Contacts of the helix formed by residues 207 - 221 (chain B) in PDB entry 3LKB
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 VAL 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B THR* 3.8 35.9 - - + +
22B ASP* 4.6 3.8 - - + -
23B ALA* 4.0 16.8 - - + +
151B HIS* 4.8 5.6 - - + -
155B PHE* 4.0 10.4 - - + -
206B ASN* 1.3 90.4 + - - +
208B ALA* 1.3 67.5 + - - +
209B GLY 3.4 0.9 + - - -
210B PRO* 3.5 18.6 - - + +
211B VAL* 3.4 15.4 - - - +
232B TYR* 3.3 10.8 - - + +
233B THR* 4.2 1.8 - - - -
393B VAL 4.5 1.3 - - - +
4571B IPA 3.6 35.7 - - + +
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Residues in contact with ALA 208 (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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22B ASP* 4.8 8.2 + - + +
207B VAL* 1.3 77.8 - - - +
209B GLY* 1.3 58.3 + - - +
211B VAL* 3.4 3.1 + - - +
212B ALA* 2.9 32.6 + - - +
232B TYR 3.4 5.6 + - - +
233B THR 3.6 24.0 - - - +
234B GLY 5.1 1.3 - - - +
237B ASP* 4.2 15.5 - - + +
238B LEU* 4.0 24.9 - - - +
241B LEU* 4.7 4.7 - - + -
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Residues in contact with GLY 209 (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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22B ASP* 3.4 20.6 + - - -
182B SER* 6.1 0.2 - - - -
208B ALA* 1.3 78.5 - - - +
210B PRO* 1.4 68.9 - - - +
212B ALA* 3.2 6.4 + - - +
213B ASN* 3.1 28.7 + - - -
241B LEU* 4.7 10.1 - - - -
4571B IPA 5.5 0.4 - - - -
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Residues in contact with PRO 210 (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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151B HIS* 5.1 1.1 - - + -
180B VAL* 4.2 4.0 - - + +
181B GLY* 3.7 33.7 - - - +
182B SER* 3.9 15.9 - - - +
184B ASN* 3.1 25.5 + - - +
206B ASN* 3.8 28.0 - - - +
207B VAL* 3.5 22.4 - - + +
209B GLY* 1.4 84.6 - - - +
211B VAL* 1.3 64.3 + - - +
213B ASN 3.2 1.2 + - - -
214B ILE* 3.1 22.3 + - + +
4571B IPA 4.5 0.7 - - - +
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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
----------------------------------------------------------
204B HIS* 3.7 37.7 - - + +
206B ASN* 3.8 16.6 - - + -
207B VAL 3.4 15.9 + - - +
208B ALA* 3.4 8.5 + - - +
209B GLY 3.3 0.4 - - - -
210B PRO* 1.3 74.4 - - - +
212B ALA* 1.3 65.5 + - - +
214B ILE* 3.0 6.4 + - - +
215B LEU* 2.9 30.6 + - + +
233B THR* 4.0 9.6 - - + +
238B LEU* 4.4 6.3 - - + -
249B PHE* 3.6 33.7 - - + -
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Residues in contact with ALA 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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208B ALA 2.9 17.9 + - - +
209B GLY 3.5 4.0 - - - +
211B VAL* 1.3 76.5 - - - +
213B ASN* 1.3 63.9 + - - +
215B LEU* 3.2 5.2 + - - +
216B LYS* 3.1 29.6 + - + +
238B LEU* 4.6 4.2 - - + +
241B LEU* 3.5 34.3 - - + +
242B ALA* 3.6 21.3 - - + -
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Residues in contact with ASN 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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216A LYS* 5.3 5.9 + - - -
183B GLY 4.9 4.2 - - - +
184B ASN* 3.0 50.2 + - - +
185B LEU* 4.6 10.6 - - - +
187B ASN* 3.6 7.9 + - - +
209B GLY 3.1 18.3 + - - +
210B PRO 3.2 1.5 + - - +
212B ALA* 1.3 77.4 - - - +
214B ILE* 1.3 61.0 + - - +
216B LYS* 3.4 24.2 + - - +
217B ASP* 3.2 21.5 + - - +
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Residues in contact with ILE 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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149B VAL* 4.1 22.0 - - + -
180B VAL* 4.3 8.3 - - + -
184B ASN* 3.7 7.4 - - - +
187B ASN* 3.6 30.3 - - + +
190B LEU* 4.3 7.9 - - + -
