Contacts of the helix formed by residues 230 - 252 (chain E) in PDB entry 1U1C
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 ASN 230 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E VAL* 6.3 0.8 - - - +
228E ILE 4.0 0.4 + - - -
229E PRO* 1.3 74.5 - - - +
231E ALA* 1.3 60.4 + - - +
232E GLU* 3.0 32.5 + - - +
233E THR* 3.2 26.4 + - - +
234E MET* 3.1 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E PRO 3.9 2.6 + - - -
230E ASN* 1.3 75.5 + - - +
232E GLU* 1.3 61.7 + - - +
234E MET* 3.5 11.5 + - - +
235E LYS* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 232 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230E ASN* 3.0 12.0 + - - +
231E ALA* 1.3 75.3 - - - +
233E THR* 1.3 65.8 + - - +
235E LYS* 3.3 7.1 + - - +
236E GLN* 3.2 40.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E VAL* 4.1 31.4 - - + +
105E GLY* 5.4 1.3 - - - -
220E ILE* 6.4 0.2 - - - -
230E ASN* 3.2 29.1 + - - +
231E ALA 3.4 0.2 - - - -
232E GLU* 1.3 76.7 - - - +
234E MET* 1.3 54.6 + - - +
236E GLN* 3.9 14.2 + - + +
237E THR* 2.7 41.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 234 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220E ILE* 3.8 48.5 - - + +
229E PRO* 3.6 31.4 - - + +
230E ASN 3.1 17.5 + - - +
231E ALA* 3.5 9.9 - - - +
232E GLU 3.2 0.2 - - - -
233E THR* 1.3 77.2 - - - +
235E LYS* 1.3 60.6 + - - +
237E THR* 3.5 2.3 + - - -
238E GLU* 3.2 23.7 + - - +
5041E BAU 5.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E ALA 3.4 7.7 + - - +
232E GLU* 3.3 10.8 + - - +
234E MET* 1.3 76.1 - - - +
236E GLN* 1.3 63.4 + - + +
238E GLU* 3.3 20.9 - - - +
239E SER* 3.2 21.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 236 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E GLU* 3.2 31.6 + - - +
233E THR* 3.9 14.2 + - - +
235E LYS* 1.3 76.7 - - + +
237E THR* 1.3 63.6 + - - +
239E SER* 3.4 6.9 + - - -
240E HIS* 3.1 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 237 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E VAL* 4.8 0.7 - - - +
105E GLY* 3.4 31.2 + - - +
218E GLY* 3.7 10.3 - - - -
219E VAL 3.3 37.6 + - - +
220E ILE* 4.1 9.3 - - + +
233E THR* 2.7 26.9 + - - +
234E MET 3.8 4.5 - - - -
235E LYS 3.4 0.2 - - - -
236E GLN* 1.3 75.3 - - - +
238E GLU* 1.3 64.9 + - - +
240E HIS* 3.3 6.9 + - - +
241E ALA* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ARG* 4.0 31.7 + - + +
33E LYS* 4.0 23.2 + - - +
92E ILE* 4.7 2.2 - - - +
94E THR* 6.0 6.3 - - + -
218E GLY* 6.2 0.4 - - - -
220E ILE* 5.5 1.5 - - + +
234E MET 3.2 13.1 + - - +
235E LYS* 3.3 23.6 - - - +
236E GLN 3.4 0.2 - - - -
237E THR* 1.3 79.8 - - - +
239E SER* 1.3 58.6 + - - +
241E ALA* 3.4 4.5 + - - +
242E VAL* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 5.4 3.1 - - - +
235E LYS 3.2 18.8 + - - -
236E GLN* 3.7 7.6 - - - -
237E THR 3.3 0.2 - - - -
238E GLU* 1.3 80.2 + - - +
240E HIS* 1.3 62.8 + - - +
242E VAL* 4.1 6.0 - - - +
243E LYS* 3.3 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E GLY 5.2 9.4 + - - +
107E VAL* 6.3 1.6 - - + -
147E ILE* 3.5 30.2 - - + +
148E GLY 4.2 12.8 - - - -
149E ALA* 3.9 12.4 - - + +
236E GLN* 3.1 19.3 + - + +
237E THR* 3.6 10.8 - - - +
238E GLU 3.3 0.2 - - - -
239E SER* 1.3 77.3 - - - +
241E ALA* 1.3 63.1 + - - +
243E LYS* 3.4 7.4 + - - +
244E ILE* 3.3 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ILE* 3.8 20.7 - - + +
93E GLY 5.2 0.2 - - - +
107E VAL* 4.4 10.1 - - + +
216E VAL* 4.4 3.0 - - + +
217E ALA* 4.5 1.3 - - - -
218E GLY* 4.0 24.5 - - - +
237E THR 3.1 13.2 + - - +
238E GLU* 4.0 4.5 - - - +
240E HIS* 1.3 77.0 - - - +
242E VAL* 1.3 60.2 + - - +
244E ILE* 3.4 13.5 + - - +
245E VAL* 3.1 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E ARG* 4.9 3.8 - - + -
33E LYS* 5.0 2.7 - - + +
34E ILE* 3.8 39.9 - - + +
