Contacts of the helix formed by residues 238 - 248 (chain W) in PDB entry 5IY8
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 238 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75W ARG* 3.2 45.6 + - + +
209W TYR* 6.1 6.3 - - + -
235W GLU* 3.1 22.8 + - - +
236W ALA 3.0 0.6 + - - -
237W HIS* 1.4 91.1 + - - +
239W ILE* 1.4 65.8 + - + +
240W ASP 3.2 1.1 + - - -
241W ASN* 3.4 10.6 + - - +
242W VAL* 3.2 32.9 + - + +
601W ARG* 5.8 1.6 + - - -
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Residues in contact with ILE 239 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209W TYR* 3.9 18.6 - - + -
213W LEU* 3.2 21.5 - - + +
233W PHE* 3.9 44.6 - - + -
236W ALA* 2.8 35.2 + - + +
237W HIS 5.2 0.4 - - - +
238W ASN* 1.4 69.6 - - + +
240W ASP* 1.3 64.8 + - + +
242W VAL* 5.2 0.2 - - - -
243W CYS* 2.9 27.4 + - - +
444W ILE* 5.5 14.6 - - + -
456W ILE* 5.2 6.5 - - + -
467W TYR* 5.7 4.5 - - + -
470W ILE* 5.1 12.1 - - + -
471W LEU* 5.2 15.0 - - + -
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Residues in contact with ASP 240 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237W HIS 4.2 7.1 + - - +
238W ASN 3.2 0.8 + - - -
239W ILE* 1.3 78.6 - - + +
241W ASN* 1.4 68.0 + - - +
243W CYS 3.4 0.5 + - - -
244W ILE* 3.3 22.5 + - - +
440W ALA* 3.4 19.1 - - + +
444W ILE* 5.6 1.1 - - - -
470W ILE* 4.5 27.2 - - + +
636W ARG* 2.7 46.7 + - - -
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Residues in contact with ASN 241 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237W HIS 5.0 1.7 + - - +
238W ASN* 3.4 11.4 + - - +
240W ASP* 1.4 82.7 + - - +
242W VAL* 1.3 70.7 + - - +
244W ILE* 3.3 16.8 - - - +
245W ASP* 3.1 26.4 + - - +
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Residues in contact with VAL 242 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209W TYR* 3.8 8.3 - - + +
210W HIS* 3.6 45.0 - - + +
213W LEU* 3.7 19.7 - - + -
238W ASN* 3.2 26.5 + - + +
241W ASN* 1.3 86.5 - - - +
243W CYS* 1.3 56.3 + - - +
245W ASP* 3.3 4.4 + - - +
246W SER* 2.9 30.9 + - - +
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Residues in contact with CYS 243 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213W LEU* 3.8 31.6 - - + -
214W ASP* 5.8 0.2 - - - -
215W PRO* 5.4 0.4 - - - -
239W ILE 2.9 19.7 + - - +
240W ASP 3.4 3.3 + - - +
241W ASN 3.4 0.2 - - - -
242W VAL* 1.3 73.9 - - - +
244W ILE* 1.4 52.4 + - - +
246W SER* 2.8 9.2 + - - -
247W MET* 2.8 38.5 + - - +
440W ALA* 4.3 2.9 - - + -
443W ALA* 3.4 31.9 - - - -
444W ILE* 3.7 26.0 - - + -
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Residues in contact with ILE 244 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240W ASP 3.3 6.4 + - - +
241W ASN* 3.3 23.3 - - - +
243W CYS* 1.4 75.6 - - - +
245W ASP* 1.3 65.4 + - + +
247W MET* 4.4 6.3 - - - -
248W SER* 2.6 34.5 + - - +
437W CYS* 3.8 24.6 - - - +
438W MET 4.3 2.7 - - - +
439W ASP* 3.8 7.6 - - - -
440W ALA* 3.4 37.2 - - + +
633W LEU* 5.4 12.1 - - + -
636W ARG* 3.8 20.9 - - - +
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Residues in contact with ASP 245 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210W HIS* 2.9 29.1 + - + +
241W ASN* 3.1 22.6 + - - +
242W VAL* 3.8 5.6 - - - +
243W CYS 3.3 0.2 - - - -
244W ILE* 1.3 81.8 - - + +
246W SER* 1.3 61.0 + - - +
248W SER* 3.6 15.3 + - - +
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Residues in contact with SER 246 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210W HIS* 3.5 44.4 + - - -
213W LEU* 4.3 1.9 - - - +
214W ASP* 3.4 35.3 + - - +
242W VAL 2.9 13.4 + - - -
243W CYS* 2.8 22.0 + - - -
245W ASP* 1.3 80.2 + - - +
247W MET* 1.4 57.9 + - - +
248W SER 3.6 4.5 + - - +
249W VAL* 5.3 1.6 - - - +
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Residues in contact with MET 247 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214W ASP* 5.1 2.7 - - - -
215W PRO* 3.8 35.7 - - + -
243W CYS* 2.8 21.4 + - - +
244W ILE 4.1 3.4 - - - +
246W SER* 1.4 70.9 + - - +
248W SER* 1.4 65.8 + - - +
249W VAL* 3.5 6.9 + - - +
410W TYR* 3.3 29.6 - - + +
414W PHE* 3.3 40.8 - - + -
437W CYS* 3.9 17.3 - - - -
442W LEU* 6.4 0.7 - - + -
443W ALA* 3.9 21.5 - - + -
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Residues in contact with SER 248 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244W ILE 2.6 23.7 + - - -
245W ASP* 3.6 10.4 + - - +
246W SER 3.4 6.8 - - - +
247W MET* 1.4 79.6 - - - +
249W VAL* 1.4 62.0 + - - +
250W ASN* 5.4 1.0 + - - -
414W PHE* 4.4 0.2 - - - -
434W HIS* 4.8 11.0 - - - -
435W PHE 3.4 15.0 - - - -
436W SER* 3.9 5.5 - - - -
437W CYS* 3.0 23.1 + - - +
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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
------------------------------------------------------------
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