Contacts of the helix formed by residues 233 - 247 (chain B) in PDB entry 1LI5
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 PRO 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B HIS* 4.3 13.2 - - + +
232B PHE* 1.3 119.1 - - + +
234B HIS* 1.3 67.8 + - - +
235B HIS 3.7 0.7 - - - -
236B GLU* 3.5 2.6 + - - +
237B ASN* 3.0 38.7 + - - +
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Residues in contact with HIS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B CYS* 3.3 10.2 - - + +
205B TRP 4.2 5.1 + - - -
206B HIS* 3.2 45.2 + - + +
208B GLU* 5.8 0.9 - - + -
209B CYS* 3.8 8.7 - - - -
230B LEU* 3.4 36.0 + - + +
232B PHE 3.9 0.2 - - - -
233B PRO* 1.3 82.4 - - - +
235B HIS* 1.3 70.2 + - - +
237B ASN* 3.2 2.6 + - - +
238B GLU* 3.0 35.2 + - + +
964B ZN 1.8 37.1 - - - -
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Residues in contact with HIS 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B CYS* 3.5 18.2 - - - -
155B LEU* 3.6 15.9 - - + -
224B HIS* 3.5 23.1 - - - -
225B GLY 3.7 12.8 + - - -
226B GLY* 4.0 3.6 - - - -
230B LEU* 2.8 36.7 + - + +
231B MET 3.4 9.2 - - - +
234B HIS* 1.3 74.5 - + - +
236B GLU* 1.3 63.2 + - - +
238B GLU* 3.1 25.8 + - - +
239B ILE* 3.1 17.7 + - - +
254B TRP* 3.5 16.3 - + + -
256B HIS* 2.7 37.0 + + - -
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B TYR* 4.1 11.9 - - + -
153B GLY* 3.2 26.5 + - - +
154B VAL* 2.9 27.4 + - - +
155B LEU* 3.0 13.0 + - - +
156B SER* 2.6 40.0 + - - -
231B MET 3.1 10.8 + - - +
232B PHE* 3.7 26.0 - - + -
233B PRO 3.9 4.0 - - - +
234B HIS 3.3 0.6 - - - -
235B HIS* 1.3 77.0 - - - +
237B ASN* 1.3 59.7 + - - +
239B ILE* 3.5 8.3 + - - +
240B ALA* 3.2 22.7 + - - +
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Residues in contact with ASN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B TYR* 2.6 35.1 + - - -
181B PHE* 3.3 33.8 - - + +
206B HIS* 3.5 29.4 + - + -
233B PRO* 3.0 29.7 + - - +
234B HIS 3.8 2.7 - - - +
236B GLU* 1.3 74.8 - - - +
238B GLU* 1.3 61.2 + - - +
240B ALA* 3.6 6.0 - - - +
241B GLN* 3.0 36.8 + - - +
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Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B CYS* 3.4 0.9 - - - -
206B HIS 4.1 8.5 - - - +
209B CYS* 3.5 22.3 - - + +
210B SER* 3.2 14.5 + - - +
224B HIS* 2.7 33.6 - - - -
234B HIS* 3.0 25.9 + - + +
235B HIS* 3.1 13.2 + - - +
237B ASN* 1.3 76.2 - - - +
239B ILE* 1.3 53.0 + - - +
241B GLN* 3.3 2.8 + - - -
242B SER* 2.8 40.0 + - - -
250B TYR* 2.7 23.1 + - + +
254B TRP* 4.9 1.1 - - + -
964B ZN 2.4 28.9 - - - -
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 5.2 2.5 - - + -
149B ASP* 5.5 0.4 - - - +
151B THR* 4.9 7.0 - - - +
154B VAL* 3.9 24.5 - - + -
155B LEU* 3.4 38.6 - - + -
235B HIS 3.1 13.2 + - - +
236B GLU* 3.6 9.9 - - - +
238B GLU* 1.3 75.9 - - - +
240B ALA* 1.3 59.5 + - - +
243B THR* 2.3 53.6 + - + +
250B TYR* 4.1 11.7 - - + -
254B TRP* 3.7 28.9 - - + +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B PHE* 3.5 23.3 - - + -
