Contacts of the helix formed by residues 242 - 257 (chain S) in PDB entry 1RZZ
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 242 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237S GLN* 2.9 18.7 + - - -
240S ASP 3.3 1.4 + - - -
241S ARG* 1.3 74.1 - - - +
243S THR* 1.3 62.3 + - - -
244S ALA 3.0 8.2 + - - -
245S ALA* 3.1 10.2 + - - +
246S GLU* 3.3 14.2 + - - +
115T VAL* 3.7 7.2 - - - -
117T ARG* 3.5 24.2 - - - -
231T ASP* 4.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 243 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R TYR* 3.4 13.9 + - - -
229S PHE* 3.8 26.0 - - + -
242S GLY* 1.3 71.2 - - - -
244S ALA* 1.3 63.1 + - - +
246S GLU* 3.5 1.2 + - - +
247S ARG* 2.9 57.7 + - - +
113T SER 3.5 13.2 + - - +
114T TRP* 4.2 1.1 - - - -
115T VAL* 3.4 12.9 - - - +
231T ASP* 2.8 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226S VAL* 3.7 12.1 - - + +
229S PHE* 3.5 31.4 - - + +
231S GLY* 3.6 22.7 - - - -
237S GLN* 3.6 21.7 - - - +
242S GLY 3.0 1.0 - - - -
243S THR* 1.3 82.1 - - - +
245S ALA* 1.3 64.5 + - - +
247S ARG* 3.9 0.2 - - - +
248S ALA* 3.1 22.6 + - - +
262S MET* 4.9 0.4 - - + -
231T ASP* 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R PHE* 5.5 0.4 - - - -
237S GLN* 3.3 19.1 + - + +
241S ARG* 3.9 17.9 - - + -
242S GLY 3.1 6.2 + - - +
244S ALA* 1.3 78.8 - - - +
246S GLU* 1.3 57.8 + - - +
248S ALA* 3.5 4.0 + - - +
249S ALA* 2.9 29.6 + - - +
262S MET* 3.6 32.8 - - + +
2008S U10 4.6 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R PHE* 3.2 34.6 - - + +
8R LYS* 2.9 17.5 + - - -
9R TYR* 2.6 33.8 + - + +
241S ARG* 2.6 46.3 + - - +
242S GLY 3.3 13.0 - - - +
243S THR 4.0 1.3 - - - +
244S ALA 3.3 1.0 - - - -
245S ALA* 1.3 74.1 - - - +
247S ARG* 1.3 62.6 + - - +
249S ALA* 3.7 0.9 - - - +
250S LEU* 2.8 36.6 + - - +
81T GLU* 4.3 0.2 - - - +
115T VAL* 3.3 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 247 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9R TYR* 3.8 16.0 - - + -
111R LEU* 2.8 49.9 + - + +
113R ILE* 3.9 16.6 - - + +
226S VAL* 4.5 2.2 - - + -
229S PHE* 3.0 36.8 - - - -
243S THR* 2.9 29.1 + - - +
244S ALA 3.9 3.1 - - - +
246S GLU* 1.3 73.1 - - - +
248S ALA* 1.3 61.5 + - - +
251S PHE* 2.9 30.3 + - - +
110T GLY 4.5 2.0 - - - -
111T PRO* 2.9 33.9 + - - +
113T SER* 2.8 34.4 + - - +
235T GLY* 3.8 8.7 - - - -
238T ALA* 4.0 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113R ILE* 5.8 0.7 - - - -
222S THR* 3.5 28.7 - - + -
226S VAL* 4.2 13.2 - - + +
244S ALA 3.1 17.3 + - - +
245S ALA* 3.7 6.3 - - - +
247S ARG* 1.3 78.4 - - - +
249S ALA* 1.3 62.9 + - - +
251S PHE* 3.3 10.0 + - - +
252S TRP* 3.3 22.7 - - - -
262S MET* 5.5 0.4 - - + -
2008S U10 3.6 19.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R LEU* 4.8 0.9 - - + -
5R PHE* 4.4 13.5 - - + -
245S ALA 2.9 17.9 + - - +
246S GLU* 3.7 7.2 - - - +
248S ALA* 1.3 76.7 - - - +
250S LEU* 1.3 57.5 + - - +
252S TRP* 3.1 4.0 + - - -
253S ARG* 3.0 23.2 + - - +
259S ASN* 3.2 32.0 - - - +
260S ALA 3.9 4.9 - - - +
261S THR* 6.0 0.2 - - - -
2008S U10 3.5 16.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 250 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R LEU* 3.6 28.0 - - + -
5R PHE* 4.2 5.4 - - + -
6R GLU* 3.6 37.2 - - + +
