Contacts of the helix formed by residues 220 - 238 (chain E) in PDB entry 1CSE
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 220 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E ALA* 3.5 16.3 - - - +
154E GLY* 3.2 38.2 + - - +
155E ASN* 2.9 19.5 + - - +
177E VAL 3.7 17.0 - - - +
178E GLY* 4.2 1.3 - - - -
179E ALA* 3.9 16.2 - - + +
189E PHE* 4.3 0.4 - - + -
190E SER* 3.8 24.0 - - - +
191E SER 4.6 0.4 - - - +
219E GLY* 1.3 73.7 - - - -
221E SER* 1.4 64.6 + - - +
223E ALA* 3.0 17.8 + - - +
224E SER 3.1 11.6 + - - -
45I LEU* 3.3 3.0 + - - +
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Residues in contact with SER 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E HIS* 2.7 33.2 + - - -
68E VAL* 3.7 2.6 - - - +
125E SER* 2.7 34.1 + - - -
152E ALA* 3.8 4.0 - - - +
220E THR* 1.4 78.9 + - - +
222E MET* 1.3 63.8 + - - +
225E PRO* 2.9 20.4 - - - +
45I LEU* 2.8 38.1 + - - +
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Residues in contact with MET 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E HIS* 4.3 8.5 - - + -
67E HIS* 3.9 25.1 - - + +
68E VAL* 4.1 12.3 - - + -
71E THR* 4.1 1.1 - - - +
201E PRO 3.5 2.0 - - - -
202E GLY* 3.9 4.7 - - - +
205E VAL* 3.7 27.6 - - + -
217E LEU* 3.6 36.8 - - + +
218E ASN 3.6 26.5 - - - +
219E GLY 3.1 9.8 + - - +
221E SER* 1.3 106.0 - - - +
223E ALA* 1.3 61.3 + - - +
225E PRO* 3.4 12.8 - - - +
226E HIS* 2.8 24.6 + - - -
46I ASP* 4.2 2.7 - - + -
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Residues in contact with ALA 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E VAL* 3.7 9.0 - - + +
178E GLY 3.3 31.4 - - - +
179E ALA* 4.1 6.1 - - + -
200E ALA* 3.2 28.7 - - + +
201E PRO 3.3 10.5 + - - +
219E GLY 3.7 1.0 + - - -
220E THR* 3.0 11.4 + - - +
222E MET* 1.3 79.6 - - - +
224E SER* 1.4 68.7 + - - +
226E HIS* 3.1 12.3 + - - +
227E VAL 3.6 1.6 + - - -
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Residues in contact with SER 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E ASN* 2.8 23.5 + - - -
124E MET 4.2 0.5 + - - -
125E SER* 3.7 9.8 + - - -
150E VAL* 3.3 14.6 + - - +
151E ALA* 3.5 13.9 - - - -
152E ALA* 3.6 19.4 + - - -
177E VAL* 3.9 11.3 - - - +
220E THR 3.1 9.6 + - - -
223E ALA* 1.4 77.1 - - - +
225E PRO* 1.4 61.8 - - - +
227E VAL* 3.0 20.1 + - - +
228E ALA 3.0 9.7 + - - -
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Residues in contact with PRO 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68E VAL* 3.5 35.4 - - + +
71E THR* 3.8 18.6 - - + +
72E VAL* 3.6 17.5 - - + +
123E ASN* 3.3 8.4 - - - +
125E SER* 3.8 4.5 - - - +
221E SER 2.9 28.5 - - - +
222E MET* 3.4 19.1 - - - +
224E SER* 1.4 83.5 - - - +
226E HIS* 1.3 51.8 + - - +
227E VAL 3.2 0.2 - - - -
228E ALA* 3.7 5.9 - - + +
229E GLY* 2.8 28.8 + - - -
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Residues in contact with HIS 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PRO* 6.1 0.8 - - - +
