Contacts of the helix formed by residues 75 - 80 (chain O) in PDB entry 2JA7
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 MET 75 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73O GLN* 2.7 25.3 - - - +
74O SER* 1.3 71.0 - - - +
76O ASP* 1.3 65.1 + - - +
77O ILE 3.1 7.6 + - - -
78O GLU* 4.6 1.9 + - - +
128O ASN* 3.7 26.3 + - + +
237O SER 4.7 1.1 - - - -
238O ILE* 4.9 1.6 - - - -
239O PRO* 3.4 37.5 - - + -
242O GLN* 5.7 4.7 - - + +
246O ARG* 2.5 34.9 + - - +
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Residues in contact with ASP 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75O MET* 1.3 81.7 - - - +
77O ILE* 1.3 66.0 + - - +
78O GLU* 3.0 4.9 - - - -
79O GLN* 2.8 44.4 + - + +
127O ARG* 3.3 16.2 - - + -
128O ASN* 2.5 45.9 + - - +
129O ILE* 4.4 6.3 - - + +
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Residues in contact with ILE 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O PRO* 3.9 23.1 - - + +
43O THR* 3.4 25.6 - - - +
44O LEU* 3.5 23.1 - - + -
74O SER* 3.2 37.8 - - - +
75O MET 3.1 3.4 - - - -
76O ASP* 1.3 75.7 - - - +
78O GLU* 1.3 60.0 + - + +
79O GLN 2.6 13.7 + - - -
80O LEU* 3.1 18.1 + - + +
129O ILE* 4.2 9.9 - - + +
161O LYS* 3.2 36.3 + - + -
246O ARG* 4.4 4.9 - - - +
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Residues in contact with GLU 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42O PRO* 6.0 3.4 - - + -
75O MET 4.6 1.5 + - - +
76O ASP* 2.9 4.1 + - - +
77O ILE* 1.3 82.4 - - + +
79O GLN* 1.3 58.2 + - - +
80O LEU 3.8 0.9 - - - -
161O LYS* 4.2 9.0 + - - +
242O GLN* 5.6 0.7 + - - -
246O ARG* 3.6 41.8 + - - +
249O ASP* 4.3 14.3 - - - +
253O LYS* 4.5 14.7 + - - +
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Residues in contact with GLN 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76O ASP* 2.8 40.5 + - + +
77O ILE 2.6 6.9 + - - -
78O GLU* 1.3 77.2 - - - +
80O LEU* 1.3 52.7 + - - +
81O GLU* 4.0 1.8 - - - -
126O GLY 5.0 2.0 + - - -
127O ARG* 2.6 66.1 + - - +
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Residues in contact with LEU 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44O LEU* 3.9 18.8 - - + -
77O ILE* 3.1 14.1 + - + +
78O GLU 3.8 0.6 - - - -
79O GLN* 1.3 79.0 - - - +
81O GLU* 1.3 71.0 + - - +
82O TYR 3.5 0.3 + - - -
93O ASP 3.5 10.1 - - - +
94O LYS 3.3 7.0 - - - +
95O CYS* 3.1 49.4 - - - +
96O SER* 3.6 5.2 - - - +
97O VAL* 4.5 5.2 - - + -
127O ARG* 3.8 11.2 - - - +
129O ILE* 3.7 29.6 - - + -
159O ALA 5.6 0.2 - - - +
161O LYS* 3.6 24.7 - - - +
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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
------------------------------------------------------------
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