Contacts of the helix formed by residues 220 - 237 (chain A) in PDB entry 1LT8
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 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A PHE* 1.3 71.8 - - - +
221A PRO* 1.3 74.4 - - + +
222A THR* 3.2 4.4 + - - -
223A ILE* 2.9 25.9 + - - +
224A SER* 2.8 24.2 + - - -
248A PRO* 3.9 1.1 - - - -
249A LEU 4.0 2.0 - - - -
251A TYR 3.0 25.0 + - - +
252A HIS* 3.7 5.6 - - - +
253A THR* 2.7 33.9 + - - +
701A CIT 2.5 32.9 - - - +
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Residues in contact with PRO 221 (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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220A ASP* 1.3 89.2 - - + +
222A THR* 1.3 64.0 + - - +
224A SER* 3.6 0.7 - - - -
225A LEU* 3.0 31.4 + - - +
248A PRO* 3.7 18.6 - - + -
249A LEU 3.3 17.9 - - - +
250A ALA* 5.1 2.0 - - - -
251A TYR 4.6 2.5 - - - +
252A HIS* 5.6 5.4 - - + +
276A ALA* 5.7 3.4 - - + -
280A ASP* 5.6 1.6 - - + +
281A ILE* 4.3 22.4 - - + -
284A TYR* 3.6 30.7 - - + -
287A GLU* 5.9 0.4 - - - -
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Residues in contact with THR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ASP* 3.2 8.3 + - - -
221A PRO* 1.3 82.5 - - - +
223A ILE* 1.3 63.7 + - + +
225A LEU* 3.4 5.4 + - - +
226A LYS* 3.4 37.6 + - + +
252A HIS* 6.2 0.3 - - - -
287A GLU* 5.0 11.5 + - - +
701A CIT 4.2 28.8 + - + +
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Residues in contact with ILE 223 (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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189A PRO* 3.6 27.4 - - + -
219A PHE* 3.7 31.4 - - + -
220A ASP* 2.9 23.6 + - - +
222A THR* 1.3 73.9 - - + +
224A SER* 1.3 62.8 + - - +
226A LYS* 3.0 31.7 + - + +
227A THR* 3.2 11.7 + - - +
253A THR* 3.5 29.2 - - - +
254A PRO* 4.6 4.9 - - + +
256A ALA 5.5 3.6 - - - +
701A CIT 4.3 7.4 - - - +
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Residues in contact with SER 224 (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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215A VAL* 3.9 18.9 - - - +
217A CYS 4.5 3.3 + - - -
219A PHE* 3.1 21.1 + - - +
220A ASP 2.8 23.7 + - - -
221A PRO* 3.6 3.6 - - - -
223A ILE* 1.3 76.9 - - - +
225A LEU* 1.3 60.7 + - - +
227A THR* 3.1 11.9 + - - -
228A VAL* 3.0 29.7 + - - +
246A SER* 5.5 1.3 - - - -
248A PRO* 3.1 23.2 - - - +
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PRO 3.0 21.3 + - - +
222A THR* 3.9 4.9 - - - +
223A ILE 3.3 0.4 - - - -
224A SER* 1.3 73.0 - - - +
226A LYS* 1.3 60.9 + - + +
228A VAL* 4.2 3.1 - - + -
229A LYS* 2.9 28.6 + - - +
246A SER* 4.2 14.4 - - - +
284A TYR* 3.9 22.0 - - + +
287A GLU* 3.6 41.7 - - + +
288A ALA* 3.6 30.3 - - + +
291A LEU* 3.5 18.5 - - + +
293A VAL* 4.6 2.9 - - + -
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Residues in contact with LYS 226 (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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189A PRO* 4.0 15.5 - - + -
222A THR* 3.4 32.6 + - + +
223A ILE* 3.0 23.8 + - + +
225A LEU* 1.3 78.2 - - - +
227A THR* 1.3 62.7 + - - +
229A LYS* 3.4 8.8 + - - +
230A LEU* 3.2 29.2 + - + +
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Residues in contact with THR 227 (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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187A ILE* 3.6 13.6 + - + +
188A GLY* 3.4 15.9 - - - +
189A PRO* 3.3 21.7 - - - +
198A PRO* 4.0 12.3 - - + +
215A VAL* 3.6 28.0 - - + -
219A PHE* 5.4 0.3 - - - -
223A ILE* 3.2 12.1 + - - +
224A SER* 3.1 11.5 + - - -
226A LYS* 1.3 79.2 - - - +
228A VAL* 1.3 60.8 + - - +
230A LEU* 3.1 10.7 + - - +
231A MET* 3.0 29.3 + - + +
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE 5.8 0.4 - - - +
214A GLY* 5.0 2.5 - - - -
215A VAL* 3.8 22.9 - - + +
224A SER 3.0 15.6 + - - +
225A LEU* 3.7 9.2 - - + +
226A LYS 3.3 0.2 - - - -
227A THR* 1.3 74.1 - - - +
229A LYS* 1.3 59.5 + - - +
231A MET* 3.2 10.4 + - + +
232A LYS* 2.9 26.7 + - - +
244A LEU* 4.4 21.5 - - + +
245A MET 4.0 15.0 - - - +
246A SER* 4.3 9.2 - - - -
291A LEU* 3.8 17.5 - - + -
293A VAL* 3.9 16.8 - - + -
