Contacts of the helix formed by residues 67 - 80 (chain A) in PDB entry 1OBA
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 ASP 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.2 16.1 + - - +
65A GLY 3.5 0.6 - - - -
66A GLY* 1.3 76.0 - - - +
68A VAL* 1.3 61.6 + - - +
69A ALA* 2.9 24.8 + - - +
70A GLU* 2.9 24.2 + - + +
71A ALA* 3.1 20.4 + - - +
73A ARG* 5.1 2.5 + - - -
107A ALA* 3.7 3.3 - - - +
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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
----------------------------------------------------------
66A GLY 3.6 6.2 + - - +
67A ASP* 1.3 70.9 + - - +
69A ALA* 1.3 64.0 + - - +
71A ALA* 3.2 2.4 + - - +
72A GLU* 3.0 35.8 + - + +
103A ALA* 6.1 0.4 - - - -
106A ASN* 4.2 13.5 - - + +
107A ALA* 3.8 27.1 - - + +
110A ARG* 3.6 31.6 - - + -
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASP* 2.9 9.0 + - - +
68A VAL* 1.3 79.7 - - - +
70A GLU* 1.3 61.3 + - - +
72A GLU* 3.6 17.4 + - - +
73A ARG* 3.4 44.0 + - - +
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 5.1 2.9 + - - -
39A THR* 4.0 22.7 + - - +
63A ARG 5.1 1.3 - - - +
64A PHE* 3.7 19.3 - - + +
67A ASP* 2.9 31.9 + - + +
69A ALA* 1.3 75.8 - - - +
71A ALA* 1.3 64.1 + - - +
72A GLU 3.2 0.4 - - - -
73A ARG* 2.9 31.8 + - - +
74A GLU* 3.0 31.5 + - - +
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Residues in contact with ALA 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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64A PHE* 3.5 34.3 - - + +
67A ASP 3.1 11.1 + - - +
68A VAL* 3.2 8.9 + - - +
70A GLU* 1.3 78.0 - - - +
72A GLU* 1.3 51.7 + - + +
74A GLU* 3.2 0.9 + - - +
75A ALA* 2.8 36.4 + - - +
107A ALA* 3.5 26.9 - - + +
110A ARG* 5.2 0.7 - - + -
111A PHE* 3.4 9.6 - - + +
114A MET* 4.5 1.1 - - - -
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Residues in contact with GLU 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* 3.0 20.4 + - - +
69A ALA* 3.7 18.0 - - - +
70A GLU 3.2 0.2 - - - -
71A ALA* 1.3 76.3 - - - +
73A ARG* 1.3 57.9 + - + +
75A ALA* 3.4 1.4 + - - +
76A GLN* 3.0 30.3 + - - +
110A ARG* 2.7 38.0 + - + +
114A MET* 3.2 29.9 - - + +
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Residues in contact with ARG 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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39A THR* 3.8 16.4 - - + +
67A ASP* 5.1 2.8 + - - -
69A ALA* 3.4 33.7 + - - +
70A GLU* 2.9 38.9 + - - +
72A GLU* 1.3 80.9 - - + +
74A GLU* 1.3 61.6 + - - +
76A GLN* 3.7 6.1 + - - +
77A PHE* 3.2 22.9 + - - +
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Residues in contact with GLU 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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38A SER* 3.2 35.7 + - - +
39A THR* 3.5 9.4 - - + -
60A HIS* 2.8 32.0 + - - +
62A ALA* 3.5 2.8 - - - -
63A ARG* 3.1 24.4 + - - +
64A PHE* 3.1 33.0 + - + +
70A GLU* 3.0 22.2 + - - +
71A ALA* 3.7 4.9 - - - +
73A ARG* 1.3 75.2 - - - +
75A ALA* 1.3 66.4 + - - +
77A PHE* 3.1 2.8 + - - +
78A PHE* 2.8 24.8 + - - +
111A PHE* 4.0 5.4 - - + -
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Residues in contact with ALA 75 (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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71A ALA 2.8 20.5 + - - +
72A GLU 3.4 4.7 + - - +
74A GLU* 1.3 72.2 - - - +
76A GLN* 1.3 55.9 + - - +
78A PHE* 3.2 3.4 + - - +
79A LEU* 2.8 38.1 + - + +
111A PHE* 3.3 33.3 - - + +
114A MET* 3.9 28.3 - - + -
115A ILE* 5.4 2.0 - - + -
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Residues in contact with GLN 76 (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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72A GLU 3.0 18.3 + - - +
73A ARG* 4.0 6.3 - - - +
75A ALA* 1.3 78.1 - - - +
77A PHE* 1.3 57.0 + - - +
79A LEU* 4.2 19.2 - - - +
80A ASP* 2.9 66.9 + - - +
114A MET* 5.0 8.9 - - - +
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Residues in contact with PHE 77 (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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36A SER* 3.5 16.2 - - - -
37A GLU 4.2 0.4 - - - -
38A SER 3.6 18.2 - - - -
39A THR* 3.6 35.4 - - - -
40A THR* 3.8 8.7 - - - -
41A TYR 3.4 19.7 - - - -
42A LEU* 3.8 25.8 - - + -
73A ARG 3.2 17.2 + - - +
74A GLU 3.1 5.3 + - - +
76A GLN* 1.3 74.1 - - - +
78A PHE* 1.3 63.6 + - - +
80A ASP* 3.6 5.5 + - + -
81A ASN* 2.6 47.4 + - - +
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Residues in contact with PHE 78 (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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35A ILE* 3.7 32.5 - - + -
36A SER* 3.4 24.5 - - - +
58A PHE* 3.4 26.5 - - + -
59A TYR 3.7 15.7 - - - -
60A HIS* 3.6 21.8 - - + +
74A GLU 2.8 13.3 + - - +
75A ALA* 3.3 8.7 - - - +
77A PHE* 1.3 77.4 - - - +
79A LEU* 1.3 64.6 + - + +
81A ASN* 2.9 15.0 + - - +
82A VAL* 3.3 11.2 + - + +
89A LEU* 3.9 30.3 - - + -
90A VAL 3.9 8.5 - - - -
111A PHE* 3.9 11.7 - + - -
115A ILE* 4.4 9.0 - - + -
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Residues in contact with LEU 79 (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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75A ALA* 2.8 32.3 + - + +
76A GLN* 3.7 24.2 - - - +
78A PHE* 1.3 75.3 - - + +
80A ASP* 1.3 59.2 + - - +
81A ASN 3.0 4.9 + - - -
82A VAL* 3.2 20.8 + - + +
89A LEU* 3.7 28.5 - - + -
114A MET* 3.8 27.4 - - + +
115A ILE* 4.5 11.2 - - + +
118A ALA* 3.8 24.0 - - + -
120A TYR* 4.2 6.1 + - + +
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Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN* 2.9 56.0 + - - +
77A PHE* 4.0 8.5 - - + +
78A PHE 3.3 0.4 - - - -
79A LEU* 1.3 73.1 - - - +
81A ASN* 1.3 65.2 + - - +
82A VAL 3.7 1.8 - - - +
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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