Contacts of the helix formed by residues 227 - 237 (chain r) 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 r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210r MET* 4.4 20.0 + - + +
214r GLU* 3.5 33.5 + - - +
226r GLY* 1.3 76.5 - - - -
228r SER* 1.3 58.7 + - - +
229r GLY 3.5 1.3 - - - -
230r ILE* 3.5 9.8 + - + +
231r ARG* 2.9 33.1 + - + +
488r ILE* 4.1 20.7 - - + +
490r LEU* 5.3 15.0 - - + +
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Residues in contact with SER 228 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226r GLY* 3.5 4.6 - - - -
227r LYS* 1.3 76.8 + - - +
229r GLY* 1.3 66.4 + - - +
231r ARG* 3.4 4.8 + - - +
232r ARG* 3.1 47.0 + - - +
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Residues in contact with GLY 229 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225r LEU 5.9 0.4 + - - -
226r GLY 5.2 1.4 + - - -
228r SER* 1.3 75.4 - - - +
230r ILE* 1.3 64.2 + - - +
232r ARG* 3.3 9.6 + - - +
233r ALA* 3.0 25.1 + - - +
239r GLY* 4.1 2.9 - - - -
240r SER 3.1 29.6 - - - -
241r ILE* 4.0 6.7 - - - -
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Residues in contact with ILE 230 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210r MET* 4.1 5.6 - - + -
214r GLU 3.9 7.0 - - - +
215r GLY* 3.8 9.2 - - - -
216r PRO* 3.9 12.8 - - + -
224r ILE* 3.6 29.4 - - + -
226r GLY 3.8 10.8 - - - +
227r LYS* 3.5 9.3 + - + +
228r SER 3.3 0.4 - - - -
229r GLY* 1.3 74.1 - - - +
231r ARG* 1.3 58.0 - - - +
233r ALA* 3.2 4.2 + - - +
234r TYR* 2.9 59.4 + - + -
241r ILE* 3.9 25.9 - - + +
488r ILE* 4.0 23.3 - - + -
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Residues in contact with ARG 231 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206r ILE* 4.8 0.4 - - - +
207r ALA* 3.5 32.5 - - - +
210r MET* 3.5 31.0 - - + +
227r LYS* 2.9 21.0 + - + +
228r SER* 3.6 5.4 - - - +
230r ILE* 1.3 76.3 - - - +
232r ARG* 1.3 55.9 + - - +
234r TYR* 3.2 2.9 + - - +
235r GLU* 2.8 69.9 + - + +
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Residues in contact with ARG 232 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228r SER* 3.1 37.5 + - - +
229r GLY* 3.6 7.3 - - - +
231r ARG* 1.3 78.5 - - - +
233r ALA* 1.3 54.3 + - - +
235r GLU* 3.4 6.0 + - - -
236r THR* 2.8 49.0 + - + +
238r ARG 3.4 12.6 - - - +
239r GLY* 4.6 5.4 - - - -
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Residues in contact with ALA 233 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229r GLY 3.0 17.6 + - - +
230r ILE* 3.4 7.9 - - - +
231r ARG 3.2 0.2 - - - -
232r ARG* 1.3 76.8 - - - +
234r TYR* 1.3 61.5 + - + +
237r GLY* 2.8 29.8 + - - -
238r ARG 3.5 11.6 + - - +
239r GLY* 4.0 4.9 - - - -
241r ILE* 4.6 2.0 - - + -
333r VAL* 3.8 36.6 - - + -
335r MET* 3.9 7.3 - - - +
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Residues in contact with TYR 234 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184r PRO* 5.6 2.7 - - + -
186r HIS* 2.6 42.9 + + - -
206r ILE* 3.5 20.6 - - + +
210r MET* 3.8 15.7 - - + -
213r ILE* 3.8 25.0 - - + +
215r GLY* 3.1 16.1 - - - -
216r PRO* 3.2 5.5 - - + +
230r ILE* 2.9 39.6 + - + +
231r ARG 3.8 3.1 - - - +
233r ALA* 1.3 80.1 - - + +
235r GLU* 1.3 62.7 + - - +
241r ILE* 6.0 1.1 - - + -
333r VAL* 6.3 1.1 - - + -
335r MET* 4.8 10.5 - - + -
347r ASN* 3.3 3.8 - - - +
348r LEU* 3.1 53.3 + - + +
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Residues in contact with GLU 235 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206r ILE* 3.8 26.4 - - - +
231r ARG* 2.8 63.5 + - + +
232r ARG* 3.7 7.9 - - - +
233r ALA 3.3 0.2 - - - -
234r TYR* 1.3 78.0 - - - +
236r THR* 1.3 68.7 + - + +
347r ASN* 3.2 20.0 + - - +
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Residues in contact with THR 236 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232r ARG* 2.8 20.6 + - + +
235r GLU* 1.3 86.1 - - + +
237r GLY* 1.3 56.3 + - - +
238r ARG* 2.8 32.1 + - - +
345r LEU* 3.5 23.9 - - - +
346r ILE 4.6 3.2 - - - +
347r ASN* 4.7 3.6 - - - -
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Residues in contact with GLY 237 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233r ALA* 2.8 20.7 + - - -
235r GLU 3.9 0.2 - - - -
236r THR* 1.3 77.7 - - - +
238r ARG* 1.3 61.3 + - - +
333r VAL* 3.7 1.8 - - - +
334r ASN* 3.4 4.5 - - - -
335r MET* 2.8 36.3 + - - +
345r LEU* 4.0 3.8 - - - -
346r ILE 3.3 23.3 + - - -
347r 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