Contacts of the helix formed by residues 67 - 82 (chain O) in PDB entry 2J28
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 ASN 67 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A A 3.2 31.3 + - + +
51A G 2.5 38.3 + - + +
35O ILE* 5.5 0.5 - - - +
65O THR* 4.4 5.2 - - - +
66O GLY* 1.3 85.6 + - - +
68O LYS* 1.3 80.5 + - - +
69O ASP* 3.1 28.1 + - - +
70O ALA* 3.0 11.1 + - - +
71O ALA* 3.3 9.5 + - - +
102O ARG* 3.7 20.3 + - - +
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Residues in contact with LYS 68 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A C 3.6 14.2 + - - -
49A C 3.1 39.9 + - - +
50A A 2.8 23.9 + - - +
67O ASN* 1.3 81.8 - - - +
69O ASP* 1.3 62.8 + - - +
71O ALA* 3.6 3.6 + - - +
72O ALA* 3.3 20.4 + - - +
101O GLY* 3.5 19.7 - - - +
102O ARG* 3.7 21.7 - - + +
105O ALA* 4.0 8.2 - - + +
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Residues in contact with ASP 69 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64O TYR 5.3 0.7 - - - +
65O THR* 3.7 19.1 - - + -
67O ASN* 3.1 17.2 + - - +
68O LYS* 1.3 78.7 - - - +
70O ALA* 1.3 65.3 + - - +
72O ALA* 3.2 8.3 + - - +
73O ALA* 2.9 23.9 + - - +
76O LYS* 5.0 0.2 + - - -
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Residues in contact with ALA 70 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O ILE* 3.9 9.9 - - + +
53O THR* 4.2 16.6 - - + +
65O THR* 3.4 14.9 - - - +
66O GLY* 3.1 32.5 - - - +
67O ASN 3.0 10.5 + - - +
69O ASP* 1.3 79.5 - - - +
71O ALA* 1.3 57.1 + - - +
73O ALA* 3.0 3.7 + - - +
74O VAL* 2.9 32.9 + - - +
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Residues in contact with ALA 71 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O ILE* 3.5 28.9 - - + +
67O ASN 3.3 3.0 + - - -
68O LYS 3.8 4.5 - - - +
70O ALA* 1.3 79.4 - - - +
72O ALA* 1.3 63.5 + - - +
74O VAL* 3.0 20.2 - - - +
75O GLY 3.0 6.2 + - - -
102O ARG* 3.1 42.8 - - + +
105O ALA* 3.9 0.4 - - + -
106O LEU* 3.5 10.1 - - - +
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Residues in contact with ALA 72 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68O LYS 3.3 10.3 + - - +
69O ASP* 3.2 12.4 + - - +
71O ALA* 1.3 78.6 - - - +
73O ALA* 1.3 58.8 + - - +
76O LYS* 2.9 36.4 + - - +
105O ALA* 4.1 10.8 - - + +
108O ASP* 5.9 0.2 - - - +
109O ALA* 3.2 19.9 - - + +
112O GLU* 4.5 8.3 - - - +
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Residues in contact with ALA 73 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62O LEU* 5.1 11.2 - - + -
65O THR* 4.3 11.2 - - + -
69O ASP 2.9 13.1 + - - +
70O ALA* 3.2 12.8 - - - +
72O ALA* 1.3 76.7 - - - +
74O VAL* 1.3 66.0 + - + +
75O GLY 3.4 0.2 + - - -
76O LYS* 3.0 21.3 + - - +
77O ALA* 3.5 17.2 + - - +
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Residues in contact with VAL 74 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O ILE* 3.3 32.1 - - + -
36O TYR 4.8 2.2 - - - +
37O ALA* 5.0 0.2 - - + -
51O ALA* 5.1 0.9 - - + -
52O SER* 4.2 12.3 - - - +
53O THR* 3.5 23.1 - - - +
62O LEU* 4.8 11.9 - - + -
70O ALA 2.9 19.5 + - - +
71O ALA 3.0 19.1 - - - +
73O ALA* 1.3 71.1 - - - +
75O GLY* 1.3 55.8 + - - +
77O ALA* 3.0 8.6 + - - +
78O VAL* 2.6 46.1 + - + +
106O LEU* 3.7 17.7 - - + -
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Residues in contact with GLY 75 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71O ALA 3.0 10.5 + - - -
