Contacts of the strand formed by residues 217 - 224 (chain D) in PDB entry 1IAS
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 GLY 217 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D LYS* 3.4 5.7 - - - +
214D GLY 3.3 25.1 + - - +
215D ARG 3.5 2.0 - - - -
216D PHE* 1.3 89.9 - - - +
218D GLU* 1.3 66.0 + - - +
233D ILE 3.6 9.0 - - - -
235D SER* 3.9 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D SER* 2.9 25.6 + - - -
212D GLY 3.4 5.6 - - - +
213D LYS* 3.4 37.8 - - + -
216D PHE* 3.7 2.6 - - - -
217D GLY* 1.3 78.5 - - - +
219D VAL* 1.3 64.8 + - - +
220D TRP* 3.4 32.5 + - + +
231D VAL 3.7 0.3 - - - +
232D LYS* 3.4 2.9 - - - +
233D ILE* 2.8 35.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D SER* 3.7 0.9 + - - -
211D ILE* 2.7 42.0 + - + -
212D GLY* 2.8 20.8 + - - +
216D PHE* 3.8 23.8 - - + -
218D GLU* 1.3 75.5 - - - +
220D TRP* 1.3 76.4 + - - +
230D ALA* 4.6 13.0 - - + -
231D VAL 3.5 7.4 - - - +
232D LYS* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D LEU* 4.0 28.9 - - + -
208D GLN 4.5 3.8 - - - -
209D GLU* 3.4 29.2 - - - -
210D SER* 3.8 15.9 - - - -
211D ILE* 3.8 5.9 - - - +
218D GLU* 3.4 47.5 + - + +
219D VAL* 1.3 81.7 - - - +
221D ARG* 1.3 64.8 + - - +
222D GLY 3.9 0.2 - - - -
230D ALA* 3.4 7.1 - - - +
231D VAL* 2.7 44.1 + - + +
233D ILE* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D SO4 2.8 44.0 + - - -
207D LEU* 4.1 0.9 - - - -
208D GLN* 2.8 47.6 + - + +
209D GLU* 2.3 51.8 + - - +
211D ILE* 3.3 21.9 - - + +
220D TRP* 1.3 74.5 - - - +
222D GLY* 1.3 62.7 + - - +
223D LYS* 3.4 11.9 - - - +
228D GLU* 2.6 24.2 + - - +
229D VAL 3.7 4.3 - - - +
282D TYR* 3.4 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 222 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D ILE* 4.4 7.4 - - - -
206D VAL 3.5 11.2 - - - -
207D LEU* 4.1 7.6 - - - -
208D GLN* 3.9 2.7 - - - -
220D TRP 3.8 1.6 + - - -
221D ARG* 1.3 75.9 - - - +
223D LYS* 1.3 61.3 + - - +
228D GLU* 3.4 4.3 - - - +
229D VAL* 2.6 45.4 + - - +
231D VAL* 4.7 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 223 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D SO4 2.9 36.3 + - - -
205D ILE* 3.5 4.4 - - - +
206D VAL* 2.8 42.1 + - + +
208D GLN* 3.6 25.0 + - + +
221D ARG* 3.4 19.5 - - - +
222D GLY* 1.3 78.8 - - - +
224D TRP* 1.3 61.5 + - - +
225D ARG 3.9 1.7 + - - -
226D GLY* 3.5 30.7 - - - +
227D GLU 3.1 7.6 - - - +
228D GLU* 4.1 13.5 - - + -
229D VAL* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ILE* 3.5 40.2 - - + -
175D THR* 3.9 3.8 - - + -
176D THR* 3.7 6.5 - - - -
177D LEU* 3.5 48.0 - - + -
180D LEU* 4.1 11.7 - - + -
200D THR* 5.8 0.4 - - + -
201D ILE* 3.6 33.5 - - + +
204D THR* 2.6 39.1 - - + +
205D ILE* 4.1 12.1 - - + +
223D LYS* 1.3 73.8 - - - +
225D ARG* 1.3 105.7 + - + +
227D GLU* 2.8 22.2 + - - +
229D VAL* 4.9 6.6 - - + +
----------------------------------------------------------
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