Contacts of the strand formed by residues 236 - 242 (chain A) in PDB entry 1Y8B
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 236 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ALA 3.2 27.1 - - - +
114A GLY* 4.2 11.4 - - - -
115A PRO* 4.3 10.8 - - + -
232A LYS* 3.5 0.9 - - - -
233A ASN 3.0 32.9 + - - +
234A ASN* 3.1 11.4 - - - +
235A GLY* 1.3 80.7 - - - +
237A HIS* 1.3 64.8 + - - +
238A ILE* 3.9 3.3 + - + +
262A GLU* 2.8 38.4 - - + +
265A ILE* 3.9 11.2 - - + -
545A ALA* 4.6 15.0 - - + -
548A TYR* 5.8 4.0 - - + -
549A HIS* 4.7 14.1 - - - +
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Residues in contact with HIS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLN* 3.1 28.6 + - - -
217A VAL* 5.2 9.4 - - + -
230A LEU* 4.6 13.1 - - + +
231A LEU 3.5 7.9 - - - +
232A LYS* 3.3 28.8 - - + +
235A GLY 3.6 9.2 - - - -
236A LEU* 1.3 77.2 - - - +
238A ILE* 1.3 61.7 + - - +
239A GLU* 3.5 8.1 - - - +
261A VAL* 4.0 4.0 - - - +
262A GLU* 3.6 34.4 + - + +
327A ILE* 6.0 2.9 - - + -
329A LEU* 4.4 31.4 - - + +
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Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.2 22.2 - - + -
177A SER* 4.7 4.0 - - - +
178A LEU* 3.8 32.1 - - + -
185A TYR* 6.3 0.7 - - + -
231A LEU* 2.7 62.8 + - + +
232A LYS* 4.3 2.2 - - - +
233A ASN* 4.7 4.3 - - + +
236A LEU 4.4 5.6 - - - +
237A HIS* 1.3 77.6 - - - +
239A GLU* 1.3 66.9 + - - +
240A LEU* 4.2 20.2 - - + -
259A VAL* 4.8 0.9 - - + -
260A ILE 4.1 1.6 - - - -
261A VAL* 4.1 17.7 - - + -
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Residues in contact with GLU 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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135A TRP* 4.6 11.9 + - - +
228A CYS* 4.8 9.4 - - - -
229A ILE 2.9 20.4 - - - +
230A LEU* 3.4 12.5 - - + +
237A HIS* 3.5 6.5 - - - +
238A ILE* 1.3 87.6 - - - +
240A LEU* 1.3 66.8 + - - +
259A VAL* 4.0 0.7 - - - +
260A ILE* 2.4 73.1 + - + +
261A VAL* 3.5 3.8 - - - -
262A GLU 4.5 1.0 + - - -
319A TYR* 5.7 4.5 - - + -
329A LEU* 3.2 31.4 - - - +
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 4.9 7.9 - - + -
185A TYR* 4.7 17.7 - - + +
191A PHE* 4.0 21.8 - - + -
228A CYS* 4.0 7.9 - - - -
229A ILE* 3.3 33.9 + - + -
231A LEU* 4.7 14.6 - - + -
238A ILE* 4.2 16.6 - - + -
239A GLU* 1.3 81.0 - - - +
241A GLN* 1.3 60.1 + - - +
242A ILE* 3.7 10.9 + - + +
256A ILE* 4.0 29.2 - - + -
258A ASP 4.4 3.1 - - - +
259A VAL* 4.0 23.8 - - + -
260A ILE* 4.9 0.7 - - - -
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Residues in contact with GLN 241 (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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135A TRP* 3.6 27.2 - - + -
227A THR 5.2 4.9 - - - +
228A CYS* 5.1 7.9 - - - -
239A GLU 4.0 1.4 + - - -
240A LEU* 1.3 71.5 - - - +
242A ILE* 1.3 67.7 + - - +
243A ASP* 3.6 13.3 + - + +
256A ILE* 5.6 0.4 - - - -
257A ASN* 4.2 1.7 - - - +
258A ASP* 3.4 55.3 + - + +
260A ILE* 3.4 29.2 - - + +
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Residues in contact with ILE 242 (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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191A PHE* 3.9 21.3 - - + -
226A PRO 4.7 11.4 - - - +
227A THR* 4.4 14.6 + - - +
228A CYS* 5.3 0.7 - - - -
229A ILE* 3.8 31.2 - - + +
240A LEU* 3.7 17.0 + - + +
241A GLN* 1.3 78.8 - - - +
243A ASP* 1.3 69.0 + - - +
244A ALA* 4.9 1.1 - - + +
255A HIS* 3.2 41.1 - - + +
256A ILE* 4.2 3.8 - - + -
257A ASN* 4.2 0.7 - - - +
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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