Contacts of the helix formed by residues 227 - 237 (chain j) in PDB entry 6QX2
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 LYS 227 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210j MET* 4.3 19.5 + - + +
214j GLU* 3.5 32.5 + - - +
226j GLY* 1.3 76.0 - - - -
228j SER* 1.3 60.0 + - - +
229j GLY 3.5 1.3 - - - -
230j ILE* 3.5 11.5 + - + +
231j ARG* 2.9 32.7 + - + +
488j ILE* 4.1 19.3 - - + +
490j LEU* 5.3 14.3 - - + +
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Residues in contact with SER 228 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226j GLY* 3.5 3.3 - - - -
227j LYS* 1.3 78.3 + - - +
229j GLY* 1.3 62.2 + - - +
231j ARG* 3.4 5.1 + - - +
232j ARG* 3.1 45.1 + - - +
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Residues in contact with GLY 229 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226j GLY 5.2 1.4 + - - -
227j LYS 3.5 0.2 - - - -
228j SER* 1.3 74.5 - - - +
230j ILE* 1.3 64.6 + - - +
232j ARG* 3.3 15.7 + - - +
233j ALA* 3.0 24.8 + - - +
239j GLY* 4.1 2.9 - - - -
240j SER 3.1 28.9 - - - -
241j ILE* 4.0 5.8 - - - -
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Residues in contact with ILE 230 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210j MET* 4.1 5.4 - - + -
214j GLU 3.9 7.6 - - - +
215j GLY* 3.8 8.7 - - - -
216j PRO* 3.9 13.2 - - + -
224j ILE* 3.6 27.6 - - + -
226j GLY 3.8 13.2 + - - +
227j LYS* 3.5 9.1 + - + +
228j SER 3.3 0.4 - - - -
229j GLY* 1.3 73.0 - - - +
231j ARG* 1.3 57.4 + - - +
233j ALA* 3.2 4.0 + - - +
234j TYR* 3.0 59.6 + - + -
241j ILE* 3.9 27.3 - - + +
488j ILE* 4.0 22.9 - - + -
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Residues in contact with ARG 231 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206j ILE* 4.8 0.4 - - - +
207j ALA* 3.5 32.3 - - - +
210j MET* 3.5 31.2 - - + +
227j LYS* 2.9 20.0 + - + +
228j SER* 3.6 6.7 - - - +
230j ILE* 1.3 76.0 - - - +
232j ARG* 1.3 52.6 + - - +
234j TYR* 3.2 3.5 + - - +
235j GLU* 2.8 69.5 + - + +
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Residues in contact with ARG 232 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228j SER* 3.1 27.8 + - - +
229j GLY* 3.6 23.1 - - - +
231j ARG* 1.3 75.3 - - - +
233j ALA* 1.3 53.5 + - - +
235j GLU* 4.3 6.3 - - - -
236j THR* 2.8 48.1 + - + +
238j ARG 3.4 12.8 - - - +
239j GLY* 4.6 7.5 - - - -
240j SER* 4.9 5.7 + - - +
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Residues in contact with ALA 233 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229j GLY 3.0 17.8 + - - +
230j ILE* 3.4 7.4 - - - +
231j ARG 3.2 0.2 - - - -
232j ARG* 1.3 77.6 - - - +
234j TYR* 1.3 62.6 + - + +
237j GLY* 2.8 29.6 + - - -
238j ARG 3.5 12.1 + - - +
239j GLY* 4.0 4.7 - - - +
241j ILE* 4.6 2.0 - - + -
333j VAL* 3.7 36.3 - - + -
335j MET* 3.9 7.4 - - - +
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Residues in contact with TYR 234 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184j PRO* 5.6 2.7 - - + -
186j HIS* 2.6 43.1 + + - -
206j ILE* 3.5 21.1 - - + +
210j MET* 3.8 18.8 - - + -
213j ILE* 3.8 25.9 - - + +
215j GLY* 3.1 15.9 - - - -
216j PRO* 3.2 5.9 - - + +
230j ILE* 3.0 39.1 + - + +
231j ARG 3.8 3.8 - - - +
233j ALA* 1.3 80.0 - - + +
235j GLU* 1.3 63.8 + - - +
241j ILE* 6.0 1.3 - - + -
333j VAL* 6.3 0.7 - - + -
335j MET* 4.8 11.7 - - - -
347j ASN* 3.3 3.6 - - - +
348j LEU* 3.1 54.4 + - + +
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Residues in contact with GLU 235 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206j ILE* 3.8 25.6 - - + +
231j ARG* 2.8 66.4 + - + +
232j ARG* 3.7 7.4 - - - +
233j ALA 3.3 0.2 - - - -
234j TYR* 1.3 77.8 - - - +
236j THR* 1.3 66.7 + - + +
347j ASN* 3.2 19.9 + - - +
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Residues in contact with THR 236 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232j ARG* 2.8 18.9 + - + +
235j GLU* 1.3 87.0 - - + +
237j GLY* 1.3 58.2 + - - +
238j ARG* 2.8 32.0 + - - +
345j LEU* 3.5 23.9 - - - +
346j ILE 4.6 3.0 - - - +
347j ASN* 4.6 4.0 - - - -
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Residues in contact with GLY 237 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233j ALA* 2.8 20.4 + - - -
235j GLU 3.9 0.4 - - - -
236j THR* 1.3 75.8 - - - +
238j ARG* 1.3 60.6 + - - +
333j VAL* 3.7 1.7 - - - +
334j ASN* 3.4 5.4 + - - -
335j MET* 2.8 35.0 + - - +
345j LEU* 3.7 4.7 - - - +
346j ILE 3.3 23.0 + - - -
347j ASN* 4.3 1.4 - - - +
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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