72O ALA 3.7 0.2 + - - -
73O ALA 3.2 0.4 - - - -
74O VAL* 1.3 80.2 - - - +
76O LYS* 1.3 61.1 + - - +
77O ALA 3.0 1.0 + - - -
78O VAL* 3.3 9.2 + - - +
79O ALA* 3.3 9.0 + - - +
106O LEU* 3.7 17.9 - - - -
109O ALA* 3.5 17.5 - - - -
110O ALA* 3.3 22.4 - - - -
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Residues in contact with LYS 76 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69O ASP 5.0 0.4 + - - -
72O ALA* 2.9 35.1 + - - +
73O ALA* 3.0 25.5 - - - +
74O VAL 3.4 0.2 - - - -
75O GLY* 1.3 73.4 - - - +
77O ALA* 1.3 60.1 + - - +
79O ALA* 3.8 5.8 - - - +
80O GLU* 3.7 16.5 + - - +
109O ALA 3.8 12.6 + - - +
110O ALA* 4.8 0.4 - - - +
112O GLU* 3.7 26.7 - - + +
113O ALA* 4.6 14.2 - - + +
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Residues in contact with ALA 77 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O ALA* 4.2 12.1 - - + -
56O LYS* 5.0 9.6 - - - -
62O LEU* 6.6 0.2 - - + -
73O ALA 3.5 11.3 + - - +
74O VAL* 3.0 13.2 + - - +
75O GLY 2.9 1.2 - - - -
76O LYS* 1.3 76.6 - - - +
78O VAL* 1.3 67.2 + - - +
79O ALA 2.9 3.5 + - - -
80O GLU* 3.0 15.5 + - - +
81O ARG* 3.3 20.3 + - - -
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Residues in contact with VAL 78 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26O LEU* 5.6 10.5 - - + -
37O ALA* 3.9 23.6 - - + -
38O GLN 5.2 1.1 - - - +
39O VAL* 5.0 10.2 - - + +
50O ALA* 3.5 25.7 - - + +
51O ALA* 3.8 22.8 - - + +
74O VAL* 2.6 35.3 + - + +
75O GLY* 3.8 7.2 - - - +
77O ALA* 1.3 72.0 - - - +
79O ALA* 1.3 62.9 + - - +
81O ARG* 3.6 6.2 + - - +
82O ALA* 3.4 16.1 + - - +
106O LEU* 4.6 7.4 - - + -
110O ALA* 5.5 3.4 - - + -
115O LEU* 6.0 4.9 - - + -
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Residues in contact with ALA 79 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75O GLY 3.3 9.2 + - - +
76O LYS 3.8 10.8 - - - +
77O ALA 2.9 1.6 + - - -
78O VAL* 1.3 76.2 - - - +
80O GLU* 1.3 57.1 + - - +
82O ALA* 2.7 35.5 + - - +
110O ALA* 3.8 12.7 - - + +
113O ALA* 4.4 5.8 - - + -
114O GLY* 4.4 7.9 - - - +
115O LEU* 3.4 32.5 - - + +
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Residues in contact with GLU 80 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56O LYS* 5.2 6.4 + - - -
76O LYS 3.7 9.0 + - - +
77O ALA* 3.0 9.2 + - - +
79O ALA* 1.3 79.1 - - - +
81O ARG* 1.3 66.2 + - - +
82O ALA 3.3 5.4 + - - +
83O LEU* 4.4 16.7 - - - +
113O ALA* 5.7 0.8 - - - +
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Residues in contact with ARG 81 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A A 6.2 0.2 - - - -
49O VAL* 5.1 12.3 - - - +
50O ALA* 3.1 30.8 + - - +
51O ALA* 3.7 25.7 - - - +
55O GLU* 4.3 18.0 + - - +
56O LYS* 2.9 52.1 - - - +
77O ALA 3.3 16.5 + - - +
78O VAL* 3.8 6.5 - - - +
79O ALA 3.1 0.8 - - - -
80O GLU* 1.3 81.8 - - - +
82O ALA* 1.3 54.2 + - - +
83O LEU* 2.8 3.7 + - - +
84O GLU* 2.7 28.2 - - - +
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Residues in contact with ALA 82 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O VAL* 5.7 10.3 - - + -
78O VAL 3.4 9.2 + - - +
79O ALA* 2.7 19.9 + - - +
80O GLU 4.2 0.4 - - - -
81O ARG* 1.3 74.8 - - - +
83O LEU* 1.3 66.1 + - - +
84O GLU* 4.5 0.7 - - - -
87O ILE* 3.3 39.5 - - + +
115O LEU* 5.0 11.0 - - + -
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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