Contacts of the helix formed by residues 215 - 232 (chain E) in PDB entry 1S9C
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 HIS 215 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185E ALA* 3.6 31.0 - - - -
188E TYR* 3.3 33.9 - + + +
189E ARG* 3.6 13.7 - - + +
193E ASP* 3.2 40.9 + - + +
198E HIS* 3.3 49.9 + + + +
214E LEU* 1.3 75.2 - - - +
216E GLY* 1.3 68.5 + - - +
217E LEU* 4.1 2.9 - - + +
218E CYS* 2.9 18.1 + - + +
219E THR* 3.4 6.6 + - - -
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Residues in contact with GLY 216 (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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198E HIS* 4.8 2.6 - - - -
214E LEU 3.4 4.5 + - - -
215E HIS* 1.3 71.4 - - - +
217E LEU* 1.3 60.4 + - - +
218E CYS 3.1 0.3 + - - -
219E THR* 3.3 8.0 + - - -
220E PHE 3.1 17.3 + - - -
246E PHE* 3.3 33.0 - - - -
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Residues in contact with LEU 217 (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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30E TYR* 4.3 2.8 + - - -
62E VAL* 3.3 34.3 - - + -
66E GLN* 3.3 30.3 - - + +
89E HIS* 3.8 27.1 + - + +
92E GLN* 3.8 21.5 - - + -
142E PHE* 4.9 2.2 - - + -
188E TYR* 3.3 24.3 + - + +
193E ASP* 5.8 0.7 - - - +
215E HIS* 3.1 2.5 - - + +
216E GLY* 1.3 76.0 - - - +
218E CYS* 1.3 56.4 + - - +
220E PHE* 3.2 17.2 - - + +
221E GLY* 2.9 22.3 + - - -
246E PHE* 3.9 9.8 - - + -
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Residues in contact with CYS 218 (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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33E GLY 3.4 26.2 - - - -
34E VAL* 3.6 2.0 - - - +
184E GLN* 4.0 13.5 - - - -
188E TYR* 3.8 33.6 - - + -
214E LEU* 4.0 14.8 - - + -
215E HIS* 2.9 13.2 + - + +
217E LEU* 1.3 77.2 - - - +
219E THR* 1.3 66.5 + - - +
220E PHE 3.0 1.1 - - - -
221E GLY* 2.9 11.6 + - - -
222E PHE* 3.0 34.0 + - - -
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Residues in contact with THR 219 (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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214E LEU* 3.9 15.0 + - - +
215E HIS 3.4 8.9 + - - -
216E GLY* 3.3 9.8 + - - -
218E CYS* 1.3 76.7 - - - +
220E PHE* 1.3 64.5 + - - +
222E PHE* 3.1 4.5 + - - +
223E SER* 3.0 23.7 + - - -
246E PHE* 6.1 0.2 - - - -
250E VAL* 3.9 12.4 - - + +
256E LEU* 3.7 37.7 - - + -
271E THR* 4.1 5.2 - - + -
280E VAL* 3.9 15.7 - - + -
281E ILE* 3.7 18.4 - - + -
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Residues in contact with PHE 220 (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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30E TYR* 5.1 0.9 - - - -
59E THR* 3.5 25.1 - - + -
62E VAL* 3.7 20.2 - - + -
92E GLN* 4.0 20.4 - - + -
94E LEU* 5.3 0.7 - - + -
216E GLY 3.1 11.5 + - - +
217E LEU* 3.2 26.5 - - + +
219E THR* 1.3 79.7 - - - +
221E GLY* 1.3 64.7 + - - +
223E SER* 4.0 1.5 - - - -
224E ALA* 2.9 28.2 + - + +
242E VAL* 3.0 35.0 - - + -
244E ALA* 3.6 32.8 - - + -
246E PHE* 4.1 11.4 - + + -
269E PHE* 5.2 6.1 - + - -
281E ILE* 3.7 10.7 - - + +
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Residues in contact with GLY 221 (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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30E TYR* 4.0 9.0 - - - -
34E VAL* 3.3 27.3 - - - +
59E THR* 4.1 9.9 + - - -
217E LEU 2.9 10.4 + - - -
218E CYS 2.9 4.4 + - - -
220E PHE* 1.3 78.3 - - - +
222E PHE* 1.3 51.5 + - - +
224E ALA* 3.4 2.1 + - - +
225E ARG* 2.8 36.8 + - - +
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Residues in contact with PHE 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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34E VAL 3.3 22.9 + - - -
35E GLY* 3.6 22.2 - - - -
178E ASP* 3.7 36.8 - - + -
179E THR 4.9 7.2 - - - -
180E THR* 4.6 9.6 - - - -
184E GLN* 3.7 30.7 - - + -
214E LEU* 5.2 1.3 - - + -
218E CYS* 3.0 37.3 + - - -
219E THR* 3.2 8.1 - - - +
221E GLY* 1.3 73.2 - - - +
223E SER* 1.3 65.8 + - - +
225E ARG* 2.9 25.1 + - - +
226E ARG* 3.0 17.7 + - - +
256E LEU* 3.6 22.4 - - + -
258E THR* 5.6 0.7 - - - +
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Residues in contact with SER 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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219E THR 3.0 10.4 + - - -
220E PHE 4.1 1.8 - - - -
222E PHE* 1.3 79.9 - - - +
224E ALA* 1.3 64.3 + - - +
226E ARG* 3.1 4.2 + - - +
227E VAL* 2.9 28.2 + - - +
258E THR* 2.7 32.3 + - - +
