Contacts of the strand formed by residues 82 - 87 (chain D) 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 GLU 82 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D SER* 4.4 14.6 + - - -
78D ARG* 5.1 9.4 + - - -
80D THR* 4.2 8.2 - - - +
81D ARG* 1.3 94.2 + - - +
83D CYS* 1.3 59.4 + - - +
84D SER* 3.6 6.8 + - - +
95D VAL* 3.5 27.8 - - + +
96D ILE 3.0 16.6 - - - +
97D PRO* 4.1 7.4 - - + -
98D LEU* 4.1 5.6 - - - +
91E ASP* 3.6 9.2 - - - +
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Residues in contact with CYS 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D GLU* 1.3 71.0 - - - +
84D SER* 1.3 59.4 + - - +
85D VAL* 4.4 13.2 - - - -
95D VAL* 3.8 0.2 - - - -
96D ILE* 2.9 30.3 + - + +
98D LEU* 3.7 12.7 - - + +
90E GLU* 3.6 20.9 - - - -
91E ASP* 3.7 10.1 - - - -
120E ARG* 3.7 16.8 - - - +
122E THR* 4.5 2.0 - - - -
134E LEU* 3.4 12.7 - - + +
137E SER* 3.5 36.1 - - - -
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Residues in contact with SER 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLU* 3.8 6.6 + - - +
83D CYS* 1.3 73.0 - - - +
85D VAL* 1.3 65.5 + - - +
86D THR* 5.2 3.1 - - - +
93D THR* 4.7 7.9 - - - -
94D GLN 3.5 7.0 - - - -
95D VAL* 4.4 14.8 - - - -
89E LYS 4.1 0.2 - - - +
90E GLU* 3.9 0.3 - - - -
91E ASP* 3.3 46.1 + - - +
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Residues in contact with VAL 85 (chain D).
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* 4.4 9.2 - - - -
84D SER* 1.3 79.5 - - - +
86D THR* 1.3 68.8 + - - +
93D THR* 3.4 7.5 - - - +
94D GLN* 3.1 37.1 + - + +
88E LEU* 3.7 33.9 - - + -
89E LYS 3.5 14.8 - - - +
90E GLU* 4.6 2.7 - - - -
124E TYR* 4.1 13.2 - - + +
134E LEU* 3.5 39.3 - - + -
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Residues in contact with THR 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D SER 5.2 2.0 - - - +
85D VAL* 1.3 78.1 - - - +
87D SER* 1.3 66.8 + - - +
93D THR* 3.9 18.8 - - + +
88E LEU* 3.1 23.5 - - - +
89E LYS* 3.1 35.1 + - + +
90E GLU 5.5 1.6 - - - +
91E ASP* 6.2 1.3 - - - -
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Residues in contact with SER 87 (chain D).
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* 1.3 81.7 + - - +
88D ASP* 1.3 60.0 + - - +
89D LEU* 3.3 10.0 + - - +
90D ASP* 3.7 8.5 + - - -
91D PHE* 3.7 30.3 + - - +
92D PRO 5.6 1.1 - - - -
93D THR* 4.7 3.0 + - - -
94D GLN* 6.1 2.0 - - - -
86E ASN* 2.8 32.7 + - - -
87E SER 4.0 4.7 - - - -
88E LEU* 4.5 1.8 - - - +
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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