Contacts of the helix formed by residues 82 - 86 (chain E) in PDB entry 3MP4
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 VAL 82 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45E GLN* 3.8 33.9 - - + +
77E VAL* 3.0 47.2 - - + +
78E SER 3.2 5.7 + - - +
79E PRO* 3.7 2.9 - - - +
81E TRP* 1.3 80.1 - - + +
83E PRO* 1.3 64.6 - - - +
84E GLN* 3.2 17.9 - - + +
85E MET* 3.2 19.3 + - + +
86E GLY 3.6 5.4 + - - -
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Residues in contact with PRO 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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50E ILE* 5.2 9.4 - - + -
79E PRO* 3.2 21.5 - - + +
80E LYS 4.9 2.0 - - - +
81E TRP 3.7 5.8 - - - +
82E VAL* 1.3 81.8 - - - +
84E GLN* 1.3 70.7 + - - +
85E MET 3.0 2.9 - - - -
86E GLY* 2.7 25.7 + - - +
87E ASP* 4.7 0.5 + - - -
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Residues in contact with GLN 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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44E LEU* 3.9 17.0 - - + +
45E GLN* 3.9 13.1 - - - +
47E GLU 4.2 10.8 - - - +
48E LYS 5.6 0.5 - - - +
50E ILE* 3.5 35.4 - - + +
56E LYS* 3.2 32.1 + - - +
82E VAL* 3.2 23.1 - - + +
83E PRO* 1.3 90.1 - - - +
85E MET* 1.3 72.5 + - + +
86E GLY 3.9 0.2 + - - -
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Residues in contact with MET 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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40E PRO 3.9 18.6 - - - +
41E MET* 3.1 32.1 - - + +
44E LEU* 3.9 9.2 - - + -
45E GLN* 3.6 29.6 - - + +
56E LYS* 4.7 5.8 - - - -
74E THR* 3.9 16.2 - - - +
75E SER* 3.7 22.0 - - - +
77E VAL* 4.3 3.8 - - + -
82E VAL* 3.2 24.0 + - + +
83E PRO 3.0 0.4 - - - -
84E GLN* 1.3 97.9 - - + +
86E GLY* 1.3 54.2 + - - +
87E ASP* 3.1 7.2 - - - -
88E HIS* 2.8 40.1 + - - +
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Residues in contact with GLY 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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79E PRO* 4.0 28.9 - - - +
82E VAL 3.6 1.8 + - - -
83E PRO* 2.7 16.9 + - - -
84E GLN 3.4 0.2 - - - -
85E MET* 1.3 76.9 - - - +
87E ASP* 1.3 55.2 + - - +
88E HIS* 3.2 22.2 + - - -
89E THR 4.9 0.2 + - - -
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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