Contacts of the helix formed by residues 222 - 240 (chain A) in PDB entry 2PWA
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 222 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASN* 3.8 1.6 - - - -
182A ALA* 4.2 0.7 - - - -
192A PHE* 3.4 19.0 - - - -
205A GLY* 2.8 16.7 + - - +
221A SER* 1.3 76.4 - - - +
223A THR* 1.3 63.6 + - - -
224A SER 3.0 2.0 - - - -
225A MET* 2.9 17.6 + - - -
226A ALA 3.3 7.3 + - - -
2002A B2A 3.2 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 223 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ALA* 3.5 2.6 - - - +
159A ALA* 3.8 2.7 - - + -
160A GLY 3.0 36.4 + - - +
161A ASN* 2.8 23.2 + - - +
180A VAL 3.8 15.9 - - - +
181A GLY* 4.2 1.1 - - - -
182A ALA* 3.8 18.8 - - + +
192A PHE* 3.6 1.0 - - + -
193A SER* 3.7 23.3 - - - +
222A GLY* 1.3 72.1 - - - -
224A SER* 1.3 59.7 + - - +
226A ALA* 3.2 3.0 + - - +
227A THR* 2.8 29.8 + - - -
2001A B2A 2.9 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 224 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS* 3.2 17.7 + - - -
73A CYS* 3.4 5.4 - - - -
132A SER* 2.7 36.7 + - - +
222A GLY* 3.0 0.4 - - - -
223A THR* 1.3 77.6 - - - +
225A MET* 1.3 66.7 + - - +
228A PRO* 2.8 13.6 - - - +
2001A B2A 2.5 38.8 + - - -
2002A B2A 2.8 14.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 225 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A HIS* 4.2 2.5 - - + +
72A HIS* 3.8 20.4 - - + +
73A CYS* 3.8 12.3 - - - -
76A THR* 3.9 1.8 - - - +
204A PRO 3.6 2.0 - - - -
205A GLY 3.9 2.2 - - - +
208A ILE* 3.7 26.5 - - + -
220A ILE* 3.5 34.3 - - + +
221A SER 3.5 17.0 - - - -
222A GLY 2.9 8.9 + - - +
224A SER* 1.3 92.7 - - - +
226A ALA* 1.3 63.1 + - - +
227A THR 3.4 0.2 - - - -
228A PRO* 3.3 13.1 - - - +
229A HIS* 2.9 22.5 + - - -
2002A B2A 3.1 32.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A VAL* 3.7 9.9 - - + +
181A GLY 3.3 18.8 - - - +
182A ALA* 3.9 11.7 - - + -
203A GLY* 3.3 26.7 - - - +
204A PRO 3.1 12.5 + - - +
222A GLY 3.3 2.0 + - - -
223A THR* 3.2 7.7 + - - +
225A MET* 1.3 78.1 - - - +
227A THR* 1.3 66.1 + - - +
229A HIS* 3.0 16.1 + - - +
230A VAL* 3.3 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 227 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A SER* 3.7 12.6 - - - +
131A LEU 4.0 3.6 - - - +
132A SER* 3.6 11.0 - - - +
156A ALA* 3.5 35.7 - - + +
157A VAL* 3.5 8.9 + - - +
158A ALA* 3.0 21.4 - - - +
180A VAL* 3.8 10.6 - - - +
223A THR 2.8 20.9 + - - -
226A ALA* 1.3 75.8 - - - +
228A PRO* 1.3 65.4 - - - +
230A VAL* 3.0 8.1 + - - +
231A ALA* 2.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 228 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A CYS* 3.3 31.9 - - + +
76A THR* 3.8 17.2 - - + +
77A VAL* 3.4 19.6 - - + +
130A SER* 3.5 11.9 - - - +
132A SER* 3.6 4.7 - - - +
224A SER 2.8 28.5 - - - +
225A MET* 3.3 17.7 - - - +
227A THR* 1.3 85.8 - - + +
229A HIS* 1.3 59.1 + - - +
231A ALA* 3.7 1.3 - - + -
232A GLY* 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 6.3 0.4 - - - +
9A GLY* 3.8 26.8 - - - -
10A LEU* 4.1 6.9 + - + +
13A ILE* 3.7 30.8 - - + +
76A THR* 3.4 18.8 - - + +
82A TYR 5.7 0.2 + - - -
84A VAL* 3.8 25.0 - - + +
204A PRO* 3.2 32.5 + - + -
208A ILE* 3.8 18.7 - - + +
225A MET 2.9 21.0 + - - -
226A ALA 3.0 8.7 + - - +
228A PRO* 1.3 78.6 - - - +
230A VAL* 1.3 61.3 + - + +
233A LEU* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MET* 4.4 2.7 - - + -
156A ALA* 4.4 7.0 - - + -
178A CYS* 4.2 19.7 - - - -
180A VAL* 3.7 39.3 - - + -
201A ILE* 3.9 14.6 - - + -
202A PHE 4.7 2.2 - - - +
203A GLY* 4.7 2.2 - - - -
226A ALA 3.3 2.7 + - - +
227A THR 3.0 8.3 + - - +
229A HIS* 1.3 76.3 - - - +
231A ALA* 1.3 60.0 + - - +
233A LEU* 3.2 6.5 + - - +
