Contacts of the strand formed by residues 325 - 333 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LEU 3.4 2.3 - - - +
67A GLN* 3.1 4.2 - - - -
68A THR* 3.1 26.8 + - - -
97A VAL* 3.9 10.8 - - + -
98A LYS 3.3 10.1 - - - +
99A HIS* 2.7 38.9 + - + +
101A GLN* 3.0 10.1 + - - +
320A GLN* 3.0 23.6 + - - +
324A GLY* 1.3 76.5 - - - +
326A ILE* 1.3 63.0 + - - +
327A PHE* 3.7 28.2 + - + -
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Residues in contact with ILE 326 (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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52A SER 3.6 20.2 - - - +
53A SER* 3.8 7.0 - - - +
54A GLY* 3.8 21.8 - - - +
63A ASP 4.4 6.7 - - - +
64A LYS 4.9 0.2 - - - -
65A GLY* 3.8 29.2 - - - +
66A LEU 3.3 2.5 - - - -
67A GLN* 3.9 19.7 - - + +
96A THR* 3.8 1.4 + - - +
97A VAL* 3.6 3.3 - - - -
98A LYS* 2.9 57.2 + - + +
100A GLU* 4.4 3.8 - - - +
324A GLY 3.7 9.6 - - - +
325A THR* 1.3 77.4 - - - +
327A PHE* 1.3 66.3 + - - +
328A ASP* 4.2 3.6 + - + +
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Residues in contact with PHE 327 (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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27A PHE* 3.8 4.7 - - - -
49A PHE* 4.0 26.0 - + - -
65A GLY* 3.2 4.1 - - - -
66A LEU* 2.9 46.6 + - + +
68A THR* 4.5 4.7 - - + -
95A PHE* 4.5 6.7 - + - -
96A THR 3.4 5.2 - - - +
97A VAL* 4.0 17.9 - - + -
107A GLY 4.4 1.8 - - - -
108A GLY* 3.5 37.5 - - - -
109A TYR 4.4 0.2 - - - -
316A LEU* 4.1 21.8 - - + -
318A LEU* 3.9 15.7 - - + -
320A GLN* 5.0 0.2 - - - -
325A THR* 3.7 27.4 - - + -
326A ILE* 1.3 72.7 - - - +
328A ASP* 1.3 61.0 + - - +
330A PHE* 3.6 19.5 - - + -
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Residues in contact with ASP 328 (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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26A GLN* 3.0 14.7 - - - +
27A PHE* 3.6 6.3 - - - -
62A LYS 3.1 8.3 - - - +
63A ASP* 3.7 12.2 - - - +
64A LYS 3.1 12.1 - - - +
65A GLY* 4.4 2.2 - - - -
95A PHE* 3.8 3.6 - - - +
96A THR* 2.9 40.6 + - - +
326A ILE* 4.2 5.4 + - + +
327A PHE* 1.3 74.1 - - - +
329A ASN* 1.3 91.8 + - - +
330A PHE* 3.2 7.6 + - - -
500A CA 2.3 31.4 - - - -
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Residues in contact with ASN 329 (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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25A GLU 3.3 10.5 + - - -
26A GLN* 3.6 20.8 + - - +
62A LYS 5.2 1.4 + - - -
63A ASP* 5.2 2.9 - - - +
94A GLN* 3.7 3.8 + - - +
95A PHE* 3.5 11.4 - - - -
96A THR* 3.5 15.3 + - + +
171A LEU* 5.5 1.5 - - + +
328A ASP* 1.3 108.5 + - - +
330A PHE* 1.3 65.1 + - - +
331A LEU* 3.6 1.6 + - - +
342A PHE* 3.9 9.9 - - + -
346A THR* 3.4 46.2 - - + +
350A THR* 5.3 2.1 + - - -
500A CA 4.5 1.4 - - - -
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.1 21.1 - + + -
24A LYS* 3.4 9.3 - - - +
25A GLU* 3.0 41.4 + - + +
27A PHE* 3.8 28.9 - + - -
37A TRP* 4.1 7.4 - + - -
66A LEU* 4.7 0.4 - - + -
94A GLN 3.4 7.0 - - - -
95A PHE* 3.7 18.2 - + + -
110A VAL* 3.8 23.8 - - + -
314A LEU* 3.9 27.6 - - + -
316A LEU* 4.1 15.5 - - + -
327A PHE* 3.6 34.1 - - + -
328A ASP 4.1 3.1 - - - -
329A ASN* 1.3 78.0 - - - +
331A LEU* 1.3 59.9 + - - +
342A PHE* 4.1 0.5 - - - -
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Residues in contact with LEU 331 (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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21A VAL* 4.0 19.5 - - + -
23A PHE 3.4 14.4 - - - +
24A LYS* 4.3 11.0 - - + -
92A VAL 3.6 2.4 - - - +
94A GLN* 2.8 47.4 + - + +
329A ASN 4.6 0.7 - - - +
330A PHE* 1.3 75.9 - - - +
332A ILE* 1.3 70.3 + - - +
333A THR* 3.8 19.1 - - + -
338A TYR* 4.1 15.9 - - + -
339A ALA* 3.8 30.3 - - + -
342A PHE* 3.7 30.3 - - + -
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Residues in contact with ILE 332 (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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21A VAL* 3.7 1.7 - - - -
22A TYR* 2.8 29.6 + - + -
23A PHE* 2.8 32.4 + - + +
81A PHE* 4.4 19.7 - - + -
84A PHE* 3.9 16.2 - - + -
91A LEU* 3.8 22.7 - - + -
92A VAL 3.3 9.9 - - - +
93A VAL* 4.8 6.5 - - + -
112A LEU* 4.2 21.8 - - + -
314A LEU* 3.8 26.9 - - + -
331A LEU* 1.3 77.4 - - - +
333A THR* 1.3 63.9 + - - +
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Residues in contact with THR 333 (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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19A PRO* 4.4 0.3 - - - +
20A ALA 2.6 23.9 + - - -
21A VAL* 4.7 0.7 - - - -
22A TYR* 4.0 6.7 - - - -
91A LEU* 3.8 7.3 - - - +
92A VAL* 2.8 45.4 + - + +
331A LEU* 3.8 31.0 - - + -
332A ILE* 1.3 76.2 - - - +
334A ASN* 1.3 63.4 + - - +
335A ASP* 3.5 28.9 + - - +
338A TYR* 4.0 12.6 - - + -
339A ALA* 4.2 3.1 - - + +
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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