Contacts of the helix formed by residues 220 - 228 (chain B) in PDB entry 3LSG
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 LYS 220 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B GLU 4.3 10.7 + - - +
219B LEU* 1.3 75.7 - - - +
221B ASN* 1.3 67.5 + - - +
222B TYR* 3.2 24.9 - - + -
223B GLU* 2.8 31.6 + - - +
224B ILE* 3.0 12.3 + - - +
252B ARG* 4.7 3.6 - - - +
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Residues in contact with ASN 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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214B LEU* 4.1 9.9 - - - +
220B LYS* 1.3 72.8 - - - +
222B TYR* 1.3 58.0 + - - +
224B ILE* 3.8 6.0 - - - +
225B ALA* 2.9 31.2 + - - +
233B VAL* 3.8 15.0 - - + -
236B PHE* 3.8 6.9 - - + -
237B ILE* 3.9 22.3 - - + +
248B PRO* 3.3 33.8 - - - +
249B LYS* 5.2 3.6 - - - +
252B ARG* 5.0 3.2 + - - +
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Residues in contact with TYR 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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220B LYS* 3.2 24.1 - - + -
221B ASN* 1.3 77.7 - - - +
223B GLU* 1.3 89.9 + - + +
225B ALA* 3.8 2.0 - - - +
226B GLU* 3.2 31.3 + - - +
233B VAL* 3.6 28.3 - - + +
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Residues in contact with GLU 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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218B GLU 4.7 0.2 - - - +
219B LEU* 3.7 30.0 - - + +
220B LYS* 2.8 36.6 + - - +
222B TYR* 1.3 111.8 + - + +
224B ILE* 1.3 65.6 + - - +
226B GLU* 3.2 9.6 + - - +
227B GLN* 2.9 33.0 + - - +
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Residues in contact with ILE 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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210B ALA* 4.1 16.2 - - + -
213B LEU* 4.0 32.1 - - + -
214B LEU* 3.2 36.8 - - + -
219B LEU* 3.7 29.6 - - + +
220B LYS 3.0 12.0 + - - +
221B ASN* 3.8 8.3 - - - +
223B GLU* 1.3 75.3 - - - +
225B ALA* 1.3 64.2 + - - +
227B GLN* 3.0 2.4 + - - -
228B VAL* 2.9 24.1 + - + +
236B PHE* 3.6 23.3 - - + -
252B ARG* 4.0 5.2 - - - +
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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 ASN 2.9 21.7 + - - +
222B TYR 3.8 5.2 - - - +
223B GLU 3.3 0.2 - - - -
224B ILE* 1.3 74.1 - - - +
226B GLU* 1.3 60.7 + - - +
228B VAL* 3.5 1.8 + - - +
229B GLY 3.4 2.9 + - - -
230B PHE* 2.9 33.4 + - + +
232B ASP 4.3 1.8 - - - +
233B VAL* 4.0 15.9 - - - +
236B PHE* 3.4 39.2 - - + -
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Residues in contact with GLU 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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166B THR 4.3 4.2 - - - +
222B TYR* 3.2 20.8 + - - +
223B GLU* 3.2 14.1 + - - +
224B ILE 3.2 0.2 - - - -
225B ALA* 1.3 78.8 - - - +
227B GLN* 1.3 66.4 + - + +
229B GLY* 3.3 12.3 + - - -
230B PHE 4.2 9.2 - - - +
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Residues in contact with GLN 227 (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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166B THR* 3.0 27.2 + - - +
209B LYS* 5.3 5.6 + - - +
213B LEU* 4.2 19.5 - - + +
219B LEU* 3.7 38.4 - - - +
223B GLU* 2.9 23.3 + - - +
224B ILE 3.0 3.8 + - - +
226B GLU* 1.3 79.9 - - + +
228B VAL* 1.3 60.6 + - - +
229B GLY 3.4 0.4 + - - -
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Residues in contact with VAL 228 (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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165B TYR* 4.2 4.9 - - + -
166B THR* 4.2 3.6 - - - +
206B ARG* 3.0 55.9 + - + +
209B LYS* 3.7 28.3 - - + -
210B ALA* 3.9 6.3 - - - +
213B LEU* 3.7 13.0 - - + -
224B ILE* 2.9 21.6 + - + +
225B ALA 4.0 1.6 - - - +
227B GLN* 1.3 78.6 - - - +
229B GLY* 1.3 58.2 + - - +
230B PHE* 3.8 23.1 - - + -
236B PHE* 4.2 13.7 - - + -
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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