Contacts of the strand formed by residues 242 - 250 (chain D) in PDB entry 3H90
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 242 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D GLY* 5.8 5.6 - - - -
76D GLY* 5.9 1.1 - - - -
238D GLN* 3.1 4.0 - - - +
239D SER* 3.1 34.1 + - - +
240D GLY 3.4 0.2 - - - -
241D PRO* 1.3 88.5 - - + +
243D ARG* 1.3 61.8 + - - +
244D PHE* 3.5 26.5 + - + -
277D GLY 3.8 22.2 - - - +
279D ASP* 5.0 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D LEU* 3.6 33.4 - - + -
214D GLU* 2.9 38.3 + - - -
238D GLN* 3.5 32.9 + - + +
241D PRO 3.8 5.1 + - - +
242D THR* 1.3 72.8 - - - +
244D PHE* 1.3 57.7 + - - +
245D ILE* 4.7 5.4 - - + -
275D PHE* 3.5 30.7 - - - +
276D PRO* 5.2 5.7 + - - +
278D SER* 3.3 24.2 + - - +
279D ASP* 2.7 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 6.0 1.3 - - + -
235B ARG* 4.3 2.9 - - - -
246B GLN* 5.7 1.8 - - - -
73D PHE* 3.7 28.9 - + + -
74D GLY* 3.8 21.3 - - - -
210D LEU* 5.0 0.2 - - - +
235D ARG 4.5 0.9 - - - -
236D THR* 3.4 3.7 - - - -
237D ARG* 2.6 71.9 + - + +
239D SER* 3.8 27.1 - - - -
242D THR* 3.5 24.0 - - - -
243D ARG* 1.3 72.5 - - - +
245D ILE* 1.3 67.4 + - - +
246D GLN* 5.7 1.6 - - + -
279D ASP* 3.4 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210D LEU* 4.7 4.3 - - + -
218D ILE* 3.6 37.2 - - + -
234D LEU* 4.1 18.6 - - + -
235D ARG 3.6 3.1 - - - -
236D THR* 4.3 6.1 - - + -
243D ARG* 4.7 5.8 - - + -
244D PHE* 1.3 81.8 - - - +
246D GLN* 1.3 68.5 + - - +
247D ILE* 4.9 5.8 - - + +
271D ILE* 3.8 25.4 - - + -
275D PHE* 5.1 3.6 - - + -
278D SER* 4.4 16.4 - - - +
279D ASP 2.8 8.5 + - - +
280D VAL* 3.0 26.3 - - + -
281D ILE* 2.8 27.6 + - - +
282D ILE* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 3.6 28.5 - - + -
237B ARG* 5.4 2.0 - - - +
244B PHE* 5.8 2.4 - - - -
246B GLN* 3.6 24.4 - - - +
281B ILE* 3.8 30.9 - - + +
233D ASP 4.2 1.3 - - - -
234D LEU* 3.0 9.4 - - - +
235D ARG* 2.9 68.9 + - + +
237D ARG* 5.5 1.4 - - - +
244D PHE* 5.7 0.9 - - + -
245D ILE* 1.3 79.2 - - - +
247D ILE* 1.3 61.2 + - - +
248D HIS* 5.7 0.9 - - + -
281D ILE* 3.3 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 4.6 0.5 - - - +
218D ILE* 4.8 2.5 - - + -
219D ILE* 4.7 7.4 - - + -
222D VAL* 3.8 25.4 - - + -
231D ALA* 3.7 22.4 - - + -
232D HIS 4.8 1.1 - - - +
233D ASP 3.1 13.9 - - - +
234D LEU* 3.8 29.2 - - + -
245D ILE* 5.1 5.4 - - + -
246D GLN* 1.3 76.8 - - - +
248D HIS* 1.3 78.4 + - - +
249D LEU* 4.1 12.1 - - + -
271D ILE* 5.5 1.6 - - + -
281D ILE 3.2 3.8 + - - +
282D ILE* 3.6 28.7 - - + -
283D HIS 2.9 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B ILE* 4.2 14.4 - - + +
231D ALA* 3.1 28.1 - - - +
232D HIS* 3.1 30.0 + + + +
233D ASP* 3.2 34.5 + - + +
246D GLN* 5.7 0.4 - - + -
247D ILE* 1.3 83.4 - - - +
249D LEU* 1.3 60.0 + - - +
250D GLU 4.1 0.2 - - - -
283D HIS* 3.2 32.9 - + + +
285D ASP* 3.1 4.1 + - - +
292D ZN 2.4 30.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D VAL* 3.4 33.0 - - + -
228D VAL* 4.1 14.1 - - + -
230D GLY 3.6 2.5 - - - +
231D ALA* 4.4 2.2 - - + -
247D ILE* 4.1 9.1 + - + -
248D HIS* 1.3 77.0 - - - +
250D GLU* 1.3 62.5 + - - +
251D MET* 3.4 30.1 + - + -
263D VAL* 4.4 0.7 - - + -
264D ALA* 4.1 5.8 - - - -
267D VAL* 3.9 28.0 - - + -
282D ILE* 3.7 26.9 - - + -
283D HIS 2.9 8.0 + - - +
284D GLN* 3.5 3.4 - - + +
285D ASP* 2.8 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D VAL* 3.8 1.4 - - - -
229D SER* 2.9 35.5 + - - +
230D GLY* 2.7 36.0 + - - +
231D ALA 3.8 6.1 + - - +
232D HIS* 2.9 44.3 + - + +
249D LEU* 1.3 73.0 - - - +
251D MET* 1.3 63.2 + - - +
285D ASP* 3.1 6.5 - - + +
286D PRO 3.9 12.1 - - - +
289D VAL* 4.4 19.1 - - + +
----------------------------------------------------------
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