37E LEU* 3.7 23.6 - - + -
92E ILE* 3.8 17.9 - - + -
238E GLU* 3.0 31.6 + - + +
239E SER* 4.1 6.7 - - - +
240E HIS 3.3 0.2 - - - -
241E ALA* 1.3 73.2 - - - +
243E LYS* 1.3 64.3 + - - +
245E VAL* 3.3 8.7 - - - +
246E VAL* 3.1 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E LEU* 4.6 13.9 - - + +
147E ILE* 4.7 17.0 - - + +
239E SER 3.3 15.5 + - - +
240E HIS* 3.6 7.4 - - - +
241E ALA 3.3 0.2 - - - -
242E VAL* 1.3 78.7 - - - +
244E ILE* 1.3 61.6 + - - +
246E VAL* 4.1 2.8 - - - +
247E GLU* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E VAL* 3.8 35.4 - - + -
140E LEU* 3.8 25.8 - - + +
143E ALA* 3.5 5.7 - - - +
144E ALA* 3.9 15.0 - - + +
147E ILE* 3.7 31.6 - - + -
149E ALA* 4.3 4.3 - - + -
216E VAL* 4.3 19.1 - - + -
240E HIS* 3.3 22.1 + - - +
241E ALA* 3.6 5.8 - - - +
242E VAL 3.2 0.2 - - - -
243E LYS* 1.3 78.2 - - - +
245E VAL* 1.3 58.2 + - - +
247E GLU* 3.3 3.7 + - - -
248E ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ILE* 4.1 15.0 - - + +
34E ILE* 5.2 1.1 - - + -
90E LEU* 3.8 32.5 - - + +
91E ARG 4.4 1.3 - - - +
92E ILE* 3.9 24.9 - - + -
140E LEU* 4.2 11.7 - - + -
216E VAL* 3.9 20.6 - - + -
241E ALA 3.1 15.0 + - - +
242E VAL* 3.3 17.7 - - + +
244E ILE* 1.3 76.4 - - - +
246E VAL* 1.3 65.1 + - + +
248E ALA* 3.5 1.9 + - - +
249E ALA* 3.1 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ILE* 4.1 18.2 - - + -
34E ILE* 4.2 21.5 - - + +
37E LEU* 4.8 14.1 - - + +
38E MET* 4.0 26.7 - - + -
57E LEU* 3.6 15.4 - - + +
242E VAL* 3.1 22.1 + - + +
243E LYS* 4.2 4.9 - - - +
245E VAL* 1.3 74.2 - - + +
247E GLU* 1.3 65.2 + - - +
249E ALA* 3.3 9.3 + - - +
250E ARG* 3.3 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E ALA* 3.8 18.2 - - + +
146E SER* 4.9 4.9 - - - +
147E ILE* 4.9 9.2 - - + -
243E LYS 3.2 19.6 + - - +
244E ILE* 3.6 4.7 - - - +
246E VAL* 1.3 73.8 - - - +
248E ALA* 1.3 64.0 + - - +
250E ARG* 3.2 51.3 + - - +
251E ARG* 3.3 40.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E LEU* 4.1 7.2 - - + -
139E ALA* 3.6 30.3 - - + +
140E LEU* 3.6 26.7 - - + -
143E ALA* 3.7 0.2 - - - +
244E ILE 2.9 17.4 + - - +
245E VAL 3.7 4.0 - - - +
247E GLU* 1.3 73.4 - - - +
249E ALA* 1.3 65.1 + - - +
251E ARG* 3.2 14.5 + - - +
252E LEU* 3.4 18.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 3.8 27.8 - - + +
23E ILE* 4.3 11.0 - - + -
57E LEU* 3.8 13.9 - - + -
62E VAL* 5.4 1.1 - - + -
90E LEU* 3.7 10.7 - - + +
245E VAL 3.1 14.5 + - - +
246E VAL 3.4 10.8 - - - +
248E ALA* 1.3 77.0 - - - +
250E ARG* 1.3 60.7 + - - +
252E LEU* 3.2 10.7 + - - -
253E LEU* 3.3 18.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 250 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E LEU* 3.7 29.6 - - + +
58E ASP* 3.4 39.3 + - - +
246E VAL* 3.3 8.5 + - - +
247E GLU* 3.2 45.6 + - - +
248E ALA 3.2 0.4 - - - -
249E ALA* 1.3 79.4 - - - +
251E ARG* 1.3 60.6 + - + +
252E LEU 3.4 0.7 + - - -
253E LEU* 3.8 15.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 251 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139E ALA* 4.1 31.0 - - + +
142E GLU* 3.9 32.4 + - - +
143E ALA* 4.5 5.1 - - - +
146E SER* 3.8 22.2 + - - -
247E GLU* 3.3 46.3 + - - +
248E ALA* 3.2 7.7 + - - +
250E ARG* 1.3 78.0 - - + +
252E LEU* 1.3 62.1 + - - +
253E LEU* 3.5 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 252 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21E LEU* 3.8 20.6 - - + +
88E THR* 4.6 1.6 - - + -
90E LEU* 3.8 34.8 - - + -
135E GLU* 3.6 28.3 - - + +
136E CYS* 4.0 12.6 - - - +
139E ALA* 3.8 15.9 - - + -
212E ARG* 3.1 45.3 + - - +
248E ALA* 3.4 16.8 - - + +
249E ALA 3.2 3.8 + - - -
251E ARG* 1.3 80.0 - - - +
253E LEU* 1.3 61.1 + - - +
----------------------------------------------------------
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