Contacts of the strand formed by residues 325 - 333 (chain J) in PDB entry 5LK5
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 THR 325 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66J LEU 3.4 2.1 - - - +
67J GLN* 3.1 3.3 - - - -
68J THR* 3.0 27.4 + - - -
97J VAL* 3.8 10.1 - - + -
98J LYS 3.3 9.4 - - - +
99J HIS* 2.8 38.7 + - + +
101J GLN* 3.0 10.0 + - - +
320J GLN* 2.9 23.9 + - - +
324J GLY* 1.3 76.9 - - - +
326J ILE* 1.3 61.8 + - - +
327J PHE* 3.8 29.2 + - + -
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Residues in contact with ILE 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52J SER 3.6 19.1 - - - +
53J SER* 3.7 5.8 - - - +
54J GLY 3.7 14.4 - - - +
63J ASP 4.4 7.0 - - - +
65J GLY* 3.8 29.6 - - - +
66J LEU 3.3 2.5 - - - -
67J GLN* 3.9 16.8 - - + +
96J THR* 3.8 1.0 + - - +
97J VAL* 3.6 4.0 + - - -
98J LYS* 2.9 53.6 + - + +
100J GLU* 3.6 22.0 - - - +
324J GLY 3.7 10.3 - - - +
325J THR* 1.3 76.0 - - - +
327J PHE* 1.3 65.3 + - - +
328J ASP* 4.2 4.1 + - + +
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Residues in contact with PHE 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J PHE* 3.8 4.7 - - - -
49J PHE* 4.0 26.5 - + - -
65J GLY* 3.2 3.2 - - - -
66J LEU* 2.9 43.3 + - + +
68J THR* 4.6 4.0 - - + -
95J PHE* 4.4 7.2 - + - -
96J THR 3.4 4.5 - - - +
97J VAL* 4.0 17.3 - - + -
107J GLY 4.4 2.0 - - - -
108J GLY* 3.5 38.4 - - - -
316J LEU* 4.1 22.4 - - + -
318J LEU* 3.9 16.4 - - + -
325J THR* 3.8 27.4 - - + -
326J ILE* 1.3 73.1 - - - +
328J ASP* 1.3 59.7 + - - +
330J PHE* 3.6 19.7 - - + -
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Residues in contact with ASP 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J GLN* 3.0 14.2 - - - +
27J PHE* 3.6 6.8 - - - -
62J LYS 3.2 7.6 - - - +
63J ASP* 3.7 11.7 - - - +
64J LYS 3.1 12.9 - - - +
65J GLY* 4.3 2.0 - - - -
95J PHE* 3.8 4.0 - - - +
96J THR* 2.9 42.1 + - - +
326J ILE* 4.2 6.0 + - + +
327J PHE* 1.3 74.8 - - - +
329J ASN* 1.3 93.5 + - - +
330J PHE* 3.3 6.7 + - - -
500J CA 2.3 31.2 - - - -
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Residues in contact with ASN 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25J GLU 3.2 12.4 + - - -
26J GLN* 3.4 18.5 + - - +
62J LYS 5.2 2.0 + - - +
63J ASP* 5.2 4.8 + - - -
94J GLN* 3.7 3.8 + - - +
95J PHE* 3.6 11.8 - - - -
96J THR* 3.5 17.8 + - + +
169J THR* 5.9 0.8 - - - +
171J LEU* 5.4 1.5 - - + +
328J ASP* 1.3 113.2 + - - +
330J PHE* 1.3 65.3 + - - +
331J LEU* 3.6 1.7 + - - +
342J PHE* 3.9 10.4 - - + -
346J THR* 3.4 46.6 - - + +
350J THR* 5.5 2.6 - - - +
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Residues in contact with PHE 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23J PHE* 4.1 21.8 - + + -
24J LYS* 3.3 9.3 - - - +
25J GLU* 3.0 41.6 + - + +
27J PHE* 3.9 27.4 - + - -
37J TRP* 4.1 8.3 - + - -
66J LEU* 4.7 0.4 - - + -
94J GLN 3.4 6.5 - - - -
95J PHE* 3.6 18.8 - + + -
110J VAL* 3.8 23.8 - - + -
314J LEU* 3.9 27.6 - - + -
316J LEU* 4.1 15.7 - - + -
327J PHE* 3.6 33.4 - - + -
328J ASP 4.1 2.9 - - - -
329J ASN* 1.3 77.0 - - - +
331J LEU* 1.3 60.0 + - - +
342J PHE* 4.1 0.5 - - - -
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Residues in contact with LEU 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J VAL* 4.0 18.8 - - + -
23J PHE 3.3 14.1 - - - +
24J LYS* 4.3 11.7 - - + -
92J VAL* 3.7 2.5 - - + +
93J VAL* 4.7 0.3 - - - +
94J GLN* 2.8 45.8 + - + +
314J LEU* 6.2 0.4 - - - +
329J ASN 4.6 0.9 - - - +
330J PHE* 1.3 76.1 - - - +
332J ILE* 1.3 71.3 + - - +
333J THR* 3.8 18.6 - - + -
338J TYR* 4.1 16.6 - - + -
339J ALA* 3.8 29.8 - - + -
342J PHE* 3.7 30.5 - - + -
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Residues in contact with ILE 332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J VAL* 3.7 1.9 - - - -
22J TYR* 2.8 29.3 + - + -
23J PHE* 2.8 33.7 + - + +
81J PHE* 4.4 16.4 - - + -
84J PHE* 3.9 16.2 - - + -
91J LEU* 3.8 22.7 - - + -
92J VAL 3.3 9.9 - - - +
93J VAL* 4.8 6.3 - - + -
112J LEU* 3.5 35.0 - - + -
314J LEU* 3.8 16.6 - - + -
331J LEU* 1.3 77.5 - - - +
333J THR* 1.3 63.8 + - - +
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Residues in contact with THR 333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19J PRO* 4.7 0.3 - - - +
20J ALA 2.6 24.1 + - - -
21J VAL* 4.5 1.0 - - - +
22J TYR* 4.0 7.4 - - - -
90J THR 3.9 0.2 - - - +
91J LEU* 3.7 7.1 - - - +
92J VAL* 2.8 45.1 + - + +
331J LEU* 3.8 30.5 - - + -
332J ILE* 1.3 75.0 - - - +
334J ASN* 1.3 63.0 + - - +
335J ASP* 3.5 29.8 + - - +
338J TYR* 4.0 13.1 - - + -
339J ALA* 4.1 3.4 - - + +
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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