Contacts of the strand formed by residues 235 - 240 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASP* 4.9 11.4 - - + +
231A THR 6.2 0.2 - - - +
233A VAL 3.8 11.9 - - - +
234A PRO* 1.3 76.3 - - + +
236A ILE* 1.3 60.9 + - - +
237A GLU* 3.8 12.5 + - + +
253A ARG* 4.0 28.3 - - + +
254A VAL 3.2 10.5 - - - +
255A PRO* 4.1 27.4 - - + -
248B TYR* 3.8 12.6 - - - +
249B PRO 5.7 0.5 - - - +
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A PRO 3.9 1.4 + - - -
235A LEU* 1.3 71.5 - - - +
237A GLU* 1.3 69.0 + - - +
238A TYR* 4.3 15.2 + - + -
252A VAL 3.4 1.7 - - - +
253A ARG* 3.3 4.5 - - - -
254A VAL* 2.8 48.2 + - + +
256A TYR* 3.5 18.1 - - + +
258A LYS* 4.3 4.7 - - - -
709A ASP* 5.4 1.3 - - + +
712A HIS* 3.3 48.5 - - + +
248B TYR* 4.2 7.0 - - + -
249B PRO* 3.5 36.6 - - + -
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 3.8 14.0 + - + +
236A ILE* 1.3 87.7 - - - +
238A TYR* 1.3 63.9 + - - +
251A THR* 4.2 5.6 - - + -
252A VAL 3.3 5.8 - - - +
253A ARG* 2.9 39.4 + - + -
239B SER* 3.6 10.5 + - - -
249B PRO* 4.4 19.7 + - - +
250B LYS* 5.4 0.2 - - - -
251B THR* 2.7 41.1 + - - +
253B ARG* 3.2 13.6 + - - -
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A TRP* 4.0 9.2 - - - -
236A ILE* 4.4 22.0 - - + -
237A GLU* 1.3 77.6 - - - +
239A SER* 1.3 70.9 + - - +
240A PHE* 5.1 1.8 - + - -
251A THR* 3.6 4.9 - - - +
252A VAL* 2.8 73.1 + - + +
254A VAL* 4.8 5.4 - - + -
706A THR 3.9 17.9 - - - +
707A ALA* 3.8 26.6 + - + -
708A ASP 4.9 5.4 - - - -
709A ASP* 3.6 33.7 - - + +
712A HIS* 5.3 3.1 - + + -
713A PHE* 6.2 2.2 - - + +
239B SER* 3.7 10.8 - - - +
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A TYR* 1.3 84.6 - - - +
240A PHE* 1.3 60.2 + - - +
241A TYR* 4.0 36.7 - - - -
249A PRO* 4.8 4.0 - - - -
250A LYS 3.4 7.4 - - - -
251A THR* 4.4 5.1 + - - +
706A THR* 4.4 8.7 + - - +
707A ALA* 5.1 0.3 - - - -
737A ASP* 4.6 1.4 - - - +
237B GLU 3.5 9.6 + - - -
238B TYR* 3.5 28.9 - - - +
239B SER* 4.0 7.5 + - - -
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Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A TYR* 3.8 2.2 + + - -
239A SER* 1.3 72.5 - - - +
241A TYR* 1.3 62.8 + - - +
242A SER* 3.4 33.7 - - - -
246A LEU* 4.7 0.7 - - - +
249A PRO* 3.5 1.0 - - - +
250A LYS* 2.5 58.6 + - + +
252A VAL* 3.7 24.2 - - + -
707A ALA* 4.0 18.2 - - + -
737A ASP* 3.6 37.0 - - + -
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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