Contacts of the helix formed by residues 205 - 226 (chain B) in PDB entry 1LJ1
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 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ILE 3.7 1.0 + - - -
204B ASN* 1.3 68.6 - - - +
206B PRO* 1.3 67.0 - - - +
207B ALA* 2.9 22.8 + - - +
208B LEU* 3.1 30.5 + - + +
209B VAL* 2.9 27.5 + - - +
357B LYS* 4.6 12.8 + - - +
512B ILE 5.0 2.4 - - - +
538B GLY* 2.9 23.8 + - - +
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Residues in contact with PRO 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 3.5 19.6 - - + -
197B MET* 4.3 18.6 - - + -
204B ASN 3.2 11.2 - - - +
205B ASP* 1.3 90.9 - - - +
207B ALA* 1.3 56.3 + - - +
209B VAL 4.3 0.4 - - - +
210B LYS* 2.8 29.8 + - - +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASP* 2.9 12.0 + - - +
206B PRO* 1.3 79.9 - - - +
208B LEU* 1.3 62.6 + - + +
210B LYS* 3.4 8.2 + - - +
211B VAL* 3.1 25.8 + - - +
514B THR* 3.8 20.8 - - + +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B ASP* 3.1 36.7 + - + +
207B ALA* 1.3 77.3 - - + +
209B VAL* 1.4 65.0 + - - +
211B VAL* 3.2 6.5 + - - +
212B LEU* 3.0 18.5 + - - +
357B LYS* 6.1 1.1 - - + +
512B ILE* 3.9 19.7 - - + +
513B ASP 3.7 31.9 - - - +
514B THR* 4.1 10.8 - - + +
537B GLY 4.2 6.5 - - - +
538B GLY* 3.9 24.0 - - - +
539B VAL* 4.2 16.9 - - + +
556B PHE* 3.7 19.9 - - + -
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 3.5 33.4 - - + +
196B THR* 3.8 26.9 - - + -
197B MET* 3.7 8.3 - - - -
204B ASN* 3.6 20.4 - - + +
205B ASP 2.9 20.7 + - - +
206B PRO 3.9 0.2 - - - +
208B LEU* 1.4 75.4 - - - +
210B LYS* 1.4 63.3 + - - +
212B LEU* 3.1 10.7 + - + +
213B SER* 2.9 24.2 + - - -
539B VAL* 3.5 24.7 - - + +
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 3.8 12.7 - - + -
206B PRO 2.8 18.9 + - - +
207B ALA* 3.5 9.2 - - - +
208B LEU 3.2 0.2 - - - -
209B VAL* 1.4 77.6 - - - +
211B VAL* 1.3 63.3 + - + +
213B SER* 3.4 6.8 + - - +
214B SER* 2.9 40.6 + - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ALA 3.1 16.4 + - - +
208B LEU* 3.2 8.7 + - - +
210B LYS* 1.3 75.8 - - + +
212B LEU* 1.3 65.0 + - - +
214B SER* 3.9 4.9 - - - -
215B HIS* 2.9 45.9 + - + +
514B THR* 3.9 30.7 - - + +
555B THR* 3.8 15.9 - - + +
556B PHE* 3.7 22.4 - - + -
559B LEU* 4.3 7.0 - - + -
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Residues in contact with LEU 212 (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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192B MET* 4.2 9.8 - - + +
196B THR* 4.4 15.0 - - + +
208B LEU 3.0 13.0 + - - +
209B VAL* 3.1 13.0 + - + +
211B VAL* 1.3 80.0 - - - +
213B SER* 1.3 62.6 + - - +
215B HIS* 4.2 0.5 - - - +
216B SER* 3.3 22.7 + - - -
539B VAL* 4.3 19.3 - - + -
540B HIS* 4.6 1.1 - - - +
548B ASN* 3.9 33.2 - - + +
551B SER* 3.9 11.1 + - - +
552B ASP* 3.6 41.1 - - + +
555B THR* 4.6 9.0 + - - -
556B PHE* 4.5 5.3 - - + -
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Residues in contact with SER 213 (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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175B ALA 4.6 0.3 - - - +
189B PRO* 3.6 37.5 + - - +
192B MET* 4.2 13.7 - - - -
193B PHE* 3.7 24.7 - - - +
209B VAL* 2.9 19.0 + - - -
210B LYS* 3.4 8.8 + - - +
212B LEU* 1.3 74.9 - - - +
214B SER* 1.3 66.2 + - - +
216B SER* 2.9 24.0 + - - -
217B LYS 4.8 0.2 + - - -
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Residues in contact with SER 214 (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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189B PRO* 4.6 11.3 - - - +
210B LYS* 2.9 37.4 + - - +
211B VAL* 3.9 0.7 - - - -
213B SER* 1.3 79.9 + - - +
215B HIS* 1.3 74.8 + - - +
217B LYS* 4.9 3.5 + - - +
218B ASP* 5.4 2.4 + - - +
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Residues in contact with HIS 215 (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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211B VAL* 2.9 38.1 + - + +
214B SER* 1.3 90.2 + - - +
216B SER* 1.3 63.0 + - - +
217B LYS 3.5 1.8 - - - -
218B ASP* 3.3 13.5 + - + +
219B SER* 3.0 22.4 + - - +
555B THR* 3.7 27.7 + - + +
559B LEU* 4.9 19.2 - - + +
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Residues in contact with SER 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B MET* 4.9 0.7 - - - +
173B ASN 4.0 6.9 - - - +
174B ALA* 3.4 25.4 - - - +
175B ALA 3.1 22.0 + - - -
192B MET* 3.7 7.5 - - - -
212B LEU 3.3 18.2 + - - -
213B SER 2.9 18.1 + - - -
214B SER 3.4 0.2 - - - -
215B HIS* 1.3 75.5 - - - +
217B LYS* 1.3 61.4 + - - +
219B SER* 3.3 8.5 + - - -
220B VAL* 3.1 18.7 + - - +
551B SER* 4.0 5.8 - - - -
555B THR* 4.5 2.9 - - - -
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Residues in contact with LYS 217 (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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174B ALA* 4.0 0.2 - - - +
