Contacts of the helix formed by residues 202 - 220 (chain K) in PDB entry 6AH0
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 ILE 202 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200K LYS 3.0 8.8 + - - -
201K GLU* 1.3 74.3 - - - +
203K PRO* 1.3 66.3 - - - +
204K GLU 3.1 4.1 + - - -
205K THR* 3.3 11.8 + - - -
206K THR 4.0 3.8 + - - -
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Residues in contact with PRO 203 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201K GLU 3.3 3.6 - - - +
202K ILE* 1.3 76.1 - - - +
204K GLU* 1.3 62.2 + - - +
206K THR* 2.9 14.7 + - - +
207K ARG* 2.9 12.5 + - - -
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Residues in contact with GLU 204 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K ILE 3.1 2.2 + - - -
203K PRO* 1.3 75.5 - - - +
205K THR* 1.3 56.0 + - - +
207K ARG* 4.0 1.1 - - - +
208K THR* 2.9 28.1 + - - -
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Residues in contact with THR 205 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K ILE 3.3 7.9 + - - -
203K PRO 3.2 0.6 - - - -
204K GLU* 1.3 74.6 - - - +
206K THR* 1.3 53.6 + - - +
208K THR* 5.1 0.2 - - - +
209K SER* 2.4 37.6 + - - -
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Residues in contact with THR 206 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202K ILE 4.0 3.2 + - - -
203K PRO* 2.9 8.7 + - - -
205K THR* 1.3 76.6 - - - +
207K ARG* 1.3 57.6 + - - +
210K GLN* 2.4 38.8 + - - +
211K MET 3.4 0.5 + - - -
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Residues in contact with ARG 207 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K PRO 2.9 12.6 + - - -
204K GLU* 4.0 1.8 - - - +
206K THR* 1.3 78.8 - - - +
208K THR* 1.3 58.3 + - - +
211K MET* 3.6 16.2 + - - +
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Residues in contact with THR 208 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204K GLU 2.9 17.4 + - - -
207K ARG* 1.3 78.4 - - - +
209K SER* 1.3 57.5 + - - +
212K GLN* 2.9 24.9 + - - -
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Residues in contact with SER 209 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205K THR 2.4 26.8 + - - -
208K THR* 1.3 65.6 - - - +
210K GLN* 1.3 58.0 + - - +
212K GLN* 3.2 0.9 + - - -
213K GLU* 2.9 26.3 + - - -
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Residues in contact with GLN 210 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205K THR 3.9 0.2 + - - -
206K THR* 2.4 28.8 + - - +
209K SER* 1.3 67.5 - - - +
211K MET* 1.3 54.9 + - - +
213K GLU* 3.2 2.5 + - - +
214K LEU* 2.9 26.2 + - - -
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Residues in contact with MET 211 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206K THR 3.4 5.9 + - - -
207K ARG* 3.6 15.3 + - - +
209K SER 3.3 0.2 - - - -
210K GLN* 1.3 77.4 - - - +
212K GLN* 1.3 61.8 + - - +
214K LEU* 3.2 1.7 + - - +
215K HIS* 2.9 21.7 + - - -
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Residues in contact with GLN 212 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208K THR 2.9 21.1 + - - -
209K SER* 3.7 1.6 - - - +
211K MET* 1.3 77.0 - - - +
213K GLU* 1.3 55.7 + - - +
215K HIS* 3.2 2.5 + - - +
216K LYS* 2.9 26.3 + - - -
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Residues in contact with GLU 213 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209K SER 2.9 14.4 + - - -
210K GLN* 3.2 3.1 + - - +
212K GLN* 1.3 74.6 - - - +
214K LEU* 1.3 62.9 + - - +
216K LYS* 3.2 2.6 + - - +
217K SER* 2.9 21.0 + - - -
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Residues in contact with LEU 214 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210K GLN 2.9 15.1 + - - -
211K MET* 3.7 2.7 - - - +
213K GLU* 1.3 74.4 - - - +
215K HIS* 1.3 62.4 + - - +
217K SER* 3.2 2.4 + - - +
218K LEU* 2.9 21.0 + - - -
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Residues in contact with HIS 215 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211K MET 2.9 15.2 + - - -
212K GLN* 3.7 3.1 - - - +
214K LEU* 1.3 76.1 - - - +
216K LYS* 1.3 56.4 + - - +
218K LEU* 3.2 1.7 + - - +
219K ARG* 2.8 30.7 + - - -
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Residues in contact with LYS 216 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212K GLN 2.9 14.6 + - - -
213K GLU* 3.7 2.9 - - - +
215K HIS* 1.3 73.9 - - - +
217K SER* 1.3 63.9 + - - +
219K ARG* 3.2 9.1 + - - +
220K SER* 3.2 13.7 + - - +
221K LEU 4.7 1.2 + - - -
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Residues in contact with SER 217 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213K GLU 2.9 15.1 + - - -
214K LEU* 3.7 4.0 - - - +
216K LYS* 1.3 77.1 - - - +
218K LEU* 1.3 56.8 + - - +
220K SER 4.6 1.9 + - - -
221K LEU* 4.6 8.0 + - - -
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Residues in contact with LEU 218 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214K LEU 2.9 14.6 + - - -
215K HIS* 3.6 2.0 - - - +
217K SER* 1.3 76.3 - - - +
219K ARG* 1.3 57.8 + - - +
220K SER 4.0 0.2 - - - -
221K LEU 5.5 0.7 - - - -
476K ILE* 5.9 4.5 - - - +
485K LEU* 4.9 3.4 - - - +
486K LYS* 3.6 33.9 - - - +
487K THR 4.6 2.3 + - - +
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Residues in contact with ARG 219 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215K HIS 2.8 15.3 + - - -
216K LYS* 4.0 0.7 - - - +
217K SER 3.3 0.2 - - - -
218K LEU* 1.3 81.9 - - - +
220K SER* 1.3 60.8 + - - +
221K LEU 3.9 0.2 - - - -
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Residues in contact with SER 220 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216K LYS* 3.2 12.3 + - - +
219K ARG* 1.3 79.6 - - - +
221K LEU* 1.3 68.4 + - - +
222K ASN* 3.7 1.6 + - - -
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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