Contacts of the strand formed by residues 272 - 279 (chain A) in PDB entry 5E6J
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 GLY 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265A TYR* 3.5 15.5 + - - -
266A THR 3.1 12.6 - - - -
267A GLY* 4.2 0.7 - - - -
271A CYS* 1.3 80.1 - - - +
273A HIS* 1.3 70.3 + - - -
74B ARG 3.0 8.5 + - - -
75B GLY* 4.0 5.4 - - - -
76B AYE 2.9 25.5 + - - -
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Residues in contact with HIS 273 (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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107A TRP* 3.1 43.0 - + + -
110A ASN* 5.5 2.5 - - - -
112A CYS* 4.5 0.4 - - - -
264A GLU 3.8 0.5 - - - +
265A TYR* 3.5 2.7 - - - -
266A THR* 2.8 54.0 + - - +
271A CYS* 5.0 10.3 - - - -
272A GLY* 1.3 79.9 + - - -
274A TYR* 1.3 64.5 + - - +
275A THR* 5.0 1.9 - - + +
76B AYE 3.7 21.5 - - + +
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Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A TRP* 3.6 16.3 + - - -
112A CYS* 3.7 22.3 - - + +
113A TYR* 3.9 14.6 - - + -
116A SER* 3.6 17.7 - - - +
164A GLY 3.6 20.4 - - - -
165A ASP* 3.4 1.2 + - - -
166A VAL* 3.3 42.7 + - + +
263A ASN* 4.3 8.1 - - + -
264A GLU 3.2 15.3 - - - -
265A TYR* 3.5 24.0 - + + -
273A HIS* 1.3 71.2 - - - +
275A THR* 1.3 69.9 + - - +
287A ASP* 4.3 1.2 - - - +
302A THR* 3.8 23.1 - - + +
303A ASP* 4.6 0.3 + - - -
73B LEU* 3.1 27.4 - - - +
75B GLY* 3.9 8.7 - - - -
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Residues in contact with THR 275 (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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107A TRP* 5.0 2.9 - - + -
116A SER* 4.6 5.4 - - - -
263A ASN* 3.6 4.0 - - - +
264A GLU* 2.6 67.1 + - + +
266A THR* 5.3 3.6 - - - +
273A HIS* 5.0 3.8 - - + +
274A TYR* 1.3 81.9 - - - +
276A HIS* 1.3 61.3 + - - +
277A ILE* 4.8 0.7 - - - +
285A ARG* 3.7 28.8 + - - +
286A ILE 3.9 8.1 - - - -
287A ASP* 4.1 21.1 - - + +
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Residues in contact with HIS 276 (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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116A SER* 4.1 8.7 + - - +
119A LEU* 3.6 37.3 - - + +
120A ALA* 3.8 27.1 - - + -
123A GLN* 2.9 29.2 + - - -
261A CYS* 3.8 15.0 - - + +
262A ALA 3.3 12.6 + - - -
263A ASN* 3.0 23.7 + - - +
275A THR* 1.3 73.1 - - - +
277A ILE* 1.3 73.4 + - - +
278A THR* 4.3 4.0 - - - -
285A ARG* 3.3 5.2 - - - +
286A ILE* 2.7 46.6 + - + +
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Residues in contact with ILE 277 (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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254A LEU* 3.7 33.2 - - + -
259A PHE* 4.1 10.8 - - + -
261A CYS* 3.1 6.9 - - - +
262A ALA* 2.7 45.8 + - + +
263A ASN 5.6 0.2 - - - -
264A GLU* 4.9 8.5 - - + +
275A THR* 4.8 4.3 - - - +
276A HIS* 1.3 86.5 + - - +
278A THR* 1.3 65.0 + - - +
283A LEU* 4.5 15.5 - - + -
284A TYR 3.4 4.7 - - - +
285A ARG* 3.5 33.9 - - + +
294A MET* 5.4 0.9 - - - -
297A TYR* 4.5 22.9 - - + -
301A VAL* 5.8 0.7 - - + -
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Residues in contact with THR 278 (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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100A GLY* 5.6 4.0 - - - +
102A LEU* 4.5 6.4 - - + +
123A GLN* 2.5 39.1 + - - +
260A LEU 4.1 0.4 + - - -
261A CYS* 4.1 4.7 - - - +
276A HIS* 4.3 0.7 - - - -
277A ILE* 1.3 76.1 - - - +
279A ALA* 1.3 65.0 + - - +
280A LYS* 5.8 0.7 - - - +
283A LEU* 3.8 0.7 - - - +
284A TYR* 2.8 59.4 + - + +
286A ILE* 4.2 20.4 - - + -
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Residues in contact with ALA 279 (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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256A GLN* 3.9 23.6 - - + +
259A PHE* 4.2 22.9 - - + +
260A LEU* 3.4 21.6 + - - +
278A THR* 1.3 78.7 + - - +
280A LYS* 1.3 62.3 + - - +
282A THR 3.8 4.9 - - - +
283A LEU* 4.3 13.7 - - + +
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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