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Residues in contact with LYS 229 (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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225A LEU 2.9 17.4 + - - +
226A LYS* 3.6 9.6 - - - +
227A THR 3.2 0.2 - - - -
228A VAL* 1.3 76.2 - - - +
230A LEU* 1.3 59.3 + - + +
232A LYS* 3.3 6.2 + - + +
233A GLU* 2.8 68.0 + - + +
291A LEU* 3.9 28.0 - - + +
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Residues in contact with LEU 230 (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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189A PRO* 3.7 28.7 - - + +
198A PRO* 3.4 31.4 - - + -
199A GLY* 3.4 12.1 - - - +
226A LYS* 3.4 14.6 - - + +
227A THR* 3.1 4.4 + - - +
229A LYS* 1.3 78.7 - - + +
231A MET* 1.3 59.9 + - - +
233A GLU* 3.6 18.4 + - + +
234A GLY 3.0 20.6 + - - -
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Residues in contact with MET 231 (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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185A MET* 3.8 26.5 - - + -
187A ILE* 4.1 14.6 - - + -
198A PRO* 3.5 30.5 - - + +
199A GLY* 4.1 0.2 - - - -
201A ALA* 4.5 4.3 - - + -
202A ALA* 3.6 15.3 - - + +
205A LEU* 4.9 3.6 - - + -
213A ILE* 4.3 13.9 - - + -
214A GLY* 3.5 37.7 - - - +
215A VAL* 4.9 0.7 - - + -
227A THR* 3.0 25.7 + - + +
228A VAL* 3.2 13.0 + - - +
230A LEU* 1.3 75.6 - - - +
232A LYS* 1.3 58.9 + - - +
234A GLY* 3.1 2.3 + - - -
235A LEU* 2.9 33.6 + - - +
244A LEU* 5.4 0.7 - - + -
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Residues in contact with LYS 232 (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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228A VAL 2.9 13.5 + - - +
229A LYS* 3.4 10.5 - - + +
231A MET* 1.3 77.1 - - - +
233A GLU* 1.3 60.5 + - + +
235A LEU* 3.2 8.2 + - - +
236A GLU* 2.9 54.3 + - + +
241A LYS* 4.6 8.9 + - - +
244A LEU* 3.9 28.2 - - + +
290A ASN 5.2 1.0 + - - -
291A LEU* 2.7 46.0 + - + +
292A GLY* 4.7 2.3 - - - -
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Residues in contact with GLU 233 (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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229A LYS* 2.8 54.2 + - + +
230A LEU* 3.9 22.8 - - - +
232A LYS* 1.3 76.9 - - + +
234A GLY* 1.3 66.3 + - - +
236A GLU* 3.6 18.5 - - - +
237A ALA* 3.1 24.4 + - - +
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Residues in contact with GLY 234 (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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199A GLY* 3.8 17.7 - - - -
203A VAL* 3.8 9.4 - - - +
230A LEU 3.0 15.7 + - - -
231A MET 3.1 4.2 + - - -
233A GLU* 1.3 78.4 - - - +
235A LEU* 1.3 60.2 + - - +
237A ALA* 3.4 7.7 + - - +
238A ALA* 3.2 21.0 + - - +
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Residues in contact with LEU 235 (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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202A ALA* 3.5 34.1 - - + +
203A VAL* 3.7 6.3 - - + +
206A VAL* 3.6 22.2 - - + -
213A ILE* 3.8 29.2 - - + -
231A MET 2.9 16.5 + - - +
232A LYS* 3.5 7.0 - - - +
234A GLY* 1.3 73.7 - - - +
236A GLU* 1.3 58.3 + - - +
238A ALA* 2.7 23.5 + - - -
239A GLN 3.0 8.8 + - - -
240A LEU* 3.1 24.4 + - + +
241A LYS* 4.2 18.6 - - - +
242A ALA* 4.3 12.8 - - + +
244A LEU* 4.8 3.8 - - + -
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Residues in contact with GLU 236 (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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232A LYS* 2.9 43.8 + - + +
233A GLU* 3.6 24.4 - - - +
235A LEU* 1.3 75.7 - - - +
237A ALA* 1.3 57.5 + - - +
239A GLN* 3.0 30.1 + - - +
240A LEU 4.2 5.1 + - - -
241A LYS* 5.0 10.2 + - - +
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Residues in contact with ALA 237 (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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233A GLU 3.1 17.9 + - - +
234A GLY* 3.7 7.2 - - - +
235A LEU 3.2 0.2 - - - -
236A GLU* 1.3 75.5 - - - +
238A ALA* 1.3 55.6 + - - +
239A GLN* 3.3 8.0 + - - +
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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