Contacts of the helix formed by residues 73 - 88 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B ASN 3.6 13.9 - - - +
72B PRO* 1.3 73.4 - - - +
74B VAL* 1.3 65.2 + - - +
75B THR* 3.4 6.4 + - - -
76B ALA* 3.1 26.7 + - - +
77B VAL* 3.0 24.6 + - - +
152B ILE* 3.6 4.9 - - - -
153B THR* 3.1 14.4 - - + +
155B GLU* 3.3 31.5 + - + +
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Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR* 1.3 71.9 - - - +
75B THR* 1.3 62.0 + - - +
77B VAL* 3.1 5.4 + - - +
78B LEU* 2.8 46.9 + - + +
116B GLU* 5.8 4.3 - - + +
117B VAL* 4.5 23.6 - - + +
118B LYS* 5.9 0.7 - - + +
152B ILE* 3.8 15.0 - - + -
153B THR 3.0 13.2 + - - +
154B ASP* 4.0 22.4 - - + +
155B GLU* 3.0 7.6 + - - +
156B VAL* 6.4 0.2 - - + -
161B MET* 5.1 5.4 - - - -
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Residues in contact with THR 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR* 3.7 5.6 - - - -
74B VAL* 1.3 73.1 - - - +
76B ALA* 1.3 64.7 + - - +
78B LEU* 3.1 13.1 + - + +
79B GLU* 2.9 37.7 + - + +
155B GLU* 2.7 33.7 + - - +
156B VAL* 5.7 0.3 - - - +
44C LYS* 3.6 40.4 - - + +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TYR* 3.2 29.0 + - + +
67B GLY 4.7 8.3 - - - +
68B VAL* 4.8 5.6 - - - -
69B MET 5.5 1.1 - - - +
72B PRO* 5.1 1.6 - - + -
73B THR* 3.1 25.6 + - - +
75B THR* 1.3 80.3 - - - +
77B VAL* 1.3 62.9 + - - +
79B GLU* 3.2 2.9 + - - -
80B GLY* 3.0 19.4 + - - -
103B CYS* 4.1 15.0 - - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO* 5.9 0.2 - - + -
73B THR 3.0 19.8 + - - +
74B VAL 3.4 7.6 - - - +
76B ALA* 1.3 73.8 - - - +
78B LEU* 1.3 59.3 + - + +
80B GLY* 3.2 2.6 + - - -
81B LEU* 2.9 45.4 + - + +
103B CYS* 4.1 15.0 - - - +
106B ALA* 3.6 27.1 - - + +
107B ILE* 3.7 19.1 - - + +
110B VAL* 5.0 0.2 - - + -
117B VAL* 3.7 22.0 - - + -
152B ILE* 3.8 15.7 - - + -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 2.8 34.7 + - + +
75B THR* 3.4 11.7 - - - +
77B VAL* 1.3 79.1 - - + +
79B GLU* 1.3 63.3 + - + +
81B LEU* 3.2 18.9 + - + +
82B LYS* 3.1 20.8 + - - +
116B GLU* 5.7 12.3 - - + +
117B VAL* 6.3 1.1 - - + -
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TYR* 2.9 33.8 + - + -
67B GLY* 4.8 4.5 - - - +
75B THR* 2.9 32.7 + - + +
76B ALA* 3.6 3.0 - - - +
78B LEU* 1.3 75.1 - - + +
80B GLY* 1.3 64.6 + - - +
82B LYS* 2.9 20.6 + - - +
83B ILE* 3.1 15.3 + - + +
40C ALA* 5.1 5.5 - - - +
44C LYS* 3.8 25.8 + - - +
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Residues in contact with GLY 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.7 7.7 - - - +
65B TYR* 3.9 22.1 - - - -
76B ALA 3.0 12.0 + - - -
77B VAL 3.6 3.8 - - - -
79B GLU* 1.3 77.6 - - - +
81B LEU* 1.3 54.5 + - - +
83B ILE* 3.4 2.1 + - - +
84B LEU* 3.0 26.7 + - - +
107B ILE* 3.7 22.4 - - - -
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Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 2.9 38.3 + - + +
78B LEU* 3.6 20.2 - - + +
79B GLU 3.2 0.2 - - - -
80B GLY* 1.3 73.2 - - - +
82B LYS* 1.3 60.6 + - - +
84B LEU* 3.4 8.9 - - + +
85B LYS* 2.8 30.5 + - - +
107B ILE* 3.5 33.2 - - + +
110B VAL* 3.8 22.4 - - + -
111B ALA* 3.9 20.4 - - + +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU 3.1 11.1 + - - +
79B GLU* 2.9 14.0 + - - +
81B LEU* 1.3 74.1 - - - +
83B ILE* 1.3 67.6 + - + +
85B LYS* 3.3 14.2 + - + +
86B ASP* 2.8 65.4 + - - +
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.7 20.4 - - + -
63B ALA* 4.1 8.1 - - + -
64B VAL 4.2 13.5 - - - +
65B TYR* 4.4 18.6 - - + -
79B GLU 3.1 13.1 + - - +
80B GLY* 3.7 6.5 - - - +
82B LYS* 1.3 81.3 - - + +
84B LEU* 1.3 66.0 + - - +
86B ASP* 3.5 5.1 + - + +
87B ASN* 2.8 48.2 + - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.8 11.4 - - + +
80B GLY 3.0 14.2 + - - +
81B LEU* 3.4 13.5 - - + +
83B ILE* 1.3 76.8 - - - +
85B LYS* 1.3 57.1 + - - +
87B ASN 3.5 0.2 - - - -
88B ASN* 2.6 34.3 + - - -
89B SER* 3.3 38.0 + - - +
92B VAL* 4.5 1.8 - - + -
107B ILE* 3.7 26.0 - - + +
111B ALA* 3.7 27.8 - - + -
131B LEU* 3.9 13.2 - - + -
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Residues in contact with LYS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU 2.8 17.2 + - - +
82B LYS* 3.5 14.8 - - + +
84B LEU* 1.3 80.9 - - + +
86B ASP* 1.3 75.9 + - - +
87B ASN 3.0 1.6 + - - -
88B ASN* 3.0 17.4 + - - +
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LYS* 2.8 59.0 + - - +
83B ILE* 4.1 8.5 + - + +
85B LYS* 1.3 82.9 + - - +
87B ASN* 1.3 65.7 + - - +
88B ASN* 5.4 0.2 - - - -
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ASN* 2.7 35.0 + - - +
61B ASN* 5.7 0.9 - - - +
63B ALA* 3.5 20.5 - - + +
83B ILE* 2.8 45.9 + - - +
85B LYS 3.0 0.4 - - - -
86B ASP* 1.3 84.1 - - - +
88B ASN* 1.3 63.2 + - - +
89B SER* 4.0 6.7 - - - +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ASN* 3.5 4.9 + - - +
84B LEU* 2.6 18.7 + - - -
85B LYS* 3.0 11.3 + - - +
86B ASP 5.4 0.2 - - - -
87B ASN* 1.3 76.8 - - - +
89B SER* 1.3 67.0 - - - +
90B ASP* 3.5 4.3 + - - +
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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