Contacts of the helix formed by residues 66 - 74 (chain A) in PDB entry 2BO1
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ALA* 4.0 2.7 - - - -
39A ARG* 5.3 0.9 - - + -
40A ASN* 3.3 23.3 - - + +
65A GLY* 1.3 77.7 - - - -
67A ASN* 1.3 57.2 + - - +
68A VAL* 3.4 14.3 + - + +
69A GLU* 3.0 34.0 + - - +
70A LEU* 2.8 33.3 + - - +
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ALA* 3.6 9.7 - - + +
40A ASN* 2.7 43.2 + - - +
41A THR* 5.1 2.9 - - - +
66A THR* 1.3 67.7 - - - +
68A VAL* 1.3 81.1 + - - +
71A GLY 3.0 9.5 + - - -
79A THR* 3.4 24.4 + - - +
80A VAL 3.0 45.3 + - - +
81A SER* 4.4 4.6 - - - +
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Residues in contact with VAL 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A ASN* 5.7 0.2 - - - +
66A THR* 3.1 12.3 - - - +
67A ASN* 1.3 93.7 + - - +
69A GLU* 1.3 66.6 + - + +
71A GLY* 3.3 4.3 + - - -
72A THR* 3.1 26.8 + - - +
78A HIS 4.9 1.2 - - - +
79A THR* 3.9 17.9 - - + +
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 4.1 12.1 - - + -
65A GLY* 3.0 26.0 - - - -
66A THR* 3.0 23.1 + - - +
68A VAL* 1.3 82.6 - - + +
70A LEU* 1.3 60.2 - - - +
72A THR* 3.2 8.9 + - - -
73A ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.3 15.9 - - + -
36A ILE* 3.9 26.2 - - + +
38A ALA* 4.0 18.2 - - + +
63A PHE* 3.6 32.6 - - + -
66A THR 2.8 14.6 + - - +
67A ASN* 3.9 0.4 - - - +
68A VAL 3.3 0.2 - - - -
69A GLU* 1.3 77.2 - - - +
71A GLY* 1.3 60.2 + - - +
73A ALA* 3.2 6.2 + - + +
74A VAL* 3.2 21.8 + - - +
80A VAL* 3.5 26.7 - - + +
81A SER 4.1 4.7 - - - +
82A VAL 4.2 0.2 - - - +
83A VAL* 4.0 25.6 - - + -
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Residues in contact with GLY 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ASN 3.0 12.3 + - - -
68A VAL 3.7 1.8 - - - -
70A LEU* 1.3 74.6 - - - +
72A THR* 1.3 62.2 + - - +
74A VAL* 3.2 3.2 + - - +
75A GLY 3.2 4.0 + - - -
76A LYS* 3.0 30.7 + - - -
78A HIS 3.5 22.0 - - - -
80A VAL* 3.6 17.6 - - - +
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 3.1 17.6 + - - +
69A GLU* 3.2 12.0 + - - +
71A GLY* 1.3 75.6 - - - +
73A ALA* 1.3 64.4 + - - +
75A GLY* 3.0 14.8 + - - -
76A LYS 4.1 7.2 + - - +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ALA* 4.2 25.3 - - + +
7A LEU* 4.0 25.5 - - + +
8A ARG* 4.1 21.5 - - - +
11A ILE* 4.5 0.2 - - - +
63A PHE* 4.9 7.0 - - + -
69A GLU 2.9 13.4 + - - +
70A LEU* 3.2 15.5 + - + +
72A THR* 1.3 78.2 - - - +
74A VAL* 1.3 59.2 + - - +
75A GLY 3.6 0.3 + - - -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.3 18.4 - - + -
11A ILE* 3.6 30.9 - - + +
16A TYR* 4.8 8.2 + - + -
18A LEU* 4.4 14.1 - - + -
70A LEU* 3.4 13.0 - - + +
71A GLY* 3.3 17.9 - - - +
72A THR 3.2 0.2 - - - -
73A ALA* 1.3 78.3 - - - +
75A GLY* 1.3 60.4 + - - +
76A LYS* 4.0 14.0 - - + +
80A VAL* 3.9 16.8 - - + -
83A VAL* 4.0 25.4 - - + -
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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