9 37.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D TYR* 3.6 24.6 + - + +
110D ILE* 4.6 0.8 - - - +
200D VAL 3.5 11.1 + - - +
202D SER* 3.8 11.2 + - - +
203D SER* 3.8 6.0 - - - -
204D ASP* 3.2 31.7 + - - +
213D PHE* 3.7 18.4 - - - -
233D THR* 1.3 87.2 - - + +
235D ALA* 1.3 59.0 + - - +
236D GLU* 3.2 39.2 + - - +
275D ILE* 3.9 26.9 - - + +
276D GLY 3.5 5.2 - - - -
277D PHE* 3.8 7.6 - - + -
----------------------------------------------------------
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