269E PHE* 3.6 26.0 - - - -
271E THR* 2.8 24.1 + - - +
281E ILE* 5.0 0.9 - - - -
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Residues in contact with ALA 224 (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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59E THR* 3.6 29.8 - - + +
220E PHE* 2.9 22.4 + - + +
221E GLY 3.7 1.8 - - - +
223E SER* 1.3 78.2 - - - +
225E ARG* 1.3 63.1 + - - +
227E VAL* 3.2 9.4 + - - +
228E LEU* 3.0 22.5 + - - +
239E PHE* 3.9 17.3 - - + -
242E VAL* 5.1 4.3 - - + -
269E PHE* 4.9 8.2 - - + -
286E VAL* 6.0 0.9 - - - -
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Residues in contact with ARG 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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34E VAL* 2.4 35.2 + - + -
35E GLY* 3.0 25.5 + - - -
36E ALA* 3.6 20.2 - - - +
43E ASP* 4.5 11.3 + - - +
46E PHE* 5.4 4.3 - - + -
57E LEU* 4.2 34.1 - - + -
178E ASP* 3.3 23.8 + - - -
221E GLY 2.8 22.4 + - - +
222E PHE* 2.9 18.6 + - - +
224E ALA* 1.3 74.4 - - - +
226E ARG* 1.3 74.9 + - - +
228E LEU* 3.4 11.8 - - + +
229E GLN* 3.2 25.7 + - - +
234E ASN* 4.6 1.1 + - - +
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Residues in contact with ARG 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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173A ASP 4.6 5.5 + - - -
176E LEU* 3.3 41.6 - - + +
177E THR 3.1 24.5 + - - +
178E ASP* 2.7 31.7 + - - +
222E PHE 3.0 17.9 + - - +
223E SER* 3.1 10.5 + - - +
225E ARG* 1.3 88.1 - - - +
227E VAL* 1.3 59.7 + - - +
229E GLN* 2.4 41.3 + - - +
230E GLN* 2.8 33.2 + - - +
258E THR* 4.6 6.5 - - - +
260E MET* 4.3 7.4 - - + -
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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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223E SER 2.9 19.6 + - - +
224E ALA* 3.2 7.6 + - - +
226E ARG* 1.3 74.9 - - - +
228E LEU* 1.3 58.2 + - - +
231E PHE* 2.9 31.3 + - + +
232E ALA* 3.9 1.0 + - - +
258E THR* 4.8 1.1 - - + -
260E MET* 3.8 28.0 - - + -
267E ILE* 3.8 23.6 - - + -
269E PHE* 4.2 19.1 - - + -
286E VAL* 3.1 42.4 - - + -
288E LEU* 5.2 2.9 - - + -
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Residues in contact with LEU 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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46E PHE* 3.8 21.8 - - + -
57E LEU* 4.0 15.9 - - + -
58E PRO* 4.5 8.5 - - + -
224E ALA 3.0 12.7 + - - +
225E ARG* 3.4 12.6 - - + +
226E ARG 3.1 0.2 - - - -
227E VAL* 1.3 77.9 - - - +
229E GLN* 1.3 57.2 + - - +
232E ALA* 3.2 28.3 + - + +
234E ASN* 3.1 36.6 + - - +
235E ASP 3.9 30.7 - - - +
236E VAL* 4.1 5.6 - - + +
239E PHE* 4.0 27.1 - - + -
288E LEU* 5.6 0.7 - - - -
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Residues in contact with GLN 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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40E ASP* 4.0 19.4 + - - +
42E LYS* 5.8 2.0 - - - +
43E ASP* 4.4 8.7 + - - -
176E LEU* 4.4 1.4 - - + +
225E ARG* 3.2 12.0 + - + +
226E ARG* 2.4 50.5 + - - +
228E LEU* 1.3 78.5 - - - +
230E GLN* 1.3 72.7 + - + +
233E ASP* 3.9 12.5 + - - -
234E ASN* 3.0 33.5 + - - +
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Residues in contact with GLN 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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176A LEU* 3.9 2.2 - - - +
230A GLN* 2.8 42.1 + - - +
174E ALA* 3.8 12.9 - - + +
176E LEU* 3.6 25.8 - - + +
226E ARG 2.8 21.0 + - - +
229E GLN* 1.3 79.6 + - - +
231E PHE* 1.3 92.6 + - + +
233E ASP 4.9 0.9 + - - -
260E MET* 4.1 7.4 - - + -
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Residues in contact with PHE 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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173E ASP* 4.7 10.8 - - + -
174E ALA* 4.4 12.1 - - + -
227E VAL 2.9 12.7 + - - +
230E GLN* 1.3 103.1 - - + +
232E ALA* 1.3 59.2 + - - +
233E ASP* 3.8 0.9 - - - -
238E ARG* 4.0 9.4 + - - -
260E MET* 3.5 33.7 - - + -
262E LYS* 3.7 32.5 - - + -
267E ILE* 3.5 42.0 - - + -
288E LEU* 3.1 14.0 - - + +
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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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228E LEU* 3.2 24.7 + - + +
231E PHE* 1.3 80.5 - - - +
233E ASP* 1.3 75.1 + - - +
234E ASN 3.2 1.3 - - - -
235E ASP* 2.9 18.9 + - - +
238E ARG* 3.6 27.9 - - + +
288E LEU* 3.9 25.6 - - + -
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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