Contacts of the strand formed by residues 82 - 89 (chain K) in PDB entry 5LS6
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 PHE 82 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80K TYR* 3.6 15.8 + - + -
81K SER* 1.3 79.1 - - - +
83K LYS* 1.3 62.2 + - - +
376K MET* 3.7 24.2 - - + -
388K VAL* 4.2 18.8 - - + -
402K THR* 5.2 1.2 - - - +
404K LEU* 3.5 34.1 - - + +
418K PHE* 4.2 12.3 - + - -
422K SER 4.8 2.5 - - - -
425K LEU* 4.0 21.1 - - + -
437K TRP* 3.6 28.1 - - + -
438K ASP 2.9 17.3 - - - +
439K ARG* 3.2 32.3 - - + +
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Residues in contact with LYS 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K PHE* 1.3 74.3 - - - +
84K CYS* 1.3 67.9 + - - +
85K VAL* 3.1 35.1 - - + +
129K GLN* 4.8 10.9 + - - -
437K TRP* 3.3 8.6 - - - -
438K ASP* 2.8 22.4 + - + +
439K ARG 4.9 1.9 + - - +
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Residues in contact with CYS 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K LYS* 1.3 79.7 - - - +
85K VAL* 1.3 58.8 + - - +
86K ASN* 3.7 24.2 - - - -
87K SER* 5.1 0.4 - - - -
406K HIS* 4.2 25.4 - - + -
435K TRP* 4.2 18.6 - - - -
436K ARG 3.5 7.6 - - - -
437K TRP* 3.6 28.8 - - + -
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Residues in contact with VAL 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89J LEU* 3.4 21.6 - - - +
83K LYS* 3.1 34.3 - - + +
84K CYS* 1.3 73.3 - - - +
86K ASN* 1.3 64.6 + - - +
129K GLN* 4.2 9.4 - - + +
130K GLY* 3.3 31.9 - - - +
436K ARG* 2.9 10.0 + - - +
438K ASP* 3.1 40.6 - - + +
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Residues in contact with ASN 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J SER* 3.0 25.0 + - - -
88J ASP 4.1 0.9 + - - -
89J LEU* 3.7 18.4 + - - +
91J PHE* 6.2 0.2 - - - +
84K CYS* 3.7 13.6 - - - -
85K VAL* 1.3 79.8 - - - +
87K SER* 1.3 85.4 + - - +
88K LEU* 3.6 23.9 - - - +
130K GLY 3.0 23.5 + - - +
131K GLU* 4.6 0.2 - - - +
132K ILE* 4.1 19.9 + - + +
435K TRP* 3.7 1.0 - - - -
436K ARG* 3.1 26.8 + - + +
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Residues in contact with SER 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87J SER 3.6 0.2 - - - -
88J ASP* 2.8 50.5 + - - +
84K CYS* 5.1 1.1 - - - -
86K ASN* 1.3 79.6 + - - +
88K LEU* 1.3 59.6 + - - +
406K HIS* 5.5 0.7 - - - -
408K LYS* 5.6 0.7 - - - +
433K SER* 5.9 0.6 - - - -
434K ILE 3.3 9.2 - - - -
435K TRP* 3.1 45.8 - - - -
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Residues in contact with LEU 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J VAL* 4.2 16.8 - - + -
86J THR* 3.0 21.5 - - - +
87J SER* 4.2 5.6 - - - +
94J GLN* 5.6 2.9 - - - +
86K ASN* 3.6 14.6 - - - +
87K SER* 1.3 74.5 - - - +
89K LYS* 1.3 57.2 + - - +
113K PHE* 5.6 0.4 - - + -
124K TYR* 4.3 9.4 - - + -
132K ILE* 3.6 48.9 - - + +
433K SER* 3.3 4.6 - - - -
434K ILE* 2.7 74.1 + - + +
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Residues in contact with LYS 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85J VAL* 3.7 5.6 - - - -
86J THR* 3.1 42.9 + - + +
88K LEU* 1.3 79.8 - - - +
90K GLU* 1.3 78.3 + - - +
93K ASN* 4.3 12.3 + - - +
431K ASP* 3.5 38.1 + - - +
432K ALA 3.6 6.1 - - - +
433K SER* 4.2 13.9 - - - -
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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