Contacts of the strand formed by residues 222 - 233 (chain D) in PDB entry 1UDY
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 222 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D TRP* 3.7 29.1 - - - -
167D ILE 3.3 9.2 - - - -
168D THR* 4.7 0.9 - - - -
211D LYS* 4.0 3.4 - - - +
212D GLU* 3.0 35.3 + - + +
214D ASN* 3.4 26.9 - - - +
217D GLN 5.6 1.8 - - - +
220D SER* 3.7 15.4 + - - +
221D ASP* 1.3 78.5 + - - +
223D ARG* 1.3 65.9 + - - +
3399D FAD 4.3 17.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D MET* 4.6 0.2 - - - -
166D TRP 4.0 4.0 - - - +
167D ILE* 2.9 35.6 + - - +
170D GLY 4.2 3.4 - - - -
171D GLY* 3.7 23.0 + - - +
172D LYS* 4.5 12.1 - - - +
208D ILE* 3.4 22.3 - - - +
209D GLY 2.8 24.7 + - - +
210D ARG* 2.9 27.2 + - - +
211D LYS* 3.9 22.6 - - - +
212D GLU* 4.0 8.1 - - - -
221D ASP* 3.1 28.5 + - - +
222D THR* 1.3 77.7 + - - +
224D GLY* 1.3 65.7 + - - +
225D ILE* 4.3 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163D GLN* 4.3 2.0 - - - -
164D LYS 3.4 14.4 - - - -
165D MET* 3.9 25.7 - - - +
209D GLY* 3.0 28.5 + - - -
210D ARG 4.8 1.0 + - - -
212D GLU* 4.8 3.0 + - - +
223D ARG* 1.3 75.2 - - - +
225D ILE* 1.3 69.7 + - - +
226D VAL* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D CYS* 4.5 4.7 - - - -
163D GLN* 3.3 5.4 + - - +
164D LYS* 2.9 35.5 + - + -
167D ILE* 4.3 14.1 - - + -
170D GLY* 3.7 20.6 - - - +
176D TYR* 3.5 34.8 - - + +
206D VAL* 4.2 13.0 - - + -
207D GLN 3.4 17.0 - - - +
208D ILE* 4.3 6.1 - - + -
209D GLY 4.7 0.2 - - - +
223D ARG 4.3 5.2 - - - +
224D GLY* 1.3 81.0 - - - +
226D VAL* 1.3 63.7 + - - +
227D PHE* 3.3 31.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D GLY 3.8 6.5 - - - +
163D GLN* 2.8 25.8 - - + +
205D GLY 3.4 2.4 - - - +
206D VAL* 3.8 1.7 - - - -
207D GLN* 2.9 60.7 + - + +
225D ILE* 1.3 71.9 - - - +
227D PHE* 1.3 77.0 + - - +
228D GLU* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D CYS* 4.8 9.6 - - - -
149D THR* 5.7 1.6 - - + -
160D ILE* 3.3 19.9 - - + +
161D ASN* 3.2 25.3 + - - -
162D GLY* 2.8 29.7 + - - +
164D LYS* 4.0 16.6 - - + -
176D TYR* 4.9 10.1 - + + -
178D LEU* 4.1 24.2 - - + -
199D VAL* 4.6 13.9 - - + -
205D GLY 3.6 3.4 - - - -
206D VAL* 4.5 13.2 - - + -
225D ILE* 3.3 41.5 - - + -
226D VAL* 1.3 77.3 - - - +
228D GLU* 1.3 60.3 + - - +
230D VAL* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D ASN* 3.8 6.5 - - - +
205D GLY* 3.0 26.9 + - - +
207D GLN* 3.7 28.3 + - - +
226D VAL* 4.0 10.1 - - + +
227D PHE* 1.3 69.5 - - - +
229D ASP* 1.3 78.2 + - - +
230D VAL* 2.9 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D GLU* 5.4 1.0 - - - +
159D ILE* 3.5 19.0 - - + +
160D ILE 3.4 5.9 + - - -
161D ASN* 3.2 30.9 + - - +
204D PRO 4.6 2.8 - - - +
228D GLU* 1.3 77.6 - - - +
230D VAL* 1.3 62.5 + - - +
231D ARG* 3.2 13.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
158D TYR 3.2 4.2 - - - +
159D ILE* 4.5 0.2 - - - -
160D ILE* 2.8 43.3 + - + +
199D VAL* 4.4 14.1 - - + -
203D THR* 3.9 21.1 - - + -
204D PRO 4.1 4.7 - - - -
205D GLY 3.6 30.1 - - - +
206D VAL* 4.3 4.7 - - + +
227D PHE* 3.6 32.8 - - + -
228D GLU 2.9 5.8 + - - +
229D ASP* 1.3 69.2 - - - +
231D ARG* 1.3 65.7 + - - +
232D VAL* 4.2 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D LYS* 3.6 17.2 - - - +
157D GLU* 2.6 46.8 + - - +
158D TYR 3.5 4.5 - - - -
159D ILE* 3.7 18.6 - - + +
203D THR* 3.8 20.6 + - + +
204D PRO 4.7 1.4 + - - -
229D ASP 3.2 11.9 + - - +
230D VAL* 1.3 72.2 - - - +
232D VAL* 1.3 64.7 + - - +
233D PRO* 4.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D GLU* 3.2 4.8 - - - +
158D TYR* 2.8 43.3 + - + +
160D ILE* 4.3 9.2 - - + -
197D PHE* 4.2 17.0 - - + -
198D ILE 4.4 4.5 - - - +
199D VAL* 3.6 29.4 - - + -
203D THR* 5.8 0.9 - - + +
230D VAL* 4.1 14.6 - - + +
231D ARG* 1.3 79.9 - - - +
233D PRO* 1.3 81.8 - - + +
236D ASN* 3.5 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ASP 4.1 9.0 - - - +
157D GLU* 4.3 2.0 - - + -
158D TYR* 5.0 0.7 - - - -
231D ARG 4.4 3.1 - - - +
232D VAL* 1.3 92.6 - - + +
234D LYS* 1.3 60.7 + - - +
235D GLU* 3.7 23.3 - - + +
236D ASN* 3.0 54.2 + - - +
237D VAL* 4.3 0.3 + - - +
----------------------------------------------------------
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