Contacts of the helix formed by residues 220 - 228 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218D GLU 4.3 10.1 + - - +
219D LEU* 1.3 76.6 - - - +
221D ASN* 1.3 68.8 + - - +
222D TYR* 3.2 33.0 - - + -
223D GLU* 2.9 23.5 + - - +
224D ILE* 2.9 20.2 + - - +
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Residues in contact with ASN 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D LEU* 4.8 9.2 - - - +
219D LEU 5.2 0.5 - - - +
220D LYS* 1.3 75.5 - - - +
222D TYR* 1.3 58.8 + - - +
224D ILE* 3.2 16.4 + - - +
225D ALA* 2.7 30.5 + - - +
233D VAL* 3.6 17.3 - - + +
236D PHE* 4.2 10.6 - - + -
237D ILE* 3.7 27.4 - - + +
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Residues in contact with TYR 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D LYS* 3.2 31.7 - - + +
221D ASN* 1.3 78.2 - - - +
223D GLU* 1.3 81.5 + - + +
225D ALA* 3.5 2.7 - - - +
226D GLU* 3.1 38.2 + - - +
233D VAL* 3.5 28.9 - - + +
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Residues in contact with GLU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D LEU* 3.5 29.6 - - + +
220D LYS* 2.9 47.3 + - + +
222D TYR* 1.3 104.5 + - + +
224D ILE* 1.3 65.8 + - - +
226D GLU* 2.9 21.8 - - - +
227D GLN* 2.9 31.5 + - - +
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Residues in contact with ILE 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210D ALA* 3.8 25.4 - - + +
213D LEU* 4.1 16.8 - - + +
214D LEU* 4.0 39.0 - - + +
219D LEU* 3.9 30.3 - - + +
220D LYS 2.9 17.2 + - - +
221D ASN* 3.7 10.8 - - - +
223D GLU* 1.3 74.8 - - - +
225D ALA* 1.3 64.0 + - - +
227D GLN* 3.1 6.5 + - - +
228D VAL* 3.0 23.4 + - + +
236D PHE* 3.7 24.0 - - + -
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Residues in contact with ALA 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ASN 2.7 21.0 + - - +
222D TYR 3.5 6.5 - - - +
224D ILE* 1.3 74.8 - - - +
226D GLU* 1.3 61.6 + - - +
228D VAL* 3.3 4.5 + - - +
229D GLY 3.4 0.2 + - - -
230D PHE* 3.1 29.1 + - + +
232D ASP 4.4 2.5 - - - +
233D VAL* 3.8 20.4 - - + +
236D PHE* 3.8 34.7 - - + -
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Residues in contact with GLU 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D THR 3.6 8.5 - - - +
168D SER* 6.0 0.3 - - - -
222D TYR* 3.1 18.5 + - - +
223D GLU* 2.9 44.1 - - - +
225D ALA* 1.3 79.6 - - - +
227D GLN* 1.3 70.6 + - + +
228D VAL 3.4 0.9 + - - -
229D GLY* 3.4 9.5 + - - -
230D PHE 4.3 8.2 - - - +
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Residues in contact with GLN 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D THR* 3.2 28.0 - - - +
209D LYS* 4.8 5.6 + - - +
213D LEU* 4.1 17.8 - - + +
219D LEU* 3.5 36.6 - - - +
223D GLU* 2.9 23.7 + - - +
224D ILE 3.1 2.9 + - - +
226D GLU* 1.3 87.6 + - + +
228D VAL* 1.3 61.3 + - - +
229D GLY 3.5 0.2 - - - -
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D TYR* 4.1 1.1 - - + -
166D THR* 4.0 10.3 - - - +
206D ARG* 3.0 44.6 + - + +
209D LYS* 3.8 17.0 - - + -
210D ALA* 3.7 30.5 - - - +
213D LEU* 4.1 6.5 - - + -
224D ILE 3.0 20.4 + - - +
225D ALA 3.6 6.3 - - - +
227D GLN* 1.3 79.5 - - - +
229D GLY* 1.3 58.0 + - - +
230D PHE* 3.6 16.1 + - + -
236D PHE* 4.0 18.4 - - + -
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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