Contacts of the strand formed by residues 82 - 87 (chain B) in PDB entry 5ELI
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 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TRP* 4.1 4.7 - - + -
63B VAL* 4.0 27.8 - - + +
64B VAL* 4.2 7.1 - - + +
77B ARG 3.7 0.3 - - - +
78B TRP* 3.2 6.9 - - - -
79B ASN 2.9 38.0 + - - -
80B GLY 3.2 0.6 - - - -
81B SER* 1.3 86.3 + - - +
83B ALA* 1.3 62.0 + - - +
95B ILE* 4.0 15.7 - - + -
96B THR 3.5 4.5 - - - +
97B LEU* 3.9 27.1 - - + +
104B ASP* 5.6 1.9 + - - -
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 4.9 0.4 - - - -
76B ARG* 3.7 20.2 - - + -
77B ARG 3.1 5.8 - - - +
78B TRP* 3.5 32.7 - - + -
82B THR* 1.3 75.3 - - - +
84B ILE* 1.3 61.0 + - - +
94B THR 4.5 0.4 - - - -
95B ILE* 3.3 10.2 - - - +
96B THR* 2.9 43.6 + - - +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LYS 4.2 6.7 - - - +
50B TRP* 4.4 7.2 - - + +
64B VAL* 4.0 23.8 - - + +
65B SER 3.7 23.3 - - - +
66B THR* 3.6 31.8 - - + +
75B LEU 3.6 2.3 - - - +
76B ARG* 3.2 2.4 - - - -
77B ARG* 2.9 44.9 + - + +
83B ALA* 1.3 75.5 - - - +
85B THR* 1.3 69.0 + - - +
93B LEU* 3.8 16.2 - - + -
94B THR 3.5 4.3 - - - -
95B ILE* 3.5 26.5 - - + -
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR* 5.0 0.7 - - - -
73B SER 4.2 3.4 - - - -
74B PHE* 3.3 27.8 - - + +
75B LEU 4.4 0.9 - - - -
76B ARG* 3.0 34.3 + - - +
84B ILE* 1.3 70.3 + - - +
86B ASP* 1.3 67.3 + - - +
92B THR 4.1 0.5 - - - +
93B LEU* 3.4 4.6 - - - +
94B THR* 2.9 42.6 + - - -
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B TYR* 2.5 31.2 + - - -
46B ARG 4.5 1.6 - - - +
48B LYS* 3.2 35.1 + - - +
66B THR* 3.6 16.1 + - + +
70B TRP* 4.8 0.7 + - - -
73B SER* 3.1 32.7 + - - +
74B PHE* 3.4 16.6 + - - +
85B THR* 1.3 78.9 - - - +
87B ASP* 1.3 64.0 + - - +
88B THR* 3.4 17.9 + - - +
92B THR 3.9 1.2 - - - +
93B LEU* 3.7 6.0 - - + +
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Residues in contact with ASP 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A ARG* 2.6 45.0 + - - -
78A TRP* 4.0 11.3 + - + -
38B TYR* 3.4 0.3 + - - -
85B THR* 6.3 0.4 - - + -
86B ASP* 1.3 72.0 + - - +
88B THR* 1.3 52.9 + - - +
89B LEU* 3.6 2.6 + - - +
90B GLY* 3.5 10.0 + - - -
91B GLY* 2.7 32.9 + - - -
92B THR* 2.9 38.3 + - - +
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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