Contacts of the helix formed by residues 79 - 86 (chain M) in PDB entry 2O5J
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 PRO 79 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78M PHE* 1.4 84.0 - - + +
80M GLN* 1.3 67.4 + - - +
81M ASP* 4.9 1.8 - - + +
82M GLU* 2.9 43.7 + - + +
83M CYS* 2.9 20.6 + - - -
90M TYR* 3.3 12.3 - - + +
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Residues in contact with GLN 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M PRO* 1.3 70.5 - - - +
81M ASP* 1.3 55.2 + - - +
83M CYS* 2.6 32.1 + - - +
84M ARG* 2.8 35.7 + - - +
90M TYR* 2.9 42.6 + - + +
120M LEU* 5.7 0.5 - - - +
122M THR* 3.2 39.3 + - - +
123M GLU* 4.8 3.8 + - - +
128M ILE* 3.7 16.1 - - + +
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Residues in contact with ASP 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79M PRO* 3.5 2.1 - - + +
80M GLN* 1.3 78.7 - - - +
82M GLU* 1.3 58.0 + - - +
84M ARG* 2.9 21.3 + - - +
85M GLU* 2.8 36.7 + - - +
629M TYR* 3.2 35.6 + - - -
802M ARG* 4.2 16.6 + - - -
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Residues in contact with GLU 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M PHE* 3.0 37.6 - - + +
79M PRO* 2.9 35.1 + - + +
81M ASP* 1.3 78.6 - - - +
83M CYS* 1.3 56.7 + - - +
85M GLU* 4.0 17.4 - - - +
86M LYS* 3.1 52.4 + - - +
88M LEU* 4.5 2.1 - - - +
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Residues in contact with CYS 83 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M PHE* 4.3 14.1 - - - -
79M PRO 2.9 9.0 + - - -
80M GLN 2.6 17.4 + - - +
82M GLU* 1.3 69.1 - - - +
84M ARG* 1.3 53.1 + - - +
86M LYS 2.7 19.7 - - - +
88M LEU* 3.1 42.8 + - + +
89M THR 4.1 1.8 - - - -
90M TYR* 3.3 52.0 - - + +
128M ILE* 4.8 5.6 - - + +
131M GLY 3.9 6.8 + - - -
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Residues in contact with ARG 84 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M GLN* 2.8 50.8 + - - +
81M ASP* 2.9 23.5 + - - +
83M CYS* 1.3 79.1 - - - +
85M GLU* 1.3 67.2 + - - +
86M LYS 3.7 2.5 - - - +
87M ASP* 5.3 1.2 - - - +
128M ILE* 3.9 18.3 - - + +
131M GLY* 3.1 29.5 - - - +
133M ASP* 3.6 31.3 + - - -
626M ARG* 5.7 5.1 - - - +
629M TYR* 5.2 10.3 - - - -
707M ARG* 4.2 14.7 + - - -
826M TYR* 5.2 2.6 + - - -
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Residues in contact with GLU 85 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M ASP* 2.8 21.5 + - - +
82M GLU* 4.0 21.8 - - - +
84M ARG* 1.3 80.5 - - - +
86M LYS* 1.3 75.8 + - + +
87M ASP* 4.7 1.0 - - - +
707M ARG* 5.0 1.7 + - - -
802M ARG* 5.3 10.3 - - - +
804M VAL* 4.8 24.9 - - + +
806M LEU* 5.8 2.4 - - + +
824M ARG* 3.0 26.9 + - - +
826M TYR* 5.9 2.5 - - - -
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Residues in contact with LYS 86 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M PHE* 5.7 1.7 - - + -
82M GLU* 3.1 30.9 + - - +
83M CYS 2.7 26.5 - - - +
84M ARG 3.7 1.4 - - - -
85M GLU* 1.3 98.3 - - + +
87M ASP* 1.3 60.1 + - - +
88M LEU* 2.7 16.2 + - + -
806M LEU* 5.5 7.0 - - + -
811M PRO* 3.5 17.0 - - - +
812M GLY* 3.1 40.3 + - - +
813M VAL* 3.3 35.4 - - + +
824M ARG* 4.1 6.5 - - - +
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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