Contacts of the helix formed by residues 206 - 210 (chain B) in PDB entry 3L43
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 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B SER* 2.7 31.3 + - - -
42B ALA 3.8 14.1 - - - -
176B PRO* 3.9 15.7 - - + -
177B ALA* 3.9 5.7 - - - +
178B ASN* 4.0 18.3 + - - +
205B THR* 1.4 80.8 - - - +
207B LEU* 1.4 56.1 + - - +
208B ASP* 3.1 8.5 - - - -
209B LEU* 2.9 46.1 + - + +
210B MET 3.8 3.1 + - - -
234B VAL 4.0 0.4 + - - -
901B GDP 3.0 59.6 + - + -
178C ASN 5.2 5.5 + - - -
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Residues in contact with LEU 207 (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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177B ALA* 3.7 24.0 - - + -
204B ILE* 3.4 27.6 - - + +
205B THR 3.2 2.6 - - - -
206B LYS* 1.4 74.5 - - - +
208B ASP* 1.3 61.0 + - - +
210B MET* 3.5 18.7 - - - +
216B ALA* 3.7 15.5 - - + -
220B LEU* 3.9 8.7 - - + -
233B GLY* 3.7 11.9 - - - -
234B VAL 3.7 10.8 + - - +
235B VAL* 4.1 0.9 - - + +
258B PHE* 3.4 26.1 - - + -
259B PHE* 3.7 25.1 - - + -
262B HIS* 5.4 1.7 + - - -
265B TYR* 3.3 30.6 + - + +
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Residues in contact with ASP 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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206B LYS* 3.6 4.5 - - - -
207B LEU* 1.3 78.6 - - - +
209B LEU* 1.4 63.2 + - - +
210B MET 3.4 4.7 + - - +
235B VAL* 3.8 21.5 - - + +
236B ASN 4.8 0.7 - - - +
238B SER* 5.1 1.7 - - - -
258B PHE* 3.6 25.2 - - + -
901B GDP 2.7 46.8 + - - +
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Residues in contact with LEU 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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178B ASN* 3.7 33.0 - - - +
206B LYS* 2.9 31.5 + - + +
208B ASP* 1.4 82.5 - - - +
210B MET* 1.3 64.8 + - - +
211B ASP 3.7 1.0 + - - -
901B GDP 3.5 27.4 - - + +
178C ASN* 5.0 0.4 + - + -
209C LEU* 4.4 22.4 - - - +
210C MET 5.5 0.4 - - - +
211C ASP* 3.4 45.8 - - + +
212C GLU 5.3 0.7 - - - +
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Residues in contact with MET 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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177B ALA* 3.7 44.0 - - + +
178B ASN* 4.7 5.4 - - - +
206B LYS 3.8 0.2 + - - -
207B LEU* 3.5 17.5 - - - +
208B ASP 3.4 4.9 - - - +
209B LEU* 1.3 80.1 - - - +
211B ASP* 1.3 64.7 + - - +
212B GLU* 3.6 1.9 + - - -
214B THR* 3.6 24.0 - - - +
215B ASP* 3.6 23.1 - - - +
216B ALA* 3.5 22.9 - - + +
262B HIS* 6.3 0.9 - - - +
265B TYR* 3.6 12.3 - - - -
209C LEU* 5.0 1.4 - - - +
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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