Contacts of the helix formed by residues 201 - 215 (chain B) in PDB entry 1KCX
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 ASN 201 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B MET 4.4 0.9 - - - -
200B GLU* 1.3 69.3 - - - +
202B GLY* 1.3 57.7 + - - +
203B ASP* 3.1 11.6 + - - +
204B LEU* 2.9 51.9 + - + +
205B ILE* 3.0 33.5 + - - +
231B LEU* 3.2 17.9 + - + +
234B GLU* 2.9 30.2 + - - +
235B ALA* 3.8 0.2 - - - +
238B ARG* 3.2 17.5 - - - +
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Residues in contact with GLY 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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168B MET 3.2 6.7 + - - -
169B ALA* 3.8 15.0 - - - -
170B TYR 4.3 3.4 - - - -
171B LYS* 4.1 4.5 + - - +
175B GLN* 3.0 21.7 - - - +
200B GLU 3.2 8.1 + - - -
201B ASN* 1.3 69.6 + - - +
203B ASP* 1.3 60.3 + - - +
205B ILE* 3.8 5.1 - - - +
206B ALA* 3.0 29.6 + - - +
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Residues in contact with ASP 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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171B LYS* 3.3 31.7 + - + +
175B GLN* 3.0 26.3 + - - +
201B ASN* 3.1 8.3 + - - +
202B GLY* 1.3 75.5 - - - +
204B LEU* 1.3 66.0 + - + +
206B ALA* 3.4 4.2 + - - +
207B GLN* 3.1 30.1 + - + +
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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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201B ASN* 2.9 33.6 + - + +
203B ASP* 1.3 76.8 - - + +
205B ILE* 1.3 60.3 + - - +
207B GLN* 3.6 12.6 - - + +
208B GLU* 3.0 34.8 + - + +
231B LEU* 3.9 31.2 - - + -
234B GLU* 5.2 4.9 - - + +
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Residues in contact with ILE 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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169B ALA* 4.5 5.2 - - + -
200B GLU* 3.6 22.0 - - + +
201B ASN 3.0 27.5 + - - +
202B GLY* 3.8 5.6 - - - +
204B LEU* 1.3 74.0 - - - +
206B ALA* 1.3 57.1 + - - +
208B GLU* 3.2 1.4 + - - +
209B GLN* 2.8 53.0 + - - +
226B SER 3.8 11.6 - - - +
227B ARG* 3.3 54.3 - - + +
231B LEU* 3.6 19.1 - - + -
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Residues in contact with ALA 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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171B LYS* 4.1 23.3 - - + -
202B GLY 3.0 17.7 + - - +
203B ASP 3.6 5.6 - - - +
205B ILE* 1.3 77.7 - - - +
207B GLN* 1.3 65.9 + - - +
209B GLN* 3.5 17.2 + - - +
210B LYS* 3.3 27.8 + - - +
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Residues in contact with GLN 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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171B LYS* 5.8 5.5 - - - +
203B ASP* 3.1 22.9 + - + +
204B LEU* 3.6 17.0 - - + +
206B ALA* 1.3 79.7 - - - +
208B GLU* 1.3 68.1 + - + +
210B LYS* 3.4 14.2 + - - +
211B ARG* 3.1 22.2 + - - +
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Residues in contact with GLU 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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204B LEU* 3.0 21.7 + - + +
205B ILE 3.9 0.2 - - - +
207B GLN* 1.3 77.5 - - + +
209B GLN* 1.3 61.6 + - - +
211B ARG* 3.0 45.6 + - - +
212B ILE* 2.8 38.9 + - + +
225B LEU 4.5 8.5 - - - +
226B SER* 3.8 24.5 - - - +
228B PRO* 5.4 4.3 - - + -
231B LEU* 5.1 6.3 - - + -
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Residues in contact with GLN 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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205B ILE* 2.8 34.6 + - + +
206B ALA* 3.7 20.5 + - - +
208B GLU* 1.3 73.9 - - - +
210B LYS* 1.3 65.2 + - + +
212B ILE* 3.7 0.9 - - - +
213B LEU* 2.9 30.2 + - + +
223B HIS* 5.8 1.2 + - - -
226B SER* 3.9 23.0 + - - +
227B ARG* 4.7 10.2 + - - -
348B PHE* 4.2 5.3 - - + -
349B THR* 4.1 31.2 - - + +
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Residues in contact with LYS 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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206B ALA 3.3 13.1 + - - +
207B GLN* 3.6 16.2 - - - +
208B GLU 3.3 0.2 - - - -
209B GLN* 1.3 80.6 - - + +
211B ARG* 1.3 58.6 + - - +
213B LEU* 3.0 8.2 + - - +
214B GLU* 2.7 54.8 + - + +
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Residues in contact with ARG 211 (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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207B GLN 3.1 14.8 + - - +
208B GLU* 3.0 42.0 + - - +
210B LYS* 1.3 80.2 - - - +
212B ILE* 1.3 75.3 + - - +
214B GLU* 3.4 10.8 + - + +
215B MET* 3.2 53.4 + - + +
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Residues in contact with ILE 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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208B GLU* 2.8 30.4 + - - +
209B GLN 3.8 2.9 - - - +
211B ARG* 1.3 98.9 - - - +
213B LEU* 1.3 62.4 + - - +
215B MET* 3.3 24.0 + - - +
217B ILE* 3.4 44.1 + - + +
222B GLY* 4.2 7.9 - - - -
225B LEU* 4.4 21.1 - - + +
226B SER* 4.2 15.7 - - - +
348B PHE* 4.1 13.0 - - + -
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Residues in contact with LEU 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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209B GLN* 2.9 21.1 + - + +
210B LYS* 3.6 6.1 - - - +
212B ILE* 1.3 72.7 - - - +
214B GLU* 1.3 61.4 + - + +
215B MET 3.0 2.0 - - - -
216B GLY* 2.8 22.0 + - - -
217B ILE 3.6 8.7 - - - +
218B THR* 4.2 17.8 - - + +
347B ASN* 3.8 34.3 - - - +
348B PHE* 3.5 28.7 - - + -
349B THR* 3.8 13.7 - - + +
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LYS* 2.7 56.0 + - - +
211B ARG* 3.5 10.8 - - - +
212B ILE 3.3 0.2 - - - -
213B LEU* 1.3 77.1 - - - +
215B MET* 1.3 60.8 + - + +
216B GLY 3.4 0.3 + - - -
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Residues in contact with MET 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 ARG* 3.2 44.0 - - + +
212B ILE* 3.4 19.7 - - - +
213B LEU 3.0 1.0 - - - -
214B GLU* 1.3 79.8 - - + +
216B GLY* 1.3 57.2 + - - +
217B ILE* 3.5 19.2 + - + +
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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