Contacts of the helix formed by residues 205 - 218 (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 SER 205 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201B ALA 5.6 0.4 - - - -
202B ASP* 3.7 20.9 + - - -
203B LEU 3.3 1.6 - - - +
204B LYS* 1.3 80.9 - - - +
206B LEU* 1.3 66.7 + - - +
207B ALA 3.7 0.4 - - - -
208B LYS* 3.5 10.5 + - - +
209B ARG* 3.1 32.2 + - - +
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Residues in contact with LEU 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 4.1 8.4 + - - +
203B LEU* 3.1 27.4 + - + +
204B LYS 3.1 2.0 - - - -
205B SER* 1.3 78.9 + - - +
207B ALA* 1.3 59.2 + - - +
209B ARG* 2.8 23.1 + - - +
210B ILE* 2.9 39.5 + - + -
294B ILE* 5.6 0.4 - - + -
295B PRO* 3.7 23.6 - - + -
403B GLY 3.4 31.4 - - - +
404B ILE* 4.0 13.9 - - + -
407B VAL* 3.9 11.7 - - + -
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LEU 4.5 1.2 + - - -
204B LYS 4.5 3.9 + - - +
205B SER 3.7 0.2 - - - -
206B LEU* 1.3 78.9 - - - +
208B LYS* 1.3 57.3 + - - +
210B ILE* 3.9 0.9 - - - +
211B TYR* 3.0 30.0 + - - +
377B LEU* 4.0 27.3 - - + +
407B VAL* 3.5 24.4 - - + +
411B HIS* 4.9 12.1 - - + -
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Residues in contact with LYS 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 LYS 5.0 2.5 + - - +
205B SER* 3.5 14.0 + - - +
206B LEU 3.2 1.0 - - - -
207B ALA* 1.3 78.0 - - - +
209B ARG* 1.3 63.4 + - + +
211B TYR* 4.3 6.3 - - - +
212B GLU* 2.7 65.4 + - + +
700F TRP* 4.0 14.4 - - + -
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Residues in contact with ARG 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 SER* 3.1 31.4 + - - +
206B LEU* 2.8 8.4 + - - +
208B LYS* 1.3 78.6 - - + +
210B ILE* 1.3 60.2 + - - +
212B GLU* 3.4 4.3 + - - +
213B ALA* 3.0 29.1 + - - +
293B ALA* 2.7 34.8 + - - +
295B PRO* 3.9 27.4 - - + +
700F TRP* 3.2 43.3 - - + -
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B LEU* 2.9 40.8 + - + +
209B ARG* 1.3 76.9 - - - +
211B TYR* 1.3 58.1 + - - +
213B ALA* 3.4 4.9 + - - -
214B TYR* 3.0 24.8 + - - +
290B PHE* 3.5 15.7 - - + -
294B ILE* 4.4 9.0 - - + +
295B PRO* 3.9 12.3 - - + -
376B SER* 3.9 20.0 - - - +
377B LEU* 3.5 30.7 - - + -
380B ALA* 4.0 17.9 - - + -
404B ILE* 4.4 16.2 - - + -
407B VAL* 5.8 0.4 - - + -
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Residues in contact with TYR 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 ALA 3.0 19.3 + - - +
208B LYS* 4.3 6.3 - - - +
210B ILE* 1.3 78.4 - - - +
212B GLU* 1.3 62.0 + - + +
214B TYR* 3.3 0.5 + - - +
215B LEU* 2.9 61.6 + - + +
223B VAL* 6.1 0.9 - - - +
371B ASP* 5.6 0.9 + - - -
372B ASP* 4.0 9.2 - - + +
373B SER* 3.8 37.6 + - - +
376B SER* 3.4 23.8 - - - +
377B LEU* 5.4 0.4 - - + -
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Residues in contact with GLU 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 LYS* 2.7 42.3 + - + +
209B ARG 3.9 3.1 - - - +
210B ILE 3.3 0.2 - - - -
211B TYR* 1.3 80.0 - - + +
213B ALA* 1.3 60.3 + - - +
214B TYR 3.2 0.2 - - - -
215B LEU* 4.1 9.2 - - + +
216B LYS* 3.0 29.8 + - - +
700F TRP* 2.7 58.8 + - + -
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Residues in contact with ALA 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 ARG* 3.0 18.9 + - - +
210B ILE* 3.6 6.7 - - - +
211B TYR 3.2 0.2 - - - -
212B GLU* 1.3 78.4 - - - +
214B TYR* 1.3 61.1 + - - +
216B LYS* 4.0 4.2 - - - +
217B ASN* 3.2 27.3 + - - +
290B PHE* 3.6 15.4 - - + -
293B ALA* 3.2 39.3 - - + +
294B ILE* 5.4 0.2 - - - -
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Residues in contact with TYR 214 (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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210B ILE 3.0 11.7 + - - +
211B TYR* 3.5 2.5 - + - +
212B GLU 3.2 0.2 - - - -
213B ALA* 1.3 77.7 - - - +
215B LEU* 1.3 79.5 + - + +
216B LYS 3.2 0.2 - - - -
218B PHE* 3.2 55.3 + + + +
220B MET 5.1 1.2 + - - -
221B ASN* 4.3 13.7 - - + -
222B LYS* 4.5 1.2 + - - +
290B PHE* 3.6 15.7 - + + -
320B MET* 4.4 9.0 - - - +
323B SER* 5.4 2.1 + - - -
372B ASP* 2.9 40.9 + - + -
375B ILE* 3.9 22.6 - - + +
376B SER* 3.1 44.4 - - - +
379B VAL* 5.3 1.1 - - + -
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Residues in contact with LEU 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 TYR* 2.9 62.2 + - + +
212B GLU* 4.1 9.0 - - + +
214B TYR* 1.3 92.0 - - + +
216B LYS* 1.3 63.7 + - - +
218B PHE 4.0 10.7 - - - +
221B ASN* 4.5 21.1 + - + +
372B ASP* 4.6 5.2 - - + -
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Residues in contact with LYS 216 (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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212B GLU 3.0 19.7 + - - +
213B ALA* 4.0 5.6 - - - +
215B LEU* 1.3 81.4 - - - +
217B ASN* 1.3 81.6 + - - +
218B PHE 3.9 1.7 + - - +
289B GLU* 5.7 1.2 + - - -
698F ASP* 2.5 43.2 + - - +
699F GLN* 5.2 1.3 - - - +
700F TRP* 5.0 18.4 - - + +
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Residues in contact with ASN 217 (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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213B ALA* 3.2 22.9 + - - +
216B LYS* 1.3 102.0 + - - +
218B PHE* 1.3 61.1 + - - +
219B ASN 4.0 0.2 - - - -
286B GLU* 3.1 30.4 - - - +
289B GLU* 3.1 43.5 + - + +
290B PHE* 3.8 16.6 - - + +
293B ALA* 4.4 6.6 - - - +
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Residues in contact with PHE 218 (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* 3.2 62.3 + + + +
215B LEU* 4.0 12.1 - - - +
216B LYS 4.8 1.4 - - - +
217B ASN* 1.3 79.2 - - - +
219B ASN* 1.3 62.4 + - - +
220B MET 3.3 15.6 + - - +
221B ASN* 4.6 6.0 + - - +
224B LYS* 4.7 4.2 + - - -
283B THR* 5.3 2.0 - - + -
286B GLU* 3.8 16.8 - - + +
287B LEU* 4.0 25.4 - - + -
290B PHE* 3.7 38.4 - + + -
320B MET* 3.3 37.0 - - + -
379B VAL* 5.0 0.7 - - + -
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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