234A ALA* 2.8 28.2 + - - +
252A ILE* 4.1 14.7 - - + +
273A ALA* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A VAL* 4.4 4.9 - - + -
77A VAL* 4.4 3.6 - - + -
128A VAL* 3.6 26.3 - - + +
130A SER* 3.5 35.4 - - - +
154A MET* 5.1 0.2 - - - -
156A ALA* 4.2 10.2 - - + +
227A THR 2.9 9.5 + - - +
228A PRO* 3.9 3.6 - - + +
230A VAL* 1.3 75.8 - - - +
232A GLY* 1.3 63.2 + - - +
234A ALA* 3.3 5.6 + - - +
235A ALA* 3.0 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 4.0 22.1 - - - +
84A VAL* 3.5 15.9 - - - -
85A ALA* 3.5 8.4 - - - +
228A PRO 2.9 17.2 + - - -
229A HIS 3.9 0.7 - - - -
231A ALA* 1.3 75.4 - - - +
233A LEU* 1.3 58.9 + - - +
235A ALA* 3.2 1.8 + - - -
236A TYR* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 4.6 10.8 - - + -
23A TYR* 6.1 0.2 - - - +
84A VAL* 3.4 10.2 - - + +
229A HIS 2.9 18.5 + - - +
230A VAL* 3.2 5.8 + - - +
232A GLY* 1.3 75.7 - - - +
234A ALA* 1.3 63.1 + - - +
236A TYR* 3.2 10.2 + - + +
237A LEU* 2.9 46.8 + - + +
252A ILE* 4.0 20.9 - - + -
273A ALA* 3.9 27.6 - - + -
274A TYR 3.9 17.5 - - - +
275A ASN* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.3 2.0 - - + -
154A MET* 3.9 39.9 - - + -
230A VAL 2.8 13.8 + - - +
231A ALA 3.5 7.9 - - - +
233A LEU* 1.3 77.4 - - - +
235A ALA* 1.3 56.9 + - - +
237A LEU* 3.2 5.1 + - - +
238A MET* 2.8 39.5 + - - +
243A THR* 4.9 0.2 - - - +
248A ALA* 4.2 6.3 - - + -
252A ILE* 4.0 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLY* 4.4 0.7 - - - -
33A SER* 3.4 26.1 + - - +
35A VAL* 3.8 21.1 - - + -
85A ALA* 4.3 8.3 - - + -
88A THR* 4.3 0.2 - - - +
128A VAL* 3.9 9.8 - - + +
231A ALA 3.0 13.8 + - - +
232A GLY 3.6 7.6 - - - +
234A ALA* 1.3 76.2 - - - +
236A TYR* 1.3 58.1 + - - +
238A MET* 3.3 4.0 + - - +
239A THR* 2.9 33.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 4.9 1.6 - - - -
25A TYR* 3.8 10.0 - + + -
26A ASP* 2.8 49.7 + - + +
28A SER* 5.0 0.6 + - - -
29A ALA* 4.2 17.7 - - - -
30A GLY* 4.1 10.5 - - - -
84A VAL* 4.6 13.7 - - + -
85A ALA* 4.3 7.3 - - + +
232A GLY 2.9 16.9 + - - +
233A LEU* 3.2 14.6 + - + +
235A ALA* 1.3 76.3 - - - +
237A LEU* 1.3 79.1 + - + +
239A THR* 3.4 3.8 + - - -
240A LEU* 3.1 44.9 + - + +
275A ASN* 4.0 22.9 - - + -
277A TYR* 3.7 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 2.9 36.2 + - + +
234A ALA 3.8 3.4 - - - +
236A TYR* 1.3 93.4 - - + +
238A MET* 1.3 64.1 + - - +
240A LEU* 3.3 5.7 + - + +
241A GLY 3.2 3.8 + - - -
242A LYS* 3.0 44.7 + - + +
243A THR* 3.8 15.2 + - + -
251A TYR* 3.7 29.8 - - + +
252A ILE* 3.7 28.0 - - + -
255A THR* 5.3 1.6 - - - +
274A TYR 5.4 1.6 - - - +
275A ASN* 4.4 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER* 5.3 1.1 - - - -
125A LYS* 3.4 21.6 - - - +
126A GLY* 3.7 11.4 - - - -
127A VAL 3.6 37.2 - - - +
128A VAL* 3.8 19.1 - - + -
154A MET* 4.3 5.6 - - - -
234A ALA* 2.8 23.9 + - - +
235A ALA* 3.7 4.9 - - - +
237A LEU* 1.3 74.3 - - - +
239A THR* 1.3 65.9 + - - +
241A GLY* 2.9 14.6 + - - -
243A THR* 3.7 29.2 - - + +
244A THR* 4.1 6.3 - - - +
245A ALA* 3.9 26.9 - - + +
248A ALA* 4.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER* 3.8 28.9 - - - +
30A GLY* 3.1 19.7 + - - -
31A GLN* 2.9 35.3 + - + +
33A SER* 3.6 1.6 - - - -
125A LYS* 3.6 35.1 + - + +
235A ALA 2.9 16.2 + - - -
236A TYR 3.6 4.7 - - - -
238A MET* 1.3 77.6 - - - +
240A LEU* 1.3 60.5 + - - +
241A GLY* 3.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ASP* 3.6 19.3 - - + +
28A SER* 3.5 22.7 - - - +
236A TYR* 3.1 52.6 + - + +
237A LEU* 3.6 9.0 - - - +
238A MET 3.2 0.6 - - - -
239A THR* 1.3 75.6 - - - +
241A GLY* 1.3 59.8 + - - +
242A LYS* 3.4 36.1 + - + +
----------------------------------------------------------
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