Contacts of the strand formed by residues 83 - 90 (chain E) 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 LYS 83 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82E PHE* 1.3 74.2 - - - +
84E CYS* 1.3 63.3 + - - +
85E VAL* 3.2 30.7 + - + +
437E TRP* 3.3 8.9 - - - -
438E ASP* 3.0 31.7 + - - +
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Residues in contact with CYS 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ASP* 6.0 1.6 - - - -
83E LYS* 1.3 73.5 - - - +
85E VAL* 1.3 61.9 + - - +
86E ASN 3.7 20.4 - - - -
87E SER* 4.6 0.7 - - - -
406E HIS* 4.7 19.2 + - + -
435E TRP* 3.8 29.2 - - - -
436E ARG 3.3 10.5 - - - +
437E TRP* 3.8 28.8 - - + -
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Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LEU* 3.4 24.1 - - + +
83E LYS* 3.2 39.5 + - - +
84E CYS* 1.3 74.5 - - - +
86E ASN* 1.3 58.8 + - - +
129E GLN* 4.3 7.9 - - + -
130E GLY* 3.3 31.0 - - - +
436E ARG* 3.2 7.3 + - - +
438E ASP* 3.2 37.0 - - + +
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Residues in contact with ASN 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D SER* 2.8 24.8 + - - -
88D ASP* 5.1 2.9 - - - -
89D LEU* 3.8 21.5 + - + +
84E CYS* 3.7 10.1 - - - -
85E VAL* 1.3 77.6 - - - +
87E SER* 1.3 82.6 + - - +
88E LEU* 3.6 25.1 - - - +
130E GLY 3.0 28.5 + - - +
131E GLU* 4.6 0.4 - - - +
132E ILE* 3.7 18.4 + - + +
436E ARG* 3.3 25.9 + - + +
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Residues in contact with SER 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D THR* 5.4 0.2 + - - -
87D SER* 4.0 0.2 - - - -
88D ASP* 3.1 43.6 + - - +
84E CYS* 4.6 1.6 - - - -
86E ASN* 1.3 79.5 + - - +
88E LEU* 1.3 60.4 + - - +
132E ILE* 6.0 0.7 - - - -
408E LYS* 5.9 0.3 - - - +
434E ILE 3.4 9.0 - - - -
435E TRP* 3.2 49.4 - - - -
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Residues in contact with LEU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D VAL* 3.7 21.5 - - + -
86D THR* 3.1 22.4 - - - +
87D SER* 4.5 4.0 - - - +
94D GLN* 5.4 2.9 - - - +
86E ASN* 3.6 22.9 - - - +
87E SER* 1.3 75.0 - - - +
89E LYS* 1.3 60.2 + - - +
124E TYR* 3.9 8.5 - - + -
132E ILE* 3.6 36.6 - - + +
433E SER* 3.3 6.1 - - - -
434E ILE* 2.8 69.3 + - + +
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Residues in contact with LYS 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D VAL* 3.5 7.3 - - - -
86D THR* 3.1 44.7 + - + +
88E LEU* 1.3 81.1 - - - +
90E GLU* 1.3 75.4 + - - +
93E ASN* 3.8 20.5 + - - +
431E ASP* 3.7 27.5 + - - +
432E ALA 3.3 13.9 - - - +
433E SER* 4.3 12.3 - - - -
434E ILE 4.7 0.2 - - - +
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Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D CYS* 3.6 14.9 - - - -
84D SER 4.1 4.9 - - - -
85D VAL* 4.6 3.1 - - + -
86D THR* 5.5 1.4 - - - +
89E LYS* 1.3 90.8 - - - +
91E ASP* 1.3 67.4 + - - +
92E HIS* 3.5 32.5 + - + +
93E ASN* 3.7 6.5 + - - +
96E LEU* 3.3 13.5 - - + +
115E THR* 2.7 28.8 + - - +
120E ARG* 4.2 1.4 - - - +
122E THR* 3.0 22.2 + - - -
124E TYR* 3.0 24.2 + - - +
432E ALA* 3.1 11.8 + - - +
434E ILE* 4.6 4.5 - - + -
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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