9R TYR* 3.2 50.7 - - + -
111R LEU* 4.1 11.2 - - + -
246S GLU 2.8 23.0 + - - +
247S ARG 4.0 2.7 - - - +
249S ALA* 1.3 71.2 - - - +
251S PHE* 1.3 65.4 + - - +
253S ARG* 3.8 6.5 - - - -
254S TRP* 3.0 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 251 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R GLU* 3.7 37.0 - - + -
107R ILE* 3.7 16.3 - - + +
108R CYS* 3.7 11.4 - - - -
111R LEU* 3.6 11.2 - - + +
113R ILE* 3.8 20.9 - - + -
117R ILE* 3.3 39.7 - - + -
222S THR* 5.9 0.7 - - + -
247S ARG 2.9 18.4 + - - +
248S ALA* 3.5 7.4 - - - +
249S ALA 3.2 0.4 - - - -
250S LEU* 1.3 77.2 - - - +
252S TRP* 1.3 93.1 + + - +
254S TRP 4.0 0.7 - - - -
255S THR* 2.7 51.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 252 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104R GLU* 4.1 1.3 - - - -
117R ILE* 3.6 22.2 - - + +
2006R BPH 3.5 43.3 - - - -
218S MET* 3.6 36.8 - - + -
222S THR* 3.0 23.9 + - - +
248S ALA 3.3 21.8 - - - -
249S ALA 3.1 6.1 + - - +
251S PHE* 1.3 102.7 - + - +
253S ARG* 1.3 60.6 + - - +
255S THR* 4.2 4.3 - - + -
256S MET* 2.8 51.8 + - + +
258S PHE 3.2 17.6 - - - +
2008S U10 3.3 35.5 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 253 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1R ALA 4.0 11.4 + - - -
3R LEU* 3.3 32.2 - - - +
6R GLU* 3.8 15.3 - - - -
28R PRO* 3.0 48.4 - - + +
249S ALA 3.0 11.9 + - - +
250S LEU* 4.0 10.1 - - - +
252S TRP* 1.3 75.6 - - - +
254S TRP* 1.3 60.6 + - + +
257S GLY* 3.0 33.7 + - - +
258S PHE* 3.5 13.1 + - - +
259S ASN* 3.1 28.5 + - - +
40T TYR* 2.9 33.9 + - - -
42T LEU* 3.8 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 254 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R GLU* 2.6 27.0 + - - -
9R TYR* 3.5 33.0 - - + -
10R ARG* 3.3 20.4 - - - -
25R TRP* 3.4 21.4 - + - +
28R PRO 3.3 17.7 - - - -
29R PHE* 3.4 1.9 - - - -
30R TYR* 2.8 26.7 + + + +
103R ARG* 2.7 27.5 + - - -
107R ILE* 3.9 26.9 - - + -
110R LYS* 3.4 28.0 - - + -
111R LEU* 3.7 27.8 - - + -
250S LEU* 3.0 30.7 + - + +
251S PHE 4.1 0.9 - - - +
253S ARG* 1.3 83.4 - - + +
255S THR* 1.3 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 255 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R PHE* 4.0 3.5 - - - -
100R TRP* 3.3 33.4 - - + +
103R ARG* 3.1 31.9 + - - +
104R GLU* 3.8 23.5 - - + +
107R ILE* 3.3 15.1 - - - +
2006R BPH 4.0 5.6 - - - +
251S PHE* 2.7 34.9 + - - -
252S TRP* 3.2 11.4 + - + -
254S TRP* 1.3 78.3 - - - +
256S MET* 1.3 60.0 + - - +
257S GLY 3.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 256 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29R PHE* 3.4 14.9 - - - -
100R TRP* 4.7 0.4 - - + -
2006R BPH 3.5 26.2 - - - +
218S MET* 4.3 0.9 - - + -
252S TRP* 2.8 32.0 + - + +
255S THR* 1.3 78.1 - - + +
257S GLY* 1.3 55.6 + - - +
258S PHE* 3.5 45.2 + - + +
2008S U10 3.6 85.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 257 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R PRO* 3.6 21.8 - - - +
29R PHE* 3.5 23.9 - - - -
252S TRP 3.5 0.2 + - - -
253S ARG* 3.0 29.0 + - - -
255S THR 3.7 0.2 - - - -
256S MET* 1.3 76.9 - - - +
258S PHE* 1.3 59.1 + - - +
----------------------------------------------------------
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