Contacts of the strand formed by residues 325 - 333 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C LEU 3.4 2.1 - - - +
67C GLN* 3.1 3.8 - - - -
68C THR* 3.0 26.7 + - - -
97C VAL* 3.9 9.4 - - + -
98C LYS 3.3 9.4 - - - +
99C HIS* 2.7 38.9 + - + +
101C GLN* 3.0 10.7 + - - +
320C GLN* 2.9 24.8 + - - +
324C GLY* 1.3 75.7 - - - +
326C ILE* 1.3 63.7 + - - +
327C PHE* 3.7 29.2 - - + -
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Residues in contact with ILE 326 (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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52C SER 3.5 19.7 - - - +
53C SER* 3.7 17.3 - - - +
54C GLY 3.8 2.5 - - - +
63C ASP 4.4 6.1 - - - +
65C GLY* 3.8 28.9 - - - +
66C LEU 3.3 2.5 - - - -
67C GLN* 3.9 15.7 - - + +
96C THR* 3.8 1.2 + - - +
97C VAL* 3.6 3.6 - - - -
98C LYS* 2.9 53.4 + - + +
100C GLU* 3.6 21.8 - - - +
324C GLY 3.7 10.3 - - - +
325C THR* 1.3 76.5 - - - +
327C PHE* 1.3 67.1 + - - +
328C ASP* 4.2 4.5 + - + +
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Residues in contact with PHE 327 (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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27C PHE* 3.7 4.9 - - - -
49C PHE* 4.0 24.0 - + - -
65C GLY* 3.2 4.4 - - - -
66C LEU* 2.9 41.3 + - + +
68C THR* 4.6 5.2 - - + -
95C PHE* 4.5 6.7 - + - -
96C THR 3.4 4.5 - - - +
97C VAL* 4.1 18.2 - - + -
107C GLY 4.4 2.0 - - - -
108C GLY* 3.5 38.6 - - - -
109C TYR 5.0 0.2 - - - -
316C LEU* 4.1 22.9 - - + -
318C LEU* 3.9 16.2 - - + -
325C THR* 3.7 27.1 - - + -
326C ILE* 1.3 74.0 - - - +
328C ASP* 1.3 60.0 + - - +
330C PHE* 3.6 20.2 - + + -
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Residues in contact with ASP 328 (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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26C GLN* 3.0 15.1 - - - +
27C PHE* 3.6 6.7 - - - -
62C LYS 3.2 8.0 - - - +
63C ASP* 3.7 11.7 - - - +
64C LYS 3.1 12.3 - - - +
65C GLY* 4.3 2.2 - - - -
95C PHE* 3.8 4.3 - - - +
96C THR* 2.9 40.9 + - - +
326C ILE* 4.2 5.1 + - + +
327C PHE* 1.3 75.2 - - - +
329C ASN* 1.3 92.1 + - - +
330C PHE* 3.3 6.1 + - - -
500C CA 2.3 30.3 - - - -
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Residues in contact with ASN 329 (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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25C GLU 3.3 10.5 + - - -
26C GLN* 3.4 28.2 + - - +
62C LYS 5.2 1.8 + - - +
63C ASP* 5.1 5.5 + - - -
94C GLN* 3.7 3.5 + - - +
95C PHE* 3.5 12.3 + - - -
96C THR* 3.6 22.0 + - + +
171C LEU* 5.4 1.5 - - + +
328C ASP* 1.3 108.0 + - - +
330C PHE* 1.3 64.4 + - - +
331C LEU* 3.6 1.2 + - - +
342C PHE* 3.9 10.5 - - + -
346C THR* 3.4 37.0 - - + +
347C TRP 4.8 0.2 - - - +
350C THR* 5.2 1.4 + - - -
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Residues in contact with PHE 330 (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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23C PHE* 4.1 21.3 - + + -
24C LYS* 3.4 8.5 - - - +
25C GLU* 2.9 42.8 + - + +
27C PHE* 3.8 28.9 - + - -
37C TRP* 4.1 7.2 - + - -
66C LEU* 4.7 0.4 - - + -
94C GLN 3.4 6.5 - - - -
95C PHE* 3.7 20.9 - + + -
110C VAL* 3.8 23.6 - - + -
314C LEU* 4.0 25.8 - - + -
316C LEU* 4.1 17.5 - - + -
327C PHE* 3.6 32.1 - - + -
328C ASP 4.1 3.4 - - - -
329C ASN* 1.3 75.7 - - - +
331C LEU* 1.3 59.8 + - - +
342C PHE* 4.1 0.5 - - - -
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Residues in contact with LEU 331 (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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21C VAL* 4.0 19.5 - - + -
23C PHE 3.3 14.1 - - - +
24C LYS* 4.3 11.2 - - + -
92C VAL* 3.7 1.1 - - + +
93C VAL* 3.6 1.7 - - - +
94C GLN* 2.8 48.8 + - + +
329C ASN 4.6 0.7 - - - +
330C PHE* 1.3 75.1 - - - +
332C ILE* 1.3 69.8 + - - +
333C THR* 3.9 17.9 - - + -
338C TYR* 4.1 15.9 - - + -
339C ALA* 3.8 30.5 - - + -
342C PHE* 3.7 30.3 - - + -
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Residues in contact with ILE 332 (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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21C VAL* 3.7 2.1 - - - -
22C TYR* 2.9 29.4 + - + -
23C PHE* 2.8 32.3 + - + +
81C PHE* 4.4 19.7 - - + -
84C PHE* 3.9 17.0 - - + -
91C LEU* 3.8 21.5 - - + -
92C VAL 3.3 11.2 - - - +
93C VAL* 4.8 6.5 - - + -
112C LEU* 4.2 21.8 - - + -
314C LEU* 3.8 27.4 - - + -
331C LEU* 1.3 78.6 - - - +
333C THR* 1.3 64.9 + - - +
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Residues in contact with THR 333 (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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19C PRO 4.9 0.5 - - - -
20C ALA 2.6 22.9 + - - -
21C VAL* 4.5 1.2 - - - +
22C TYR* 4.0 7.4 - - - -
91C LEU* 3.7 7.8 - - - +
92C VAL* 2.8 45.8 + - + +
331C LEU* 3.9 30.7 - - + -
332C ILE* 1.3 75.9 - - - +
334C ASN* 1.3 60.7 + - - +
335C ASP* 3.5 30.0 + - - +
338C TYR* 4.0 12.3 - - + -
339C ALA* 4.1 3.8 - - + +
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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