7E GLY* 3.8 27.4 - - - -
8E ILE* 4.6 5.0 - - + +
11E ILE* 3.9 9.3 - - + +
71E THR* 3.2 23.3 - - + +
84E VAL* 3.9 26.7 - - + +
200E ALA* 3.7 10.8 - - + -
201E PRO* 3.3 35.9 + - + -
205E VAL* 4.0 16.1 - - + +
222E MET 2.8 26.1 + - - -
223E ALA 3.1 8.2 + - - +
224E SER 3.1 1.0 + - - -
225E PRO* 1.3 77.4 - - - +
227E VAL* 1.3 54.9 - - - +
229E GLY* 3.4 1.4 + - - -
230E ALA* 2.8 32.2 + - - +
268E ILE* 3.8 3.8 - - + +
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Residues in contact with VAL 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E VAL* 4.0 19.1 - - + -
175E ILE* 4.3 22.4 - - + -
177E VAL* 3.7 28.0 - - + -
198E VAL* 4.0 14.8 - - + -
200E ALA* 3.9 8.7 - - + -
223E ALA 4.0 0.2 - - - +
224E SER 3.0 7.0 + - - +
226E HIS* 1.3 73.6 - - - +
228E ALA* 1.3 63.4 + - - +
229E GLY 3.3 0.7 - - - -
230E ALA* 3.1 2.1 + - - +
231E ALA* 2.8 23.7 + - - +
250E LEU* 4.0 19.5 - - + +
268E ILE* 3.8 23.6 - - + -
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Residues in contact with ALA 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E VAL* 4.7 5.0 - - + +
72E VAL* 4.6 8.5 - - + -
121E VAL* 3.9 27.5 - - + +
123E ASN* 3.8 31.6 - - + +
150E VAL* 3.9 8.3 - - + +
224E SER 3.0 5.7 + - - -
225E PRO* 3.8 8.5 - - + +
227E VAL* 1.3 77.1 - - - +
229E GLY* 1.4 62.2 + - - +
231E ALA* 3.3 4.1 + - - +
232E ALA* 3.1 21.8 + - - +
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Residues in contact with GLY 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E VAL* 4.2 15.5 - - - +
84E VAL* 3.3 23.1 - - - +
85E ALA* 3.8 5.9 - - - +
225E PRO 2.8 18.6 + - - -
228E ALA* 1.4 73.8 - - - +
230E ALA* 1.3 59.0 + - - +
232E ALA* 3.1 5.5 + - - +
233E LEU* 3.0 29.1 + - - +
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E VAL* 3.5 5.1 - - - +
226E HIS 2.8 18.3 + - - +
227E VAL 3.1 4.9 + - - +
229E GLY* 1.3 77.2 - - - +
231E ALA* 1.3 61.7 + - - +
233E LEU* 3.2 5.5 + - - +
234E ILE* 3.0 29.0 + - - +
250E LEU* 3.8 12.3 - - + -
268E ILE* 3.7 12.3 - - + -
270E VAL* 3.4 31.3 - - + +
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Residues in contact with ALA 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E VAL* 4.3 11.4 - - + -
148E VAL* 4.2 18.2 - - + -
150E VAL* 5.5 0.7 - - + -
227E VAL 2.8 16.2 + - - +
228E ALA* 3.7 8.7 - - - +
230E ALA* 1.3 72.3 - - - +
232E ALA* 1.4 54.9 + - - +
234E ILE* 3.3 4.8 + - - +
235E LEU* 3.0 34.6 + - - +
246E VAL* 3.7 26.1 - - + +
250E LEU* 4.1 10.2 - - + +
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Residues in contact with ALA 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLY* 3.7 3.5 - - - -
26E VAL* 3.6 26.2 - - + +
28E VAL* 3.8 10.3 - - + -
85E ALA* 4.0 3.1 - - + -
88E VAL* 3.4 33.0 - - + -
121E VAL* 4.4 1.9 - - + +
228E ALA 3.1 9.6 + - - +
229E GLY* 3.1 8.7 + - - +
231E ALA* 1.4 71.1 - - - +
233E LEU* 1.3 66.4 + - - +
235E LEU* 3.4 0.4 + - - -
236E SER* 2.9 24.6 + - - -
