Contacts of the helix formed by residues 237 - 247 (chain s) in PDB entry 6QY3
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 ASN 237 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236s ASN* 1.3 79.2 - - - +
238s PHE* 1.3 62.1 + - - +
239s VAL* 3.1 8.1 + - + +
240s LYS* 3.2 9.6 + - + +
241s ILE* 2.9 25.7 + - - +
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Residues in contact with PHE 238 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172s ASP* 4.4 23.8 - - + +
176s ALA* 6.4 1.8 - - + -
236s ASN 3.9 0.4 + - - -
237s ASN* 1.3 74.5 - - - +
239s VAL* 1.3 56.2 + - - +
241s ILE* 3.7 9.0 - - - +
242s LYS* 2.9 29.1 + - - +
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Residues in contact with VAL 239 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237s ASN* 3.1 6.1 - - + +
238s PHE* 1.3 76.3 - - - +
240s LYS* 1.3 61.2 + - - +
242s LYS* 3.1 7.9 + - - +
243s LYS* 2.9 27.7 + - - +
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Residues in contact with LYS 240 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233s ASN* 5.5 0.7 - - - -
236s ASN* 4.1 17.3 - - + -
237s ASN* 3.2 13.7 + - + +
239s VAL* 1.3 77.7 - - - +
241s ILE* 1.3 57.9 + - - +
243s LYS* 3.3 8.2 + - - +
244s GLU* 2.9 29.3 + - - +
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Residues in contact with ILE 241 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176s ALA* 4.9 17.7 - - + +
230s VAL* 6.3 2.2 - - - -
233s ASN* 4.4 28.0 - - + +
236s ASN* 4.9 1.7 - - - +
237s ASN 2.9 17.2 + - - +
238s PHE* 3.7 9.4 - - - +
240s LYS* 1.3 76.7 - - - +
242s LYS* 1.3 58.0 + - - +
244s GLU* 3.5 2.0 + - - +
245s LEU* 2.9 27.5 + - - +
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Residues in contact with LYS 242 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176s ALA* 6.5 0.2 - - - -
238s PHE 2.9 17.6 + - - +
239s VAL* 3.1 8.3 + - - +
241s ILE* 1.3 74.7 - - - +
243s LYS* 1.3 59.3 + - - +
245s LEU* 3.3 8.8 + - - +
246s PHE* 2.9 26.2 + - - +
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Residues in contact with LYS 243 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239s VAL 2.9 13.8 + - - +
240s LYS* 3.7 11.0 - - - +
242s LYS* 1.3 73.9 - - - +
244s GLU* 1.3 59.9 + - - +
246s PHE* 3.0 10.8 + - - +
247s SER* 2.9 26.2 + - - -
110t TYR* 5.0 18.2 - - + +
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Residues in contact with GLU 244 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229s ILE* 4.9 16.8 - - + +
233s ASN* 4.8 12.6 - - + -
240s LYS 2.9 17.3 + - - +
241s ILE* 3.8 8.1 - - - +
243s LYS* 1.3 76.5 - - - +
245s LEU* 1.3 61.0 + - - +
247s SER* 3.2 21.6 + - - -
248s ILE* 3.7 4.9 + - - +
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Residues in contact with LEU 245 (chain s).
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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176s ALA 6.1 1.1 - - - +
180s GLY* 5.7 9.4 - - - +
229s ILE* 5.5 4.5 - - - +
241s ILE 2.9 17.8 + - - +
242s LYS* 3.4 9.6 - - - +
243s LYS 3.2 0.2 - - - -
244s GLU* 1.3 76.3 - - - +
246s PHE* 1.3 60.7 + - - +
248s ILE* 3.4 20.3 + - - +
249s PHE 4.6 0.5 + - - -
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Residues in contact with PHE 246 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242s LYS 2.9 13.2 + - - +
243s LYS* 3.0 12.7 + - - +
245s LEU* 1.3 72.3 - - - +
247s SER* 1.3 60.0 + - - +
248s ILE 3.1 6.1 + - - -
249s PHE* 3.5 18.7 + - - +
250s SER 4.2 1.4 + - - -
103t LEU* 4.9 9.5 - - - +
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Residues in contact with SER 247 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243s LYS 2.9 10.8 + - - -
244s GLU* 3.2 16.9 + - - -
246s PHE* 1.3 74.2 - - - +
248s ILE* 1.3 59.0 + - - +
249s PHE 3.2 0.4 - - - -
250s SER* 3.3 11.0 + - - +
251s GLU* 3.0 27.5 + - - +
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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