Contacts of the helix formed by residues 67 - 84 (chain J) in PDB entry 5OA3
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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63J LEU* 4.6 13.1 - - + +
64J ASP* 3.7 25.2 + - + +
65J GLU 3.1 1.0 - - - -
66J LYS* 1.3 76.9 - - - +
68J PRO* 1.3 75.4 - - - +
69J ARG* 2.8 38.5 + - - +
70J ARG* 3.2 13.7 + - + +
71J LEU* 3.2 17.0 + - - +
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Residues in contact with PRO 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248E ILE* 6.5 0.7 - - + -
66J LYS 3.4 5.3 - - - +
67J ASP* 1.3 96.5 - - - +
69J ARG* 1.3 57.0 + - - +
71J LEU* 3.3 14.5 + - + +
72J PHE* 2.9 33.5 + - - +
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Residues in contact with ARG 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8162 A 4.8 10.3 + - - -
8492 A 4.9 20.2 + - - -
248E ILE* 6.5 0.9 - - - -
59J GLU* 4.9 6.7 + - - +
60J LEU* 4.3 11.1 - - + +
63J LEU* 3.0 31.2 - - + +
67J ASP* 2.8 14.1 + - - +
68J PRO* 1.3 76.0 - - - +
70J ARG* 1.3 64.7 + - - +
72J PHE* 4.8 3.6 - - - -
73J GLU* 2.9 65.6 + - + +
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Residues in contact with ARG 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C ASN* 5.1 7.5 - - - +
60J LEU* 3.7 36.4 + - + +
61J LEU* 3.3 35.9 + - - +
63J LEU* 3.8 18.5 + - + +
64J ASP 3.5 19.7 - - - +
65J GLU* 3.9 33.0 - - - +
67J ASP* 3.2 14.6 + - + +
69J ARG* 1.3 78.7 - - - +
71J LEU* 1.3 64.2 + - - +
74J GLY* 2.9 23.4 + - - -
94J LEU* 4.1 19.0 - - + +
95J ASP* 5.3 0.6 + - - -
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Residues in contact with LEU 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E ARG* 6.1 1.1 - - - +
65J GLU* 3.2 34.5 - - + +
66J LYS* 3.6 18.2 - - + +
67J ASP 3.2 15.9 - - - +
68J PRO* 3.5 13.0 - - + +
70J ARG* 1.3 79.3 - - - +
72J PHE* 1.3 57.6 + - - +
74J GLY 3.8 0.2 - - - -
75J ASN* 2.9 43.5 + - - +
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Residues in contact with PHE 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8172 G 5.5 2.0 - - - -
8182 A 3.1 35.7 - - - -
8472 A 3.9 12.6 - + - -
248E ILE* 3.5 47.3 - - + -
249E ALA* 4.0 19.3 - - + +
252E ARG* 3.6 45.3 + - + +
68J PRO 2.9 20.5 + - - +
69J ARG* 4.3 2.9 - - - +
71J LEU* 1.3 70.4 - - - +
73J GLU* 1.3 73.5 + - + +
75J ASN* 3.0 5.0 + - - +
76J ALA* 2.9 24.8 + - + +
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Residues in contact with GLU 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8172 G 3.7 46.3 + - - +
8182 A 4.8 3.2 + - - +
56J ALA* 5.5 5.4 - - - +
60J LEU* 4.0 23.3 - - + +
69J ARG* 2.9 59.1 + - + +
72J PHE* 1.3 84.1 - - + +
74J GLY* 1.3 62.3 + - - +
76J ALA* 3.2 7.9 + - - +
77J LEU* 2.9 24.5 + - + +
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Residues in contact with GLY 74 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J LEU* 3.8 17.1 - - - +
70J ARG 2.9 20.8 + - - -
71J LEU 3.8 0.2 - - - -
73J GLU* 1.3 77.2 - - - +
75J ASN* 1.3 61.9 + - - +
77J LEU* 3.1 6.4 + - - +
78J LEU* 2.9 32.7 + - - +
94J LEU* 4.8 11.2 - - - -
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Residues in contact with ASN 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252E ARG* 3.3 31.8 - - - +
71J LEU* 2.9 30.8 + - - +
74J GLY* 1.3 74.4 - - - +
76J ALA* 1.3 57.5 + - - +
78J LEU* 3.5 12.5 + - - +
79J ARG* 2.9 31.5 + - - +
92J MET* 5.4 8.0 - - - +
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Residues in contact with ALA 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8182 A 3.9 33.2 - - - +
8192 G 4.1 12.8 + - - +
252E ARG* 4.6 2.8 - - - +
72J PHE* 2.9 17.6 + - + +
73J GLU* 3.4 11.0 - - - +
75J ASN* 1.3 73.9 - - - +
