Contacts of the strand formed by residues 235 - 240 (chain C) in PDB entry 5Y7K
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 LEU 235 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ASP* 4.8 11.2 - - + +
233C VAL 4.0 9.9 - - - +
234C PRO* 1.3 76.3 - - + +
236C ILE* 1.3 62.3 + - - +
237C GLU* 3.8 12.5 + - + +
253C ARG* 4.2 23.6 - - + +
254C VAL 3.2 11.9 - - - +
255C PRO* 3.9 33.0 - - + -
248D TYR* 3.8 13.8 - - - +
249D PRO 5.7 0.7 - - - +
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Residues in contact with ILE 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C PRO 4.0 1.8 + - - -
235C LEU* 1.3 70.8 - - - +
237C GLU* 1.3 69.5 + - - +
238C TYR* 4.3 16.2 - - + -
252C VAL 3.4 1.9 - - - +
253C ARG* 3.3 4.5 - - - -
254C VAL* 2.8 55.5 + - + +
256C TYR* 3.5 18.7 - - + +
258C LYS* 4.2 4.7 - - - -
709C ASP* 5.2 1.6 - - + +
712C HIS* 3.3 52.5 - - + +
248D TYR* 4.3 5.3 - - + -
249D PRO* 3.7 30.7 - - + -
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Residues in contact with GLU 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU* 3.8 13.5 + - + +
236C ILE* 1.3 91.3 - - - +
238C TYR* 1.3 65.0 + - - +
251C THR* 4.2 4.0 - - + -
252C VAL 3.2 5.4 - - - +
253C ARG* 2.9 39.0 + - + +
239D SER* 3.7 9.1 + - - -
249D PRO* 4.6 22.3 + - - +
250D LYS* 5.3 0.2 - - - -
251D THR* 2.6 43.9 + - - +
253D ARG* 3.4 9.6 + - - -
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C TRP* 4.0 8.1 - - - -
236C ILE* 4.3 18.8 - - + -
237C GLU* 1.3 79.4 - - - +
239C SER* 1.3 66.2 + - - +
240C PHE* 4.9 1.8 - + - -
251C THR* 4.5 3.8 - - - +
252C VAL* 2.8 69.7 + - + +
254C VAL* 4.8 6.7 - - + -
706C THR 3.8 21.8 - - - +
707C ALA* 3.7 28.2 + - + +
708C ASP 4.9 4.9 - - - -
709C ASP* 3.5 34.3 - - + +
712C HIS* 5.3 2.2 - + + -
713C PHE* 6.2 2.7 - - + +
239D SER* 3.7 10.1 - - - +
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Residues in contact with SER 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C TYR* 1.3 84.0 - - - +
240C PHE* 1.3 60.2 + - - +
241C TYR* 4.0 36.4 - - - -
249C PRO* 4.7 4.3 - - - -
250C LYS 3.3 7.9 - - - -
251C THR* 4.3 6.1 + - - +
706C THR* 4.6 8.7 + - - +
707C ALA* 5.2 0.3 - - - -
737C ASP* 4.7 1.0 - - - +
237D GLU 3.3 23.0 + - - -
238D TYR* 3.4 15.6 - - - +
239D SER* 4.1 7.2 + - - -
251D THR* 6.1 0.2 - - - +
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Residues in contact with PHE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C TYR* 3.8 1.5 + + - -
239C SER* 1.3 73.8 - - - +
241C TYR* 1.3 62.9 + - - +
242C SER* 3.4 30.3 - - - -
246C LEU* 4.6 0.7 - - - +
249C PRO* 3.5 1.4 - - - +
250C LYS* 2.5 61.6 + - + +
252C VAL* 3.7 25.4 - - + -
707C ALA* 3.8 23.6 - - + -
737C ASP* 3.5 42.6 - - + -
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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