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Residues in contact with LEU 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ALA* 3.9 26.9 - - - +
16E VAL* 4.0 23.1 - - + +
17E GLN* 4.3 3.1 - - + -
21E PHE* 3.5 13.5 - - - +
22E LYS* 3.5 31.0 - - - -
84E VAL* 3.2 37.2 - - + +
85E ALA* 3.7 7.0 - - + -
229E GLY 3.0 15.0 + - - +
230E ALA 3.2 8.5 + - - +
232E ALA* 1.3 77.0 - - - +
234E ILE* 1.3 61.9 + - - +
236E SER* 2.8 19.4 + - - -
237E LYS* 3.3 10.4 + - - +
270E VAL* 4.2 9.0 - - + -
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Residues in contact with ILE 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230E ALA 3.0 22.8 + - - +
231E ALA* 3.3 6.5 + - - +
233E LEU* 1.3 75.0 - - - +
235E LEU* 1.3 58.9 + - - +
237E LYS* 3.2 7.6 + - - +
238E HIS* 2.8 32.8 + - + +
241E LEU* 3.8 24.2 - - + -
246E VAL* 4.3 17.5 - - + +
249E ARG* 4.1 13.9 - - + -
250E LEU* 3.8 24.9 - - + -
270E VAL* 4.3 5.2 - - + -
273E ALA* 3.7 27.4 - - + +
274E ALA* 4.1 22.4 - - + -
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Residues in contact with LEU 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E VAL* 4.1 15.3 - - + +
120E ASP* 4.2 29.4 - - + +
121E VAL* 4.3 13.2 - - + -
148E VAL* 4.6 5.8 - - + -
231E ALA 3.0 20.8 + - - +
232E ALA 3.9 3.8 - - - +
233E LEU 3.2 0.2 - - - -
234E ILE* 1.3 77.5 - - - +
236E SER* 1.3 60.7 + - - +
238E HIS 3.9 12.6 - - - +
239E PRO* 3.2 35.7 - - + +
241E LEU* 3.9 16.8 - - + +
246E VAL* 3.6 28.3 - - + -
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Residues in contact with SER 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E PHE* 3.7 22.8 - - - +
22E LYS 4.5 1.6 - - - -
23E GLY* 3.0 44.9 + - - -
24E ALA* 4.1 9.2 - - - -
26E VAL* 4.0 3.1 - - - +
232E ALA 2.9 7.1 + - - -
233E LEU* 2.8 18.2 + - - -
235E LEU* 1.3 79.1 - - - +
237E LYS* 1.3 56.9 + - - +
239E PRO* 4.7 6.1 - - - +
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Residues in contact with LYS 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16E VAL* 5.4 0.9 - - + -
19E GLN* 3.0 28.3 + - - +
21E PHE* 3.6 44.4 - - + -
233E LEU 3.3 8.0 + - - +
234E ILE* 3.2 10.2 + - - +
236E SER* 1.3 77.1 + - - +
238E HIS* 1.3 79.1 + - + +
239E PRO* 3.4 9.2 - - - +
274E ALA* 3.0 38.1 + - + +
275E GLN* 5.0 3.6 - - - +
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Residues in contact with HIS 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E ILE* 2.8 17.5 + - + +
235E LEU* 3.5 10.7 - - - +
237E LYS* 1.3 103.1 + - + +
239E PRO* 1.3 70.9 - - - +
240E ASN 3.0 4.8 + - - -
241E LEU* 3.2 39.0 + - + +
249E ARG* 3.9 20.6 + - - -
274E ALA* 2.9 27.6 + - - -
275E GLN* 3.5 17.6 + - - -
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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
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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) + - + + + + + -
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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