175B ALA 3.9 15.7 + - - +
176B TRP 3.6 19.7 - - - +
177B THR* 4.1 22.7 - - + -
178B ASP* 3.7 30.1 + - - +
181B LYS* 6.0 1.3 - - - +
213B SER 4.8 0.4 + - - -
214B SER 4.9 3.0 + - - +
215B HIS 3.5 0.4 - - - -
216B SER* 1.3 79.7 + - - +
218B ASP* 1.3 59.4 + - - +
220B VAL* 3.2 5.2 + - - +
221B ASP* 2.8 52.9 + - - +
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Residues in contact with ASP 218 (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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214B SER 5.4 3.0 + - - +
215B HIS* 3.3 16.9 + - + +
217B LYS* 1.3 75.7 - - - +
219B SER* 1.3 63.2 + - - +
221B ASP* 3.4 11.9 + - - +
222B TRP* 2.9 29.1 + - - +
558B ARG* 3.7 17.9 + - - +
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Residues in contact with SER 219 (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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172B MET* 3.9 17.9 - - - -
215B HIS* 3.0 8.2 + - - +
216B SER* 3.6 9.0 - - - -
217B LYS 3.2 0.2 - - - -
218B ASP* 1.3 81.3 - - - +
220B VAL* 1.3 64.8 + - - +
222B TRP* 3.3 7.2 + - - +
223B MET* 3.1 27.4 + - - +
551B SER* 5.1 0.4 - - - -
554B ILE* 4.0 11.6 - - - +
555B THR* 2.7 38.4 + - - -
558B ARG* 4.9 7.7 + - - +
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Residues in contact with VAL 220 (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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172B MET* 3.9 28.5 - - + -
174B ALA* 3.7 27.1 - - + -
177B THR* 4.6 5.6 - - + -
179B GLN* 3.7 33.9 - - - +
216B SER 3.1 5.4 + - - +
217B LYS 3.6 7.9 - - - +
218B ASP 3.2 0.2 - - - -
219B SER* 1.3 76.8 - - - +
221B ASP* 1.3 57.8 + - - +
223B MET* 3.3 2.6 + - - +
224B THR* 2.8 35.1 + - - +
230B LEU* 4.1 16.4 - - + +
245B HIS* 4.6 11.7 - - + +
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Residues in contact with ASP 221 (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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178B ASP* 4.7 7.4 + - - +
179B GLN* 4.5 14.2 + - - +
217B LYS* 2.8 52.2 + - - +
218B ASP* 3.7 16.5 - - - +
219B SER 3.3 0.2 - - - -
220B VAL* 1.3 77.4 - - - +
222B TRP* 1.3 52.4 + - - +
224B THR* 3.7 6.4 - - - -
225B ALA* 2.8 34.3 + - - +
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Residues in contact with TRP 222 (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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140B SER* 3.5 47.6 - - - -
143B ILE* 4.0 16.6 - - + +
144B SER* 4.0 19.1 - - - -
147B ASP* 5.6 3.4 + - - -
218B ASP 2.9 17.2 + - - +
219B SER* 3.6 3.6 - - - +
221B ASP* 1.3 70.8 - - - +
223B MET* 1.3 69.0 + - - +
225B ALA* 3.4 7.7 + - + +
226B MET* 3.1 59.6 + - + +
261B LEU* 4.8 0.4 - - + -
554B ILE* 3.9 20.0 - - + -
558B ARG* 3.4 53.8 - - + +
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Residues in contact with MET 223 (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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172B MET* 4.5 9.9 - - + -
219B SER 3.1 19.8 + - - +
220B VAL 3.8 3.8 - - - +
222B TRP* 1.3 76.4 - - - +
224B THR* 1.3 62.7 + - - +
226B MET* 3.1 29.3 + - + +
227B GLY 3.1 1.2 + - - -
228B ALA* 2.8 24.3 + - + +
230B LEU* 3.9 15.7 - - + -
257B VAL* 3.9 30.7 - - + +
260B VAL* 4.1 21.3 - - + +
261B LEU* 3.9 23.3 - - + -
554B ILE* 3.9 30.5 - - + -
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Residues in contact with THR 224 (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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179B GLN* 3.6 23.9 + - - +
220B VAL* 2.8 23.6 + - - +
221B ASP* 3.8 7.0 - - - -
223B MET* 1.3 78.5 - - - +
225B ALA* 1.3 63.6 + - - +
227B GLY* 2.9 15.6 + - - -
228B ALA 3.5 22.0 + - - +
230B LEU* 4.3 8.9 + - - +
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Residues in contact with ALA 225 (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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221B ASP 2.8 22.6 + - - +
222B TRP* 3.9 7.4 - - + +
224B THR* 1.3 73.3 - - - +
226B MET* 1.4 59.3 + - + +
227B GLY 3.2 0.6 + - - -
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Residues in contact with MET 226 (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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143B ILE* 4.2 20.6 - - - -
222B TRP* 3.1 61.0 + - + +
223B MET* 3.1 25.5 + - + +
225B ALA* 1.4 75.9 - - + +
227B GLY* 1.3 56.0 + - - +
228B ALA 3.8 0.2 - - - -
260B VAL* 3.5 8.3 - - + +
261B LEU* 4.0 10.1 - - + -
264B ASN* 2.9 58.5 + - - +
268B ARG* 4.7 7.0 - - - +
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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
------------------------------------------------------------
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