Contacts of the helix formed by residues 227 - 237 (chain t) 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 t).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210t MET* 3.9 26.9 - - + -
214t GLU 4.8 8.5 - - - +
226t GLY* 1.3 72.4 - - - -
228t SER* 1.3 59.3 + - - +
229t GLY 3.5 1.1 - - - -
230t ILE* 4.0 9.9 - - + -
231t ARG* 2.9 58.1 + - - +
488t ILE* 5.2 6.7 - - + -
490t LEU* 5.6 5.6 - - + +
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Residues in contact with SER 228 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226t GLY* 3.5 2.7 - - - -
227t LYS* 1.3 74.8 + - - +
229t GLY* 1.3 66.4 + - - +
231t ARG* 3.4 11.4 + - - +
232t ARG* 3.1 25.0 + - - +
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Residues in contact with GLY 229 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225t LEU 5.7 1.4 + - - -
226t GLY 5.1 1.4 + - - -
227t LYS 3.5 0.2 - - - -
228t SER* 1.3 74.5 - - - +
230t ILE* 1.3 65.3 + - - +
232t ARG* 3.3 8.9 + - - +
233t ALA* 3.0 24.8 + - - +
239t GLY* 4.1 2.9 - - - -
240t SER 3.1 28.9 - - - -
241t ILE* 4.0 6.1 - - - -
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Residues in contact with ILE 230 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210t MET* 4.1 5.8 - - + -
214t GLU 3.9 7.4 - - - +
215t GLY* 3.8 9.2 - - - -
216t PRO* 3.9 20.6 - - + -
224t ILE* 3.6 28.3 - - + -
226t GLY 3.8 11.7 - - - +
227t LYS* 3.5 9.6 + - + +
228t SER 3.3 0.4 - - - -
229t GLY* 1.3 74.3 - - - +
231t ARG* 1.3 56.6 + - - +
233t ALA* 3.2 3.6 + - - +
234t TYR* 3.0 58.9 + - + -
241t ILE* 3.9 20.3 - - + +
488t ILE* 4.0 22.4 - - + -
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Residues in contact with ARG 231 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210t MET* 4.2 22.9 - - + +
227t LYS* 2.9 55.6 + - - +
228t SER* 3.6 10.4 + - - +
230t ILE* 1.3 76.6 - - - +
232t ARG* 1.3 52.3 + - - +
234t TYR* 3.2 3.3 + - - +
235t GLU* 2.8 57.2 + - + +
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Residues in contact with ARG 232 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228t SER 3.1 16.5 + - - +
229t GLY* 3.3 6.8 + - - +
231t ARG* 1.3 75.5 - - - +
233t ALA* 1.3 54.6 + - - +
235t GLU* 4.3 5.6 - - - -
236t THR* 2.8 51.7 + - + +
238t ARG* 3.4 24.2 + - - +
239t GLY* 3.8 19.1 - - - +
240t SER* 4.4 6.9 - - - +
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Residues in contact with ALA 233 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229t GLY 3.0 16.9 + - - +
230t ILE* 3.4 8.1 - - - +
231t ARG 3.2 0.2 - - - -
232t ARG* 1.3 77.4 - - - +
234t TYR* 1.3 61.5 + - + +
237t GLY* 2.8 29.8 + - - -
238t ARG 3.5 12.3 + - - -
239t GLY* 4.0 4.5 - - - -
241t ILE* 4.6 1.6 - - + -
333t VAL* 3.8 36.8 - - + -
335t MET* 3.9 7.6 - - - +
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Residues in contact with TYR 234 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184t PRO* 5.6 2.7 - - + -
186t HIS* 2.6 43.4 + + - -
206t ILE* 3.5 21.3 - - + +
210t MET* 3.8 15.7 - - + -
213t ILE* 3.8 25.7 - - + +
215t GLY* 3.1 15.7 - - - -
216t PRO* 3.2 5.5 - - + +
230t ILE* 3.0 41.6 + - + +
231t ARG 3.8 3.8 - - - +
233t ALA* 1.3 80.9 - - + +
235t GLU* 1.3 59.3 + - - +
241t ILE* 5.9 1.1 - - + -
333t VAL* 6.3 1.1 - - + -
335t MET* 4.9 10.8 - - + -
347t ASN* 3.3 6.8 - - - +
348t LEU* 3.1 53.3 + - + +
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Residues in contact with GLU 235 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206t ILE* 3.8 30.4 - - + +
207t ALA* 4.8 5.2 + - - +
210t MET* 5.8 0.2 - - - +
231t ARG* 2.8 41.9 + - + +
232t ARG* 3.7 7.9 - - - +
233t ALA 3.3 0.2 - - - -
234t TYR* 1.3 77.7 - - - +
236t THR* 1.3 67.3 + - + +
347t ASN* 3.3 19.7 + - - +
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Residues in contact with THR 236 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232t ARG* 2.8 22.5 + - + +
235t GLU* 1.3 86.1 - - + +
237t GLY* 1.3 58.5 + - - +
238t ARG* 2.8 32.2 + - - +
345t LEU* 3.5 23.6 - - - +
346t ILE 4.6 3.2 - - - +
347t ASN* 4.7 3.1 - - - -
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Residues in contact with GLY 237 (chain t).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233t ALA* 2.8 20.0 + - - -
235t GLU 3.9 0.4 - - - -
236t THR* 1.3 76.0 - - - +
238t ARG* 1.3 62.7 + - - +
333t VAL* 3.7 1.8 - - - +
334t ASN* 3.4 4.7 + - - -
335t MET* 2.8 34.7 + - - +
345t LEU* 4.0 4.3 - - - -
346t ILE 3.3 23.9 + - - -
347t ASN* 4.3 1.2 - - - +
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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