77J LEU* 1.3 66.0 + - - +
79J ARG* 3.3 5.4 + - - +
80J ARG* 3.0 29.8 + - - +
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Residues in contact with LEU 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8182 A 4.5 3.1 + - - +
53J ILE* 4.0 38.4 - - + +
56J ALA* 4.7 9.4 - - + -
57J ALA* 4.5 13.7 - - + +
60J LEU* 5.1 8.5 - - + -
73J GLU* 2.9 12.1 + - + +
74J GLY* 3.1 8.5 + - - +
76J ALA* 1.3 77.9 - - - +
78J LEU* 1.3 57.8 + - + +
80J ARG* 3.0 36.2 + - - +
81J LEU* 2.9 34.2 + - + +
94J LEU* 5.2 2.7 - - + -
97J ILE* 3.6 25.4 - - + -
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Residues in contact with LEU 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J GLY 2.9 26.0 + - - +
75J ASN* 3.9 14.1 - - - +
77J LEU* 1.3 76.7 - - + +
79J ARG* 1.3 58.9 + - - +
81J LEU* 3.3 5.3 + - - +
82J VAL* 2.9 34.3 + - - +
87J LEU* 4.0 10.4 - - + +
92J MET* 3.3 30.7 - - + +
93J LYS* 3.3 22.0 - - - +
94J LEU* 4.0 21.3 - - + -
97J ILE* 3.6 30.3 - - + -
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Residues in contact with ARG 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8192 G 3.4 28.2 + - - -
8202 U 3.1 29.7 + - - -
252E ARG* 6.5 0.7 - - - +
256E LEU* 6.0 9.0 - - - -
75J ASN 2.9 18.8 + - - +
76J ALA* 3.7 3.4 - - - +
78J LEU* 1.3 74.7 - - - +
80J ARG* 1.3 71.2 + - - +
82J VAL* 3.0 9.7 + - + +
83J ARG* 2.9 62.5 + - + +
92J MET* 5.6 3.8 - - - +
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Residues in contact with ARG 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8182 A 3.7 23.1 + - - -
8192 G 3.8 24.2 + - - -
53J ILE* 5.8 4.0 - - - +
76J ALA 3.0 15.3 + - - +
77J LEU* 3.0 49.0 - - - +
79J ARG* 1.3 89.7 - - - +
81J LEU* 1.3 62.1 + - + +
82J VAL 3.4 0.2 + - - -
83J ARG* 3.7 12.8 + - - +
84J ILE* 3.2 30.1 + - + +
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Residues in contact with LEU 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J ILE* 3.7 33.2 - - + -
77J LEU* 2.9 21.7 + - + +
78J LEU 3.3 4.2 + - - +
80J ARG* 1.3 75.0 - - + +
82J VAL* 1.3 61.7 + - - +
84J ILE* 3.5 28.1 - - + +
86J VAL* 3.5 10.4 + - + +
87J LEU* 3.2 31.1 + - + -
97J ILE* 3.7 29.8 - - + -
100J LEU* 4.3 11.0 - - + -
105J PHE* 3.9 28.0 - - + -
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Residues in contact with VAL 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J LEU 2.9 20.4 + - - +
79J ARG* 3.0 12.8 + - + +
81J LEU* 1.3 78.1 - - - +
83J ARG* 1.3 65.7 + - + +
85J GLY* 2.8 22.7 + - - -
87J LEU* 3.9 16.4 - - + +
88J ASP 4.0 14.6 - - - +
89J GLU* 3.6 26.7 - - + +
92J MET* 3.9 31.0 - - + -
151J LEU* 4.3 7.2 - - + +
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Residues in contact with ARG 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8202 U 3.4 25.7 + - - -
8212 G 3.9 13.1 + - - -
79J ARG* 2.9 47.7 + - + +
80J ARG* 3.9 14.8 - - - +
81J LEU 3.6 0.2 - - - -
82J VAL* 1.3 81.0 - - + +
84J ILE* 1.3 62.2 + - + +
85J GLY 3.2 0.2 - - - -
150J ARG* 3.5 46.7 - - + +
151J LEU* 2.8 31.4 + - - +
152J ASP* 4.6 4.4 + - - +
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Residues in contact with ILE 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80J ARG* 3.2 15.5 - - + +
81J LEU* 3.5 27.8 - - + +
83J ARG* 1.3 84.6 - - + +
85J GLY* 1.3 55.4 + - - +
86J VAL* 3.6 24.2 - - + -
105J PHE* 4.1 15.5 - - + -
108J ARG* 2.7 38.4 + - + +
148J ILE* 4.4 24.7 - - + -
149J VAL 3.6 2.8 - - - +
150J ARG* 4.4 13.7 - - + +
151J LEU 4.3 2.2 - - - +
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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
------------------------------------------------------------
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