Contacts of the helix formed by residues 201 - 220 (chain A) in PDB entry 1IL5
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 ASP 201 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 6.0 0.2 - - - -
187A GLU* 3.7 9.2 - - - +
191A ARG* 5.2 1.8 + - - +
199A ALA 3.6 3.0 + - - +
200A PRO* 1.3 74.1 - - - +
202A PRO* 1.3 75.9 - - + +
203A SER* 2.5 28.9 + - - -
204A VAL* 2.9 17.4 + - - +
205A ILE* 3.3 12.3 - - - +
235A ARG* 3.2 49.7 + - + +
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Residues in contact with PRO 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU* 6.1 3.1 - - + +
200A PRO 4.9 0.2 - - - +
201A ASP* 1.3 88.7 - - + +
203A SER* 1.3 56.5 + - - +
205A ILE* 4.5 7.8 - - + -
206A THR* 2.8 38.2 + - - +
233A GLN* 3.8 25.4 - - - +
234A ARG 3.9 11.0 - - - +
235A ARG 3.8 8.7 - - - +
236A ASN 5.2 0.2 - - - -
237A GLY* 4.1 12.8 - - - -
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Residues in contact with SER 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A TYR* 2.8 31.5 + - - -
201A ASP* 2.5 28.9 + - - -
202A PRO* 1.3 76.4 - - - +
204A VAL* 1.3 63.9 + - - +
206A THR* 4.1 1.6 - - - -
207A LEU* 3.4 26.0 + - - +
233A GLN 3.3 24.2 - - - +
234A ARG* 3.7 10.8 + - - -
235A ARG* 4.0 2.2 + - - -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 6.0 0.2 - - + -
173A GLN* 4.6 1.1 - - - +
183A TYR* 4.0 8.5 - - + -
184A ILE* 4.0 22.4 - - + +
187A GLU* 3.9 35.0 - - + +
188A MET* 5.6 3.4 - - + -
191A ARG* 5.9 0.7 - - - +
200A PRO* 3.9 20.0 - - + -
201A ASP* 2.9 19.8 + - - +
203A SER* 1.3 79.8 - - - +
205A ILE* 1.3 65.9 + - - +
207A LEU* 3.1 8.2 + - - +
208A GLU* 3.1 43.1 + - - +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 4.2 24.7 - - + +
135A GLU* 4.2 28.5 - - + +
200A PRO* 3.4 35.4 - - + +
201A ASP 3.3 17.7 + - - +
202A PRO* 3.9 8.5 - - + +
204A VAL* 1.3 78.4 - - + +
206A THR* 1.3 66.8 + - - +
208A GLU* 3.0 16.3 + - - +
209A ASN* 2.9 40.3 + - - +
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Residues in contact with THR 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A PRO* 2.8 24.8 + - - +
203A SER 4.1 2.9 - - - -
205A ILE* 1.3 75.7 - - - +
207A LEU* 1.3 59.1 + - - +
209A ASN* 3.3 6.1 + - - +
210A SER* 2.8 43.1 + - - +
231A GLN 4.4 4.7 - - - +
232A LEU* 3.9 17.0 - - + -
233A GLN* 3.1 50.6 + - + +
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Residues in contact with LEU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 3.3 29.3 - - + -
183A TYR* 3.7 39.9 - - + -
184A ILE* 4.8 4.3 - - + -
203A SER 3.4 11.2 + - - +
204A VAL 3.1 9.9 + - - +
206A THR* 1.3 76.9 - - - +
208A GLU* 1.3 58.3 + - - +
210A SER* 3.0 5.5 + - - -
211A TRP 2.9 26.2 + - - -
214A LEU* 4.1 19.0 - - + +
232A LEU* 3.9 28.0 - - + -
248A LEU* 5.5 0.4 - - + -
251A ILE* 3.9 23.1 - - + -
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Residues in contact with GLU 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A TYR* 4.1 2.7 - - + -
134A ARG* 3.0 37.1 + - - +
173A GLN* 2.9 30.3 - - - +
177A GLU* 3.5 33.2 - - - +
180A ARG* 5.4 1.6 + - - -
181A PHE* 4.3 7.2 - - - -
184A ILE* 3.7 16.3 - - + +
204A VAL* 3.2 27.5 - - - +
205A ILE* 3.0 8.5 + - - +
207A LEU* 1.3 76.6 - - - +
209A ASN* 1.3 62.0 + - - +
210A SER 3.2 0.9 + - - -
211A TRP* 3.3 14.2 + - - +
212A GLY 5.1 0.2 + - - -
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Residues in contact with ASN 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 4.9 3.8 - - - -
134A ARG* 2.9 37.9 + - - +
205A ILE* 2.9 34.5 + - - +
206A THR* 3.8 6.3 + - - +
208A GLU* 1.3 76.2 - - - +
210A SER* 1.3 60.7 + - - +
211A TRP 3.5 0.2 - - - -
212A GLY 5.1 1.2 + - - -
213A ARG* 5.2 7.7 + - - +
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Residues in contact with SER 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A THR* 2.8 29.4 + - - +
207A LEU* 3.0 5.1 + - - -
209A ASN* 1.3 80.7 - - - +
211A TRP* 1.3 53.6 + - - +
212A GLY 3.3 2.9 - - - -
213A ARG* 3.1 34.2 + - - +
