Contacts of the helix formed by residues 200 - 208 (chain B) in PDB entry 3KSA
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 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B THR 3.6 2.9 + - - +
199B ALA* 1.3 75.9 - - - +
201B ILE* 1.3 65.9 + - - +
202B ASP* 3.3 10.3 - - + +
203B LYS* 3.3 13.1 + - + +
204B LEU* 3.2 19.9 + - - +
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Residues in contact with ILE 201 (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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199B ALA 4.1 0.8 + - - -
200B LYS* 1.3 70.5 - - - +
202B ASP* 1.3 73.1 + - - +
204B LEU* 3.0 9.6 + - + +
205B MET* 2.8 43.0 + - + +
226B LYS* 4.5 7.0 - - + +
229B TYR* 3.3 18.8 - - + +
230B GLU* 3.2 48.0 - - + +
342B ILE* 5.3 3.6 - - + +
343B VAL* 4.2 20.6 - - + +
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Residues in contact with ASP 202 (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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200B LYS* 3.3 7.6 - - + +
201B ILE* 1.3 84.3 - - - +
203B LYS* 1.3 61.7 + - - +
205B MET* 3.3 17.8 - - - +
206B GLU* 3.5 5.0 + - - +
226B LYS* 5.9 3.1 - - - +
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Residues in contact with LYS 203 (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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192B TYR* 4.8 22.2 - - + +
199B ALA* 5.7 0.2 - - + -
200B LYS* 3.3 15.8 + - + +
201B ILE 3.2 0.4 - - - -
202B ASP* 1.3 76.0 - - - +
204B LEU* 1.3 67.3 + - + +
206B GLU* 3.0 23.5 + - - +
207B PHE* 3.7 10.0 - - + -
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Residues in contact with LEU 204 (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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189B ALA* 3.9 28.8 - - + +
192B TYR* 4.7 10.3 - - + -
193B MET* 3.7 35.2 - - + -
199B ALA* 4.2 12.1 - - + -
200B LYS 3.2 14.6 + - - +
201B ILE* 3.0 11.3 + - - +
203B LYS* 1.3 77.4 - - - +
205B MET* 1.3 59.0 + - + +
207B PHE* 2.9 23.2 + - + +
208B LEU* 2.9 16.1 + - + +
342B ILE* 4.1 21.5 - - + -
343B VAL* 3.7 28.9 - - + -
346B LEU* 4.3 1.6 - - + -
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Residues in contact with MET 205 (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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201B ILE* 2.8 29.5 + - + +
202B ASP* 3.3 13.0 - - - +
204B LEU* 1.3 74.9 - - + +
206B GLU* 1.3 64.4 + - - +
207B PHE 3.3 0.5 + - - -
208B LEU 3.3 13.5 - - - +
209B PRO* 3.3 33.4 - - - +
222B ARG* 4.6 4.7 - - - +
225B ILE* 4.2 7.4 - - + -
226B LYS* 3.5 42.8 - - + +
229B TYR* 3.3 29.2 - - + -
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Residues in contact with GLU 206 (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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202B ASP 3.5 5.0 + - - +
203B LYS* 3.0 18.2 + - - +
205B MET* 1.3 77.8 - - - +
207B PHE* 1.3 68.2 + - + +
209B PRO* 4.4 5.2 - - - +
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Residues in contact with PHE 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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185B GLU* 3.5 16.7 - - - +
188B ASP* 3.3 36.3 - - + +
189B ALA* 3.7 20.0 - - - +
192B TYR* 3.3 46.7 - + + -
203B LYS 3.7 15.5 - - - -
204B LEU* 2.9 11.5 + - - +
206B GLU* 1.3 83.7 - - + +
208B LEU* 1.3 54.7 + - - +
209B PRO* 2.7 23.7 - - - +
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Residues in contact with LEU 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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163B LEU* 6.3 1.1 - - + -
181B HIS* 5.7 4.7 - - + -
185B GLU* 4.1 11.4 + - + +
186B VAL* 4.9 7.6 - - + -
189B ALA* 4.3 13.9 - - + -
204B LEU 2.9 11.6 + - - +
205B MET* 3.3 18.2 - - - +
207B PHE* 1.3 71.9 - - - +
209B PRO* 1.3 59.8 - - - +
210B GLY 3.3 8.0 + - - +
229B TYR* 3.5 15.4 - - + +
342B ILE* 4.0 24.1 - - + +
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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