Contacts of the helix formed by residues 211 - 219 (chain B) in PDB entry 1L8R
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 LEU 211 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B ILE 3.1 4.7 + - - -
210B CYS* 1.3 67.5 - - - +
212B PRO* 1.3 67.3 - - + +
214B ALA* 3.2 3.8 + - - +
215B PHE* 2.8 31.5 + - + +
226B LEU* 4.3 8.3 - - + -
229B VAL* 4.2 17.0 - - + -
230B TYR* 3.8 29.2 - - + +
233B LEU* 3.9 19.5 - - + -
240B PRO* 4.6 5.4 - - + -
265B LYS* 3.1 28.1 + - + +
267B ILE* 4.0 29.2 - - + -
272B PHE* 4.2 16.8 - - + -
275B LEU* 4.3 5.8 - - + -
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Residues in contact with PRO 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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210B CYS* 3.5 5.6 - - - -
211B LEU* 1.3 95.6 - - + +
213B GLN* 1.3 56.7 + - - +
215B PHE* 3.4 9.5 + - + +
216B ASP* 2.9 38.8 + - - +
226B LEU* 4.4 22.9 - - + -
230B TYR* 6.0 1.1 - - - +
257B ILE* 3.6 13.7 - - + -
261B VAL* 6.3 0.4 - - + -
263B ARG 5.8 0.4 - - - +
264B CYS* 3.4 32.8 - - - -
265B LYS* 3.6 4.7 - - + +
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Residues in contact with GLN 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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190B MSE 5.7 2.8 - - - -
197B LYS 4.1 11.7 + - - -
198B VAL* 3.4 16.9 - - + +
199B ALA* 2.8 30.9 + - - +
210B CYS* 3.4 15.4 + - - +
211B LEU 3.2 0.4 - - - -
212B PRO* 1.3 78.0 - - - +
214B ALA* 1.3 67.6 + - - +
216B ASP* 3.3 8.3 + - + +
217B LEU* 3.1 30.3 + - + +
254B LEU 5.8 0.6 + - - -
255B GLY 5.0 1.4 + - - -
256B ALA* 3.5 44.8 + - - +
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Residues in contact with ALA 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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193B LEU* 3.7 24.5 - - + -
198B VAL* 4.7 5.4 - - + +
209B ILE* 4.3 4.7 - - + -
210B CYS 3.1 16.4 + - - +
211B LEU* 3.7 3.1 - - - +
213B GLN* 1.3 77.9 - - - +
215B PHE* 1.3 56.9 + - - +
217B LEU* 4.6 1.1 - - - -
218B PHE* 3.0 37.2 + - - +
272B PHE* 3.4 31.2 - - + -
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Residues in contact with PHE 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 LEU* 2.8 19.8 + - + +
212B PRO* 3.4 6.7 - - + +
214B ALA* 1.3 77.3 - - - +
216B ASP* 1.3 80.1 + - - +
219B LEU* 2.9 54.7 + - + -
220B LYS* 3.3 16.9 + - - -
222B LEU* 3.7 7.6 - - + -
225B GLY* 3.4 26.2 - - - -
226B LEU* 3.4 38.8 - - + -
229B VAL* 3.7 18.4 - - + -
272B PHE* 4.3 4.2 - - - -
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Residues in contact with ASP 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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212B PRO* 2.9 25.8 + - - +
213B GLN* 3.3 9.3 + - - +
215B PHE* 1.3 96.3 - - - +
217B LEU* 1.3 62.9 + - + +
220B LYS* 3.7 19.9 - - - +
256B ALA 4.6 5.9 - - - +
257B ILE* 5.9 0.7 - - - -
258B GLN* 5.5 5.7 + - - +
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Residues in contact with LEU 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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196B ALA* 4.0 22.7 - - + -
197B LYS 4.3 6.1 - - - +
198B VAL* 3.7 29.6 - - + -
213B GLN* 3.1 25.4 + - + +
215B PHE 3.2 0.2 - - - -
216B ASP* 1.3 81.5 - - + +
218B PHE* 1.3 82.6 + - + +
219B LEU 3.9 0.2 - - - -
220B LYS* 5.0 2.0 - - - +
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Residues in contact with PHE 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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193B LEU* 3.0 47.1 - - + -
194B ARG* 3.6 37.2 - - + +
196B ALA* 3.7 18.4 - - + -
214B ALA* 3.0 17.2 + - - +
217B LEU* 1.3 98.3 - - + +
219B LEU* 1.3 62.0 + - - +
220B LYS 3.7 1.3 - - - -
272B PHE* 4.1 10.8 - + + -
276B TYR* 3.4 35.5 + - + -
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Residues in contact with LEU 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 PHE* 2.9 30.9 + - + +
218B PHE* 1.3 81.5 - - - +
220B LYS* 1.3 66.5 + - - +
221B HIS 3.3 2.5 - - - -
222B LEU* 2.9 39.7 - - + +
272B PHE* 4.1 17.9 - - + -
275B LEU* 4.1 31.0 - - + -
276B TYR* 3.5 30.3 - - + -
279B CYS* 3.9 23.8 - - + -
280B THR* 4.4 6.5 - - + -
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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