214A LEU* 2.7 49.9 + - - +
230A ILE* 5.3 0.8 - - - +
231A GLN 5.3 1.9 + - - -
232A LEU* 5.3 7.0 - - - +
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Residues in contact with TRP 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.9 15.5 - - + -
78A ASN* 3.6 24.7 - - + -
180A ARG* 3.5 48.7 - - + +
181A PHE* 3.3 39.0 - + + -
207A LEU 2.9 7.2 + - - -
208A GLU 3.3 13.3 + - - +
209A ASN 3.5 0.2 - - - -
210A SER* 1.3 75.0 - - - +
212A GLY* 1.3 67.8 + - - +
214A LEU* 3.6 3.5 - - - +
215A SER* 2.9 39.7 + - - -
252A ILE* 4.5 4.5 - - + -
254A LEU 2.8 26.8 + - - -
256A VAL* 3.7 39.9 - - + -
301A DDP 4.3 9.0 - - - -
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Residues in contact with GLY 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLU 5.1 0.4 + - - -
209A ASN 5.1 1.4 + - - -
210A SER 3.3 0.4 - - - -
211A TRP* 1.3 86.5 - - - +
213A ARG* 1.3 60.2 + - - +
215A SER* 3.3 1.8 + - - -
216A THR* 2.8 27.2 + - - -
256A VAL* 5.0 0.4 - - - -
258A ARG* 2.9 23.0 + - - -
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ASN 5.2 6.1 + - - +
210A SER* 3.1 33.4 + - - +
212A GLY* 1.3 76.8 - - - +
214A LEU* 1.3 56.5 + - - +
216A THR* 3.4 5.6 + - - -
217A ALA* 3.0 28.6 + - + +
230A ILE* 3.9 35.3 - - + +
231A GLN 5.2 4.6 + - - -
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 4.3 16.6 - - + -
207A LEU* 4.1 25.4 - - + +
210A SER* 2.7 31.8 + - - +
211A TRP 3.6 3.4 - - - +
213A ARG* 1.3 71.1 - - - +
215A SER* 1.3 66.1 + - - +
216A THR 3.1 0.3 + - - -
217A ALA* 3.1 1.4 + - - -
218A ILE* 2.8 37.3 + - + +
226A PHE* 5.3 0.4 - - + -
230A ILE* 3.9 26.0 - - + -
232A LEU* 4.5 17.0 - - + -
242A VAL* 6.0 0.4 - - + -
248A LEU* 4.1 29.2 - - + -
251A ILE* 6.4 0.2 - - + -
252A ILE* 4.7 12.1 - - + -
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Residues in contact with SER 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TRP* 2.9 25.8 + - - -
212A GLY 3.6 4.7 - - - -
214A LEU* 1.3 74.8 - - - +
216A THR* 1.3 61.8 + - - +
219A GLN* 2.9 44.1 + - - +
252A ILE* 4.7 0.2 - - - +
255A MET* 3.4 35.6 - - - +
256A VAL* 3.5 12.5 + - - +
258A ARG* 3.7 12.1 - - - -
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Residues in contact with THR 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLY 2.8 13.1 + - - -
213A ARG* 3.5 9.9 - - - -
215A SER* 1.3 73.9 - - - +
217A ALA* 1.3 60.6 + - - +
219A GLN* 3.2 2.8 + - - -
220A GLU* 2.8 55.8 + - - +
258A ARG* 2.8 44.4 + - + +
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A ARG* 3.0 14.9 + - + +
214A LEU 3.7 2.0 - - - +
216A THR* 1.3 79.1 - - - +
218A ILE* 1.3 57.4 + - - +
220A GLU* 3.1 6.0 + - - -
221A SER* 2.9 29.8 + - - -
226A PHE* 3.9 19.5 - - + -
227A ALA* 5.4 3.8 + - + +
228A SER 5.6 0.9 - - - +
230A ILE* 3.5 26.5 - - + -
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Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 6.2 3.4 - - - +
42A ILE* 3.6 23.8 - - + -
214A LEU* 2.8 30.2 + - + +
217A ALA* 1.3 71.0 - - - +
219A GLN* 1.3 60.6 + - - +
221A SER* 3.0 23.1 + - - +
226A PHE* 3.7 26.5 - - + -
245A VAL* 3.7 22.9 - - + -
248A LEU* 4.1 18.2 - - + -
252A ILE* 4.2 12.3 - - + -
255A MET* 3.7 25.8 - - + -
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Residues in contact with GLN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.7 22.4 - - + +
215A SER* 2.9 35.3 + - - +
216A THR 3.7 3.1 - - - +
218A ILE* 1.3 75.0 - - - +
220A GLU* 1.3 61.2 + - + +
221A SER* 3.5 1.0 + - - +
255A MET* 3.9 24.6 - - + +
256A VAL 2.7 26.3 + - - -
257A TYR* 3.8 1.7 - - - -
258A ARG* 3.2 33.7 + - + +
259A CYS* 4.8 7.8 + - + +
260A ALA 5.6 2.4 - - - +
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A THR* 2.8 39.3 + - + +
217A ALA* 3.3 6.4 - - - +
219A GLN* 1.3 81.3 - - + +
221A SER* 1.3 64.7 + - - +
222A ASN* 3.2 4.7 + - - +
227A ALA* 5.0 10.9 + - + +
258A ARG* 5.2 0.4 - - + -
259A CYS* 3.2 34.6 - - + -
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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