Contacts of the helix formed by residues 221 - 230 (chain B) in PDB entry 1KKQ
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 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214B TYR* 4.3 15.3 - - + -
215B LEU* 4.5 17.7 + - + +
218B PHE* 4.6 7.8 + - + +
219B ASN 4.0 1.4 + - - -
220B MET* 1.3 78.2 - - - +
222B LYS* 1.3 60.6 + - - +
223B VAL* 3.3 4.8 + - - +
224B LYS* 2.6 65.2 + - - +
225B ALA* 3.3 24.1 + - - +
323B SER* 5.2 3.4 - - - -
324B VAL* 5.5 0.5 - - - +
372B ASP* 3.5 20.0 - - - +
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Residues in contact with LYS 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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214B TYR* 4.5 1.0 + - - -
221B ASN* 1.3 73.3 - - - +
223B VAL* 1.3 69.0 + - - +
225B ALA* 3.8 2.9 - - - -
226B ARG* 3.1 43.7 + - + +
323B SER* 3.7 35.9 + - - +
365B PHE* 5.9 3.0 - - - -
366B ASN* 3.4 32.3 + - - +
369B GLU* 5.0 1.0 - - - +
370B LEU* 3.1 38.7 + - - +
371B ASP* 4.8 6.5 - - - -
372B ASP* 3.0 19.4 + - - +
375B ILE* 4.9 9.5 - - + +
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Residues in contact with VAL 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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211B TYR* 6.1 0.9 - - - +
221B ASN* 3.3 8.0 + - - +
222B LYS* 1.3 80.5 - - + +
224B LYS* 1.3 69.5 + - + +
226B ARG* 3.2 11.3 + - - +
227B VAL* 3.4 18.4 + - + +
371B ASP* 6.5 0.7 - - + -
372B ASP* 3.0 22.4 + - + +
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Residues in contact with LYS 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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218B PHE 4.7 2.4 + - - -
219B ASN* 3.2 37.2 + - - +
220B MET* 3.5 20.6 - - + -
221B ASN* 2.6 42.0 + - - +
223B VAL* 1.3 78.8 - - + +
225B ALA* 1.3 61.7 + - - +
227B VAL* 3.2 17.2 + - - +
228B ILE* 3.4 17.8 + - + +
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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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220B MET* 3.9 8.7 - - - -
221B ASN 3.3 16.6 + - - +
222B LYS 4.1 1.8 - - - +
223B VAL 3.3 1.0 - - - -
224B LYS* 1.3 79.2 - - - +
226B ARG* 1.3 58.8 + - - +
227B VAL 3.1 0.4 - - - -
228B ILE* 3.4 1.3 + - - -
229B LEU* 3.1 35.4 + - + +
323B SER 3.4 22.0 - - - +
324B VAL* 3.8 22.9 - - + -
331B LEU* 3.6 9.6 - - + +
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Residues in contact with ARG 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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222B LYS* 3.1 40.4 + - + +
223B VAL* 3.8 4.5 - - - +
225B ALA* 1.3 75.6 - - - +
227B VAL* 1.3 60.5 + - + +
229B LEU* 3.1 35.9 - - - +
230B SER* 4.0 6.2 + - - -
231B GLY* 2.9 23.2 + - - -
322B SER 4.1 1.4 + - - -
323B SER 3.4 11.7 + - - -
325B MET 3.3 18.4 + - - -
326B ASN* 5.1 4.0 - - - +
363B MET* 5.5 1.6 - - - +
366B ASN* 3.8 28.3 + - - +
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Residues in contact with VAL 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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223B VAL* 3.4 16.7 + - + +
224B LYS* 3.2 11.9 + - - +
225B ALA 3.1 0.4 - - - -
226B ARG* 1.3 78.2 - - + +
228B ILE* 1.3 64.2 + - + +
229B LEU 3.5 0.2 - - - -
231B GLY* 3.3 9.3 - - - -
232B LYS* 2.8 23.6 + - - -
233B ALA* 3.7 19.0 + - + +
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Residues in contact with ILE 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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220B MET* 4.1 16.2 - - + -
224B LYS* 3.4 15.7 - - + +
225B ALA 3.4 6.5 + - - +
227B VAL* 1.3 85.9 - - + +
229B LEU* 1.3 64.6 + - - +
232B LYS* 3.9 11.2 + - - +
237B PRO* 5.4 2.1 - - - +
238B PRO* 3.9 24.3 - - + +
331B LEU* 3.6 27.1 - - + -
334B TYR 5.1 0.9 - - - +
335B GLY* 3.7 31.6 - - - +
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Residues in contact with LEU 229 (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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225B ALA 3.1 17.0 + - - +
226B ARG* 3.1 35.0 - - - +
227B VAL 3.5 0.2 - - - -
228B ILE* 1.3 81.3 - - - +
230B SER* 1.3 63.1 + - - +
232B LYS* 3.8 8.7 + - - +
238B PRO* 6.1 1.1 - - + -
323B SER 4.5 0.2 - - - +
324B VAL 4.4 10.1 - - - +
325B MET 3.9 13.2 - - - +
326B ASN* 4.1 18.2 + - + +
331B LEU* 3.5 29.6 - - + -
338B PHE* 3.8 28.3 - - + -
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Residues in contact with SER 230 (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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226B ARG* 4.0 5.1 + - - -
229B LEU* 1.3 79.9 - - - +
231B GLY* 1.3 69.8 + - - +
232B LYS* 2.6 43.9 + - - +
326B ASN* 6.2 0.9 - - - -
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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