Contacts of the helix formed by residues 80 - 90 (chain E) in PDB entry 5MS0
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 80 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E THR 5.6 5.5 + - - -
79E PRO* 1.3 77.0 - - - +
81E GLU* 1.3 66.3 + - - +
82E LYS* 3.2 11.2 - - - -
83E THR* 3.3 21.0 + - - -
84E VAL* 3.5 7.4 + - - +
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Residues in contact with GLU 81 (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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80E THR* 1.3 75.0 - - - +
82E LYS* 1.3 59.5 + - - +
84E VAL* 3.9 5.8 - - - +
85E ASP* 3.0 32.2 + - - +
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Residues in contact with LYS 82 (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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32E THR* 4.7 14.1 - - - +
80E THR* 3.2 7.3 - - - -
81E GLU* 1.3 78.0 - - - +
83E THR* 1.3 49.7 + - - +
85E ASP* 5.4 1.6 - - - -
86E ALA* 2.6 38.8 + - - +
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Residues in contact with THR 83 (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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29E ALA* 6.5 0.4 - - - -
32E THR* 4.2 19.4 + - - -
34E ALA* 5.4 5.4 - - - -
79E PRO* 3.9 21.5 - - - -
80E THR* 3.3 16.6 + - - +
81E GLU 3.2 0.4 - - - -
82E LYS* 1.3 80.7 - - - +
84E VAL* 1.3 58.3 + - - +
86E ALA* 3.3 4.6 + - - +
87E LEU* 2.9 29.8 + - - +
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Residues in contact with VAL 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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79E PRO* 6.4 0.7 - - + -
80E THR 3.5 7.7 + - - +
81E GLU* 3.3 8.5 + - - +
83E THR* 1.3 77.1 - - - +
85E ASP* 1.3 62.0 + - - +
87E LEU* 4.1 4.2 - - - +
88E MET* 2.9 26.2 + - - +
139F GLY* 5.4 2.7 - - - -
140F PRO* 3.3 26.1 - - + +
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Residues in contact with ASP 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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81E GLU 3.0 15.1 + - - +
82E LYS* 4.9 1.6 - - - +
84E VAL* 1.3 76.5 - - - +
86E ALA* 1.3 60.3 + - - +
88E MET* 3.6 8.8 - - + +
89E ARG* 2.9 29.5 + - - +
139F GLY 6.0 1.8 - - - +
140F PRO* 5.2 2.9 - - + -
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Residues in contact with ALA 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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28E THR* 6.0 7.6 - - - +
32E THR* 5.0 8.5 - - - -
82E LYS 2.6 25.4 + - - +
83E THR* 3.4 6.7 - - - +
85E ASP* 1.3 76.5 - - - +
87E LEU* 1.3 58.7 + - - +
89E ARG* 3.4 3.7 + - - +
90E LEU* 3.1 26.7 + - - +
54N PRO 5.4 1.9 - - - +
58N LEU* 3.8 30.9 - - + +
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Residues in contact with LEU 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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28E THR* 6.2 3.8 - - - -
83E THR 2.9 19.9 + - - +
84E VAL* 4.2 4.5 - - - +
86E ALA* 1.3 70.5 - - - +
88E MET* 1.3 64.7 + - - +
90E LEU* 3.5 21.7 + - - +
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Residues in contact with MET 88 (chain E).
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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84E VAL 2.9 20.3 + - - +
85E ASP* 3.8 9.9 - - + +
86E ALA 3.2 0.2 - - - -
87E LEU* 1.3 79.7 - - - +
89E ARG* 1.3 61.1 + - - +
90E LEU 3.4 5.2 + - - +
140F PRO* 3.7 29.6 - - + +
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Residues in contact with ARG 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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85E ASP 2.9 18.6 + - - +
86E ALA* 4.0 4.5 - - - +
88E MET* 1.3 74.7 - - - +
90E LEU* 1.3 64.3 + - - +
91E ASP* 3.3 5.9 + - - +
57N ASP* 5.0 26.3 - - + +
58N LEU* 5.5 2.0 - - - +
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Residues in contact with LEU 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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28E THR* 6.3 3.4 - - - -
86E ALA 3.1 17.0 + - - +
87E LEU* 3.6 20.0 - - - +
88E MET 3.2 5.1 - - - +
89E ARG* 1.3 77.2 - - - +
91E ASP* 1.3 60.8 + - - +
92E LEU* 3.4 7.4 + - + +
53N ASN 4.8 13.2 - - - +
54N PRO* 5.1 10.5 - - + +
57N ASP* 6.1 1.3 - - - -
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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