149B ASP* 3.0 26.5 - - - +
152B TYR* 3.9 11.7 - - + -
181B PHE* 4.6 1.3 - - + -
236B GLU 3.2 11.1 + - - +
237B ASN* 3.6 11.4 - - - +
239B ILE* 1.3 78.2 - - - +
241B GLN* 1.3 60.3 + - - +
243B THR* 4.0 0.4 - - - -
244B CYS* 2.9 35.5 + - - +
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Residues in contact with GLN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 5.0 2.5 - - + -
128B LEU* 3.6 11.7 - - + +
144B PHE* 4.0 9.4 - - + -
181B PHE* 3.3 23.0 - - + -
182B VAL 5.2 0.6 + - - -
183B LEU* 3.3 30.7 - - + +
206B HIS* 2.8 23.0 - - - +
207B ILE* 3.5 27.4 - - + +
210B SER* 3.1 19.9 + - - +
237B ASN 3.0 26.4 + - - +
238B GLU* 3.5 3.8 - - - +
240B ALA* 1.3 77.0 - - - +
242B SER* 1.3 57.9 + - - +
245B ALA* 3.0 31.6 + - - +
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B LEU* 5.6 0.7 - - - -
210B SER* 2.8 35.6 + - - -
238B GLU 2.8 15.8 + - - -
241B GLN* 1.3 73.8 - - - +
243B THR* 1.3 56.9 + - - +
245B ALA* 3.2 1.2 + - - -
246B HIS* 2.8 49.5 + - - +
249B GLN 4.8 1.8 - - - -
250B TYR* 3.4 38.2 - - - -
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ASP* 4.6 0.3 + - - -
151B THR* 4.5 10.6 + - - +
239B ILE* 2.3 50.2 + - + +
240B ALA* 3.6 4.3 + - - -
242B SER* 1.3 73.3 - - - +
244B CYS* 1.3 67.4 + - - +
246B HIS 3.7 5.2 + - - +
247B ASP* 3.9 10.0 + - - -
249B GLN* 4.2 15.9 + - - +
250B TYR* 4.0 21.3 - - + -
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Residues in contact with CYS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LEU* 3.9 10.4 - - + +
131B LYS* 4.7 6.9 - - - +
133B HIS* 3.6 52.3 + - + -
144B PHE* 4.1 7.6 - - + -
149B ASP* 3.8 29.8 - - - -
150B PRO* 5.4 2.0 - - - -
240B ALA 2.9 22.0 + - - +
243B THR* 1.3 83.4 + - - +
245B ALA* 1.3 61.3 + - - +
247B ASP 5.3 0.3 + - - -
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 3.8 30.5 - - + +
127B GLN* 4.9 15.9 - - + +
128B LEU* 3.7 15.7 - - + +
241B GLN 3.0 17.9 + - - +
242B SER 3.7 2.9 - - - +
244B CYS* 1.3 80.4 - - - +
246B HIS* 1.3 69.5 + - + +
247B ASP* 3.9 0.6 - - - +
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Residues in contact with HIS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B LEU* 3.5 32.2 - - + +
127B GLN* 6.1 1.8 - - + -
210B SER 5.0 1.6 + - - -
214B CYS* 4.1 15.5 - - + +
219B ASN* 3.7 48.3 + - + +
242B SER* 2.8 35.3 + - - +
243B THR 3.7 0.4 + - - -
244B CYS 3.5 0.6 - - - -
245B ALA* 1.3 89.6 + - + +
247B ASP* 1.3 84.1 + - - +
249B GLN 4.4 6.1 - - - +
250B TYR* 6.0 0.7 - + - -
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Residues in contact with ASP 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ASN* 5.1 4.5 - - - +
243B THR 3.9 11.9 + - - -
244B CYS 5.3 0.4 - - - -
245B ALA 3.9 1.2 - - - +
246B HIS* 1.3 105.4 - - - +
248B GLY* 1.3 56.0 - - - +
249B GLN* 2.7 20.6 + - - +
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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
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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