Contacts of the strand formed by residues 325 - 333 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66G LEU 3.4 2.3 - - - +
67G GLN* 3.1 4.2 - - - -
68G THR* 3.0 26.7 + - - -
97G VAL* 3.8 11.2 - - + -
98G LYS 3.3 9.2 - - - +
99G HIS* 2.7 38.5 + - + +
101G GLN* 3.0 10.8 + - - +
320G GLN* 2.9 23.9 + - - +
324G GLY* 1.3 76.7 - - - +
326G ILE* 1.3 63.0 + - - +
327G PHE* 3.8 29.7 - - + -
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Residues in contact with ILE 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G SER 3.5 19.7 - - - +
53G SER* 3.7 23.3 - - - +
54G GLY* 3.8 6.5 - - - +
63G ASP 4.4 7.0 - - - +
65G GLY* 3.8 29.2 - - - +
66G LEU 3.3 2.2 - - - -
67G GLN* 3.9 19.5 - - + +
96G THR* 3.8 0.9 + - - +
97G VAL* 3.6 4.0 + - - -
98G LYS* 2.9 55.2 + - + +
100G GLU* 4.3 6.7 - - - +
324G GLY 3.7 10.1 - - - +
325G THR* 1.3 76.7 - - - +
327G PHE* 1.3 66.8 + - - +
328G ASP* 4.2 4.1 + - + +
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Residues in contact with PHE 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G PHE* 3.7 4.9 - - - -
49G PHE* 4.0 24.2 - + - -
65G GLY* 3.2 4.6 - - - -
66G LEU* 2.9 43.0 + - + +
68G THR* 4.5 5.4 - - + -
95G PHE* 4.5 6.7 - + - -
96G THR 3.4 4.3 - - - +
97G VAL* 4.1 17.7 - - + -
107G GLY 4.4 2.0 - - - -
108G GLY* 3.5 38.8 - - - -
316G LEU* 4.1 22.9 - - + -
318G LEU* 3.9 16.6 - - + -
325G THR* 3.8 26.7 - - + -
326G ILE* 1.3 74.1 - - - +
328G ASP* 1.3 60.0 + - - +
330G PHE* 3.6 20.2 - - + -
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Residues in contact with ASP 328 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G GLN* 3.0 15.1 - - - +
27G PHE* 3.6 6.5 - - - -
62G LYS 3.2 7.8 - - - +
63G ASP* 3.7 11.7 - - - +
64G LYS 3.1 12.6 - - - +
65G GLY* 4.4 2.0 - - - -
95G PHE* 3.8 4.5 - - - +
96G THR* 2.9 41.1 + - - +
326G ILE* 4.2 5.3 + - + +
327G PHE* 1.3 75.2 - - - +
329G ASN* 1.3 93.2 + - - +
330G PHE* 3.3 6.5 + - - -
401G CA 2.3 31.2 - - - -
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Residues in contact with ASN 329 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G GLU 3.3 10.8 + - - -
26G GLN* 3.4 28.6 + - - +
62G LYS 5.2 2.0 + - - +
63G ASP* 5.1 5.5 + - - -
94G GLN* 3.7 3.6 + - - +
95G PHE* 3.5 12.0 + - - -
96G THR* 3.5 17.8 + - + +
171G LEU* 5.4 0.9 - - + +
328G ASP* 1.3 111.9 + - - +
330G PHE* 1.3 64.8 + - - +
331G LEU* 3.6 1.2 + - - +
342G PHE* 3.9 10.1 - - + -
346G THR* 3.4 36.1 - - + +
350G THR* 5.2 1.4 + - - -
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Residues in contact with PHE 330 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G PHE* 4.0 21.8 - + + -
24G LYS* 3.3 8.8 - - - +
25G GLU* 2.9 42.0 + - + +
27G PHE* 3.8 29.2 - + - -
37G TRP* 4.1 8.1 - + - -
66G LEU* 4.7 0.7 - - + -
94G GLN 3.4 6.5 - - - -
95G PHE* 3.6 20.4 - + + -
110G VAL* 3.8 24.2 - - + -
314G LEU* 4.0 26.7 - - + -
316G LEU* 4.1 16.2 - - + -
327G PHE* 3.6 31.6 - - + -
328G ASP 4.1 2.9 - - - -
329G ASN* 1.3 77.6 - - - +
331G LEU* 1.3 60.0 + - - +
342G PHE* 4.1 0.3 - - - -
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Residues in contact with LEU 331 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G VAL* 4.0 19.3 - - + -
23G PHE 3.4 13.9 - - - +
24G LYS* 4.3 11.0 - - + -
92G VAL 3.7 0.7 - - - +
93G VAL* 3.6 1.6 - - - -
94G GLN* 2.7 50.4 + - + +
329G ASN 4.6 0.4 - - - +
330G PHE* 1.3 75.1 - - - +
332G ILE* 1.3 71.0 + - - +
333G THR* 3.9 17.9 - - + -
338G TYR* 4.1 16.4 - - + -
339G ALA* 3.8 30.1 - - + -
342G PHE* 3.7 30.5 - - + -
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Residues in contact with ILE 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G VAL* 3.7 1.9 - - - -
22G TYR* 2.8 34.3 + - + -
23G PHE* 2.8 33.1 + - + +
81G PHE* 4.4 20.0 - - + -
84G PHE* 3.9 17.3 - - + -
91G LEU* 3.8 21.5 - - + -
92G VAL 3.3 10.1 - - - +
93G VAL* 4.8 7.0 - - + -
112G LEU* 4.2 21.1 - - + -
314G LEU* 3.8 26.9 - - + -
331G LEU* 1.3 78.9 - - - +
333G THR* 1.3 61.5 + - - +
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Residues in contact with THR 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G PRO 4.9 0.3 - - - -
20G ALA 2.6 24.0 + - - -
21G VAL* 4.7 1.1 - - - -
22G TYR* 4.0 6.9 - - - -
91G LEU* 3.7 7.6 - - - +
92G VAL* 2.8 45.4 + - + +
331G LEU* 3.9 30.3 - - + -
332G ILE* 1.3 75.5 - - - +
334G ASN* 1.3 61.6 + - - +
335G ASP* 3.5 29.6 + - - +
338G TYR* 4.0 12.7 - - + -
339G 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