Contacts of the helix formed by residues 60 - 83 (chain J) in PDB entry 3IT8
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 PRO 60 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J TYR* 3.7 27.6 - - + +
7J TYR* 5.2 2.2 - - - +
53J ILE* 5.1 4.5 - - - +
58J HIS 3.5 7.1 - - - +
59J THR* 1.3 99.3 - - + +
61J GLY* 1.3 63.5 + - - +
63J ASP* 4.6 0.5 + - - -
64J TYR* 3.4 28.0 + - + -
65J ASN* 3.7 19.7 - - - +
154J TYR 6.0 0.9 - - - +
158J PHE* 4.1 15.7 - - + -
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Residues in contact with GLY 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59J THR 3.6 2.7 + - - -
60J PRO* 1.3 71.8 - - - +
62J ASN* 1.3 77.7 + - - +
63J ASP 3.2 1.6 - - - -
65J ASN* 2.9 23.9 + - - +
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Residues in contact with ASN 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J GLY* 1.3 74.6 - - - +
63J ASP* 1.3 78.9 + - - +
65J ASN* 2.9 28.8 + - - +
66J PHE* 3.4 5.2 + - - +
67J ASN* 5.0 7.5 + - - +
154J TYR* 4.9 3.8 + - - -
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Residues in contact with ASP 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33J ILE* 3.6 17.6 - - + +
42J GLY 5.1 8.2 - - - +
43J ASN* 6.2 0.7 - - - -
44J VAL* 3.6 23.6 - - - +
47J ARG* 4.9 6.5 + - - +
60J PRO 4.6 0.9 + - - -
61J GLY* 3.2 1.0 - - - -
62J ASN* 1.3 82.2 - - - +
64J TYR* 1.3 72.3 + - - +
66J PHE* 3.0 25.1 + - + +
67J ASN* 5.9 1.4 + - - -
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Residues in contact with TYR 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J TYR* 3.6 17.3 - + - -
7J TYR* 2.6 36.6 + - + +
21J PHE* 3.2 31.0 - + + -
23J ASP* 2.8 29.8 + - - -
31J THR* 2.9 37.4 + - + -
33J ILE* 3.8 5.4 - - + -
44J VAL* 6.3 0.2 - - + -
47J ARG* 3.5 11.1 + - - -
51J PHE* 4.2 4.9 - - - -
53J ILE* 4.1 11.9 - - + +
59J THR* 3.4 27.0 - - + +
60J PRO* 3.4 17.9 + - + -
61J GLY 3.3 6.6 + - - -
62J ASN 3.3 0.4 - - - -
63J ASP* 1.3 82.4 - - - +
65J ASN* 1.3 74.5 + - - +
66J PHE 3.0 0.7 + - - -
170J TYR* 4.0 1.0 + - - -
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Residues in contact with ASN 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J PRO* 3.7 18.2 - - - +
61J GLY 2.9 13.2 + - - +
62J ASN* 2.9 37.6 + - - +
64J TYR* 1.3 74.8 - - - +
66J PHE* 1.3 64.8 + - - +
67J ASN 3.5 1.6 - - - -
68J PHE* 3.3 14.5 + - + +
69J TRP* 3.1 35.3 + - + +
154J TYR* 3.6 43.3 + - + +
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Residues in contact with PHE 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J TYR* 4.5 13.5 - + + -
19J GLY* 3.8 24.2 - - - -
20J VAL 3.9 12.8 - - - -
21J PHE* 3.7 28.3 - + + -
33J ILE* 3.6 20.9 - - + -
34J SER 4.1 1.6 - - - -
35J TYR* 3.8 18.6 - + + -
42J GLY* 3.8 29.8 - - - -
62J ASN 3.4 3.1 + - - +
63J ASP* 3.0 20.9 + - + +
64J TYR* 3.0 3.3 - - + +
65J ASN* 1.3 74.2 - - - +
67J ASN* 1.3