191B LEU* 4.0 25.5 - - + +
194B PHE* 6.3 0.2 - - + -
202B VAL* 5.8 1.1 - - + -
204B HIS* 4.1 24.7 - - + +
206B ASN* 5.9 0.4 - - - +
210B PRO* 3.1 16.3 + - + +
211B VAL 3.0 7.4 + - - +
213B ASN* 1.3 72.5 - - - +
215B LEU* 1.3 67.6 + - - +
216B LYS 3.2 0.2 + - - -
217B ASP* 3.3 1.7 + - - +
218B ALA* 2.9 22.2 + - - +
227B HIS* 4.1 15.3 - - + +
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Residues in contact with LEU 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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204B HIS* 4.8 0.4 - - + -
211B VAL* 2.9 27.1 + - + +
212B ALA 3.8 5.6 - - - +
214B ILE* 1.3 76.2 - - - +
216B LYS* 1.3 57.4 + - - +
218B ALA* 3.8 3.6 - - - +
219B LYS* 2.9 29.1 + - - +
227B HIS* 3.3 47.3 - - + +
238B LEU* 4.2 8.7 - - + -
242B ALA* 4.4 4.5 - - + -
245B ALA* 3.4 22.6 - - + +
246B ALA* 3.9 26.0 - - + -
249B PHE* 3.8 23.6 - - + -
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Residues in contact with LYS 216 (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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185A LEU* 4.4 22.4 - - - +
213A ASN* 5.4 4.9 + - - -
216A LYS* 5.4 8.7 - - - +
212B ALA* 3.1 21.6 + - - +
213B ASN* 3.6 22.4 + - - +
214B ILE 3.2 0.2 - - - -
215B LEU* 1.3 74.3 - - - +
217B ASP* 1.3 61.6 + - - +
219B LYS* 3.4 5.0 + - + +
220B ARG* 3.0 31.9 + - - +
241B LEU 3.6 25.8 + - - +
242B ALA* 4.1 8.3 - - - +
245B ALA* 3.8 18.2 - - + -
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Residues in contact with ASP 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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185B LEU 3.6 13.7 - - - +
186B ASP* 4.6 6.0 - - - +
187B ASN* 2.7 45.3 + - + +
188B THR* 4.9 0.9 - - - +
191B LEU* 3.9 15.0 - - + -
213B ASN 3.2 10.4 + - - +
214B ILE 3.8 3.6 - - - +
216B LYS* 1.3 79.5 - - - +
218B ALA* 1.3 56.0 + - - +
220B ARG* 3.1 10.4 + - - +
221B LEU* 2.9 35.1 + - + +
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Residues in contact with ALA 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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191B LEU* 3.5 18.4 - - + +
214B ILE 2.9 21.0 + - - +
215B LEU* 3.8 4.5 - - + +
217B ASP* 1.3 72.6 - - - +
219B LYS* 1.3 59.5 + - - +
221B LEU 3.5 0.5 + - - -
222B GLY 3.4 2.6 + - - -
223B LEU* 3.1 47.5 + - + +
227B HIS* 4.0 25.4 - - + -
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Residues in contact with LYS 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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215B LEU 2.9 18.5 + - - +
216B LYS* 3.6 6.3 - - + +
217B ASP 3.3 0.4 - - - -
218B ALA* 1.3 73.3 - - - +
220B ARG* 1.3 77.7 + - - +
222B GLY* 3.2 13.4 + - - -
244B ASP* 4.3 18.9 + - - +
245B ALA* 4.0 32.6 - - + +
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Residues in contact with ARG 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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186A ASP* 5.2 8.9 + - - -
217A ASP* 5.3 6.3 + - - -
220A ARG* 4.3 38.8 - - + +
216B LYS 3.0 15.1 + - - +
217B ASP* 3.1 15.5 + - - +
219B LYS* 1.3 87.0 - - - +
221B LEU* 1.3 61.6 + - + +
222B GLY 3.2 1.1 + - - -
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Residues in contact with LEU 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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188B THR* 4.3 20.9 - - - +
191B LEU* 4.0 18.6 - - + -
192B LYS* 4.0 32.7 + - + +
217B ASP* 2.9 20.9 + - + +
218B ALA 4.1 0.4 - - - +
219B LYS 3.1 0.8 - - - -
220B ARG* 1.3 79.1 - - + +
222B GLY* 1.3 61.7 + - - +
223B LEU* 3.3 35.5 + - + +
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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