Contacts of the helix formed by residues 228 - 244 (chain Q) in PDB entry 6AVO
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 PRO 228 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215Q TRP* 3.6 12.1 - - + -
226Q ILE 3.7 4.7 - - - +
227Q VAL* 1.3 94.8 - - + +
229Q LYS* 1.3 59.5 + - - +
230Q ASP* 3.0 20.4 - - - +
231Q ILE* 3.0 24.0 + - + -
232Q ARG* 2.8 25.6 + - - +
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Residues in contact with LYS 229 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227Q VAL 3.5 3.6 + - - -
228Q PRO* 1.3 71.6 - - - +
230Q ASP* 1.3 57.5 + - - +
232Q ARG* 3.3 27.1 + - - +
233Q GLU* 2.2 73.6 + - - +
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Residues in contact with ASP 230 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228Q PRO* 3.0 21.9 - - - +
229Q LYS* 1.3 75.7 - - - +
231Q ILE* 1.3 80.9 + - - +
233Q GLU* 3.3 8.3 + - - +
234Q GLU* 2.9 31.2 + - - +
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Residues in contact with ILE 231 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187Q ARG* 6.0 3.6 - - + +
190Q VAL* 4.2 12.3 - - + -
215Q TRP* 3.5 33.7 - - + -
219Q LEU* 5.7 1.6 - - + -
227Q VAL* 3.7 6.5 - - + -
228Q PRO* 3.0 32.7 + - + +
230Q ASP* 1.3 97.8 + - - +
232Q ARG* 1.3 57.2 + - - +
234Q GLU* 4.1 4.7 - - - +
235Q ALA* 2.9 30.8 + - - +
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Residues in contact with ARG 232 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210Q GLU* 6.1 0.6 - - - +
211Q LEU* 2.8 27.4 + - + +
212Q GLU* 4.7 3.6 - - - +
213Q LEU* 4.2 22.6 - - + +
227Q VAL* 3.8 13.4 - - + +
228Q PRO 2.8 15.3 + - - +
229Q LYS* 3.7 32.0 + - - +
231Q ILE* 1.3 76.6 - - - +
233Q GLU* 1.3 68.1 + - - +
235Q ALA* 3.5 5.5 - - - +
236Q GLU* 2.9 53.5 + - - +
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Residues in contact with GLU 233 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229Q LYS* 2.2 64.3 + - - +
230Q ASP* 3.9 6.8 - - - +
232Q ARG* 1.3 88.5 + - - +
234Q GLU* 1.3 61.1 + - - +
235Q ALA 3.2 1.1 - - - -
236Q GLU* 3.9 9.9 - - - +
237Q LYS* 2.9 29.5 + - - +
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Residues in contact with GLU 234 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Q LYS* 5.8 0.7 - - - -
230Q ASP 2.9 17.0 + - - +
231Q ILE* 4.1 5.6 - - - +
233Q GLU* 1.3 76.1 - - - +
235Q ALA* 1.3 56.6 + - - +
237Q LYS* 3.3 10.9 + - + +
238Q TYR* 2.9 30.8 + - - +
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Residues in contact with ALA 235 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190Q VAL* 3.9 24.9 - - + +
191Q LYS* 4.5 15.3 - - + -
194Q ALA* 3.8 15.7 - - + +
213Q LEU* 4.5 3.6 - - + -
231Q ILE 2.9 20.8 + - - +
232Q ARG* 3.5 7.0 - - - +
234Q GLU* 1.3 74.6 - - - +
236Q GLU* 1.3 60.8 + - + +
238Q TYR* 3.2 2.8 + - - +
239Q ALA* 2.9 30.8 + - - +
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Residues in contact with GLU 236 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194Q ALA* 4.6 0.2 - - - +
198Q TYR* 3.0 30.5 + - - +
211Q LEU* 3.1 42.0 + - + +
232Q ARG* 2.9 38.6 + - - +
233Q GLU* 3.9 10.0 - - - +
235Q ALA* 1.3 76.5 - - - +
237Q LYS* 1.3 57.9 + - - +
239Q ALA* 4.5 1.1 - - - -
240Q LYS* 2.9 37.4 + - - +
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Residues in contact with LYS 237 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233Q GLU 2.9 19.3 + - - +
234Q GLU* 3.4 10.1 - - + +
235Q ALA 3.1 0.2 - - - -
236Q GLU* 1.3 77.8 - - - +
238Q TYR* 1.3 58.8 + - - +
240Q LYS* 3.9 4.4 - - - +
241Q GLU* 2.8 64.2 + - + +
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Residues in contact with TYR 238 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Q LYS* 3.5 53.7 + - + -
192Q GLU* 5.8 3.8 - - - -
195Q LYS* 5.9 4.3 - - + -
234Q GLU 2.9 16.9 + - - +
235Q ALA 3.8 2.7 - - - +
237Q LYS* 1.3 73.4 - - - +
239Q ALA* 1.3 65.5 + - - +
241Q GLU* 3.1 20.2 + - + +
242Q SER* 2.9 37.6 + - - -
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Residues in contact with ALA 239 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191Q LYS 4.3 0.9 - - - +
194Q ALA* 3.4 12.6 - - + -
195Q LYS* 3.3 38.3 - - - +
198Q TYR* 3.5 16.6 - - + +
235Q ALA 2.9 16.8 + - - +
238Q TYR* 1.3 82.0 - - - +
240Q LYS* 1.3 62.6 + - - +
242Q SER* 2.9 17.7 + - - +
243Q LEU* 2.9 11.6 + - - +
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Residues in contact with LYS 240 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198Q TYR* 3.4 36.4 + - + -
236Q GLU* 2.9 22.3 + - - +
237Q LYS* 3.9 5.6 - - - +
239Q ALA* 1.3 75.7 - - - +
241Q GLU* 1.3 64.0 + - + +
243Q LEU* 3.1 30.2 + - + +
244Q LYS* 3.3 5.9 + - - -
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Residues in contact with GLU 241 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237Q LYS* 2.8 61.1 + - + +
238Q TYR* 3.1 20.3 + - + +
240Q LYS* 1.3 77.0 - - + +
242Q SER* 1.3 61.4 + - - +
244Q LYS* 3.4 19.4 - - - +
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Residues in contact with SER 242 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Q LYS* 3.0 44.6 + - - +
238Q TYR* 2.9 26.6 + - - -
239Q ALA* 2.9 10.3 + - - -
241Q GLU* 1.3 74.5 - - - +
243Q LEU* 1.3 67.4 + - - +
244Q LYS* 4.6 1.4 - - - +
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Residues in contact with LEU 243 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195Q LYS* 5.7 0.4 - - - +
198Q TYR* 4.8 24.0 - - + +
199Q ILE* 5.3 15.3 - - + -
239Q ALA 2.9 10.4 + - - +
240Q LYS* 3.1 20.6 + - + +
242Q SER* 1.3 81.5 - - - +
244Q LYS* 1.3 72.9 + - - +
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Residues in contact with LYS 244 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240Q LYS 3.3 7.7 + - - -
241Q GLU* 3.4 17.9 - - - +
242Q SER 4.6 1.1 - - - +
243Q LEU* 1.3 91.8 - - - +
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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