Contacts of the helix formed by residues 73 - 87 (chain A) in PDB entry 3OX4
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 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A MET* 6.0 4.5 - - + -
71A ASN 3.8 8.3 - - - +
72A PRO* 1.3 81.0 - - - +
74A VAL* 1.3 64.2 + - - +
75A THR* 2.9 20.0 + - - -
76A ALA* 3.0 27.4 + - - +
77A VAL* 3.2 10.0 + - - +
152A ILE* 3.8 5.2 - - - -
153A THR* 3.1 14.4 - - + +
155A GLU* 3.0 36.3 + - + +
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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
----------------------------------------------------------
73A THR* 1.3 72.2 - - - +
75A THR* 1.3 64.9 + - + +
77A VAL* 3.3 4.4 + - - +
78A LEU* 3.1 38.1 + - + +
116A GLU* 6.2 2.5 - - + -
117A VAL* 4.2 18.4 - - + +
118A LYS* 4.7 5.4 - - - +
152A ILE* 3.6 11.4 - - + -
153A THR 2.9 20.7 + - - +
154A ASP* 3.6 21.5 - - - +
155A GLU 5.3 0.9 - - - +
161A MET* 3.5 30.1 - - + -
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR* 2.9 21.5 + - - -
74A VAL* 1.3 76.2 - - + +
76A ALA* 1.3 64.4 + - - +
78A LEU* 3.6 11.2 + - + +
79A GLU* 3.0 33.6 + - - +
155A GLU* 3.7 18.2 + - + +
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Residues in contact with ALA 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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65A TYR* 3.2 25.8 + - + +
67A GLY 4.6 7.9 - - - +
68A VAL* 4.9 5.4 - - - -
69A MET 5.5 1.3 - - - +
72A PRO* 5.2 1.6 - - + -
73A THR* 3.0 25.4 + - - +
75A THR* 1.3 82.2 + - - +
77A VAL* 1.3 56.8 + - - +
79A GLU* 3.0 6.0 - - - +
80A GLY 2.9 23.7 + - - -
103A CYS* 3.9 17.9 - - - -
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Residues in contact with VAL 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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73A THR 3.2 11.2 + - - +
74A VAL 3.6 7.2 - - - +
75A THR 3.3 0.4 - - - -
76A ALA* 1.3 76.9 - - - +
78A LEU* 1.3 60.5 + - + +
80A GLY 2.8 4.3 + - - -
81A LEU* 2.8 50.9 + - + +
103A CYS* 4.2 8.1 - - - +
106A ALA* 3.5 31.6 - - + +
107A ILE* 3.0 17.9 - - + +
110A VAL* 4.8 2.0 - - + -
117A VAL* 4.0 20.4 - - + -
152A ILE* 4.0 18.4 - - + -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.1 33.9 + - + +
75A THR* 3.9 9.6 - - + +
77A VAL* 1.3 82.6 - - + +
79A GLU* 1.3 63.0 + - - +
81A LEU* 3.2 13.1 + - + +
82A LYS* 3.0 24.3 + - - +
110A VAL* 6.6 0.4 - - + -
116A GLU* 5.7 10.8 - - + -
117A VAL* 5.8 2.7 - - + -
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Residues in contact with GLU 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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65A TYR* 3.0 34.5 + - + +
67A GLY* 4.4 6.9 - - - +
75A THR* 3.0 22.5 + - - +
76A ALA* 3.0 14.4 - - - +
78A LEU* 1.3 78.5 - - - +
80A GLY* 1.3 57.8 + - - +
82A LYS* 3.5 6.8 + - - +
83A ILE* 3.3 26.9 + - + +
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Residues in contact with GLY 80 (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 LEU* 3.8 6.3 - - - +
65A TYR* 4.0 22.9 - - - -
76A ALA 2.9 10.0 + - - -
77A VAL 2.8 7.7 + - - -
79A GLU* 1.3 74.8 - - - +
81A LEU* 1.3 58.0 + - - +
83A ILE* 3.3 4.6 + - - +
84A LEU* 2.8 30.1 + - - +
107A ILE* 4.2 14.4 - - - -
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Residues in contact with LEU 81 (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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77A VAL* 2.8 52.4 + - + +
78A LEU* 3.2 15.2 + - + +
80A GLY* 1.3 76.7 - - - +
82A LYS* 1.3 57.0 + - - +
84A LEU* 3.3 9.9 + - + +
85A LYS* 2.9 28.8 + - - +
107A ILE* 3.4 36.1 - - + +
110A VAL* 4.2 16.6 - - + -
111A ALA* 3.9 21.5 - - + +
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Residues in contact with LYS 82 (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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78A LEU 3.0 12.6 + - - +
79A GLU* 3.6 11.2 - - - +
81A LEU* 1.3 73.8 - - - +
83A ILE* 1.3 70.2 + - + +
85A LYS* 3.0 21.4 + - - +
86A ASP* 2.9 50.4 + - - +
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Residues in contact with ILE 83 (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 LEU* 3.7 20.4 - - + -
63A ALA* 4.3 4.7 - - + -
64A VAL 4.3 14.6 - - - +
65A TYR* 4.5 17.3 - - + -
79A GLU* 3.3 14.1 + - + +
80A GLY* 3.3 8.0 + - - +
82A LYS* 1.3 78.4 - - + +
84A LEU* 1.3 63.0 + - - +
86A ASP* 3.6 9.0 + - + +
87A ASN* 2.7 45.9 + - - +
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Residues in contact with LEU 84 (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 LEU* 3.6 12.8 - - + +
80A GLY 2.8 17.0 + - - +
81A LEU* 3.3 10.3 - - + +
82A LYS 3.1 0.2 - - - -
83A ILE* 1.3 78.8 - - - +
85A LYS* 1.3 62.8 + - + +
87A ASN 3.4 0.2 + - - -
88A ASN* 2.9 23.8 + - - -
89A SER* 3.1 44.3 + - - +
92A VAL* 4.4 4.0 - - + -
107A ILE* 3.7 25.6 - - + -
111A ALA* 3.8 26.0 - - + -
131A LEU* 4.2 12.1 - - + -
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Residues in contact with LYS 85 (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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81A LEU 2.9 12.9 + - - +
82A LYS* 3.0 15.5 + - + +
84A LEU* 1.3 82.4 - - + +
86A ASP* 1.3 66.5 + - - +
87A ASN 3.1 0.2 - - - -
88A ASN* 3.0 34.7 + - - +
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Residues in contact with ASP 86 (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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82A LYS* 2.9 49.9 + - - +
83A ILE* 4.1 10.5 - - + +
84A LEU 3.4 0.2 - - - -
85A LYS* 1.3 80.5 - - - +
87A ASN* 1.3 64.8 + - - +
88A ASN* 5.4 0.2 - - - -
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Residues in contact with ASN 87 (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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33A ASN* 3.9 19.3 + - + +
63A ALA* 3.3 29.2 - - + +
83A ILE* 2.7 37.0 + - - +
85A LYS 3.1 0.6 - - - -
86A ASP* 1.3 85.7 - - - +
88A ASN* 1.3 73.3 + - - +
89A SER* 3.2 13.0 + - - +
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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