Contacts of the helix formed by residues 205 - 214 (chain B) in PDB entry 1KNY
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 TYR 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ALA* 2.7 36.1 + - - -
173B GLY* 4.1 4.3 - - - -
174B ALA* 3.0 27.5 - - - +
177B ILE* 3.8 29.4 - - + -
192B LEU* 3.6 5.4 - - - +
195B ALA* 4.1 10.1 - - + +
196B VAL* 4.6 6.5 - - - -
201B LEU* 4.2 12.1 - - + -
202B PRO* 3.4 15.4 + - + +
204B GLY* 1.3 72.5 - - - +
206B ASP* 1.3 53.1 + - - +
208B LEU* 2.7 18.5 + - + +
209B CYS* 2.7 59.8 + - - -
230B PHE* 3.6 33.7 - + + -
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Residues in contact with ASP 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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196B VAL* 4.2 26.1 - - + +
201B LEU* 4.1 15.7 - - + +
202B PRO 4.0 3.5 - - - +
204B GLY* 3.6 11.1 + - - -
205B TYR* 1.3 83.9 + - - +
207B HIS* 1.3 71.2 + - - +
209B CYS* 3.1 4.8 + - - +
210B GLN* 3.0 21.9 + - - +
213B MET* 5.6 0.3 - - - +
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Residues in contact with HIS 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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204B GLY* 3.7 10.3 - - - +
206B ASP* 1.3 85.2 + - - +
208B LEU* 1.3 57.8 + - - +
210B GLN* 2.8 53.0 + - - +
211B PHE* 3.5 36.8 + + - -
222B LYS* 6.3 1.6 - - + -
226B SER* 4.2 17.1 + - - -
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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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166B THR* 4.0 17.0 - - + -
169B VAL* 4.1 21.5 - - + -
170B ALA* 4.3 12.6 - - + -
204B GLY 3.1 10.5 + - - +
205B TYR* 2.7 36.6 + - + +
207B HIS* 1.3 75.6 - - - +
209B CYS* 1.3 59.2 + - - -
210B GLN 3.4 0.3 + - - -
211B PHE* 3.4 24.7 + - + +
212B VAL* 3.6 9.0 + - - +
223B LEU* 5.3 2.2 - - + +
226B SER* 4.4 19.5 - - - +
227B LEU* 3.8 29.2 - - + -
230B PHE* 4.1 13.2 - - + -
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Residues in contact with CYS 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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170B ALA* 4.2 12.1 - - - -
192B LEU* 4.3 13.2 - - + -
196B VAL* 4.8 5.8 - - + -
205B TYR* 2.7 62.6 + - - +
206B ASP* 3.1 10.0 + - - +
208B LEU* 1.3 74.0 - - - +
210B GLN* 1.3 58.1 + - - +
212B VAL* 3.1 6.4 + - - +
213B MET* 2.8 50.5 + - + +
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Residues in contact with GLN 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 ASP 3.0 11.3 + - - +
207B HIS* 2.8 36.2 + - + +
209B CYS* 1.3 79.0 - - - +
211B PHE* 1.3 47.9 + - + +
213B MET* 4.4 9.5 - - - +
214B SER* 2.4 40.5 + - - -
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Residues in contact with PHE 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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166B THR* 5.4 1.1 - - + -
207B HIS* 3.5 54.7 - + - -
208B LEU* 3.4 13.6 + - + +
209B CYS 3.1 0.4 - - - -
210B GLN* 1.3 77.6 - - + +
212B VAL* 1.3 57.2 + - + +
214B SER* 3.1 5.5 + - - -
215B GLY* 2.7 28.2 + - - -
216B GLN* 3.1 34.6 + - + -
217B LEU* 3.6 11.9 - - + +
219B ASP* 5.5 2.9 - - + -
222B LYS* 4.2 34.1 - - + -
223B LEU* 3.6 26.0 - - + -
226B SER* 3.9 12.8 - - - -
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Residues in contact with VAL 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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160A THR 4.3 0.3 - - - +
163A PRO* 3.1 27.5 - - - +
164A SER* 3.6 17.2 + - - +
166B THR* 3.6 43.3 - - + +
167B VAL* 4.1 13.9 - - + +
170B ALA* 3.8 12.3 - - + -
171B MET* 5.8 0.4 - - + -
192B LEU* 3.6 24.2 - - + -
208B LEU 3.7 9.2 - - - +
209B CYS 3.1 6.7 + - - +
211B PHE* 1.3 74.3 - - - +
213B MET* 1.3 64.9 + - - +
215B GLY* 3.6 0.9 + - - -
217B LEU* 4.3 9.6 - - + -
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Residues in contact with MET 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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159A THR 4.0 1.2 - - - +
160A THR* 3.3 50.8 - - + +
163A PRO* 3.6 5.7 - - - +
192B LEU* 3.6 20.0 - - + -
193B THR* 3.8 37.9 - - - -
196B VAL* 4.2 21.3 - - + -
206B ASP 5.6 0.2 - - - +
209B CYS* 2.8 38.5 + - + +
210B GLN* 4.4 6.3 - - - +
212B VAL* 1.3 74.9 - - - +
214B SER* 1.3 59.7 + - - +
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Residues in contact with SER 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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163A PRO* 4.1 2.2 - - - +
217A LEU 4.0 2.1 - - - +
218A SER* 3.6 21.1 - - - +
210B GLN* 2.4 28.3 + - - +
211B PHE* 3.1 10.2 + - - -
213B MET* 1.3 78.9 - - - +
215B GLY* 1.3 63.4 + - - +
216B GLN* 3.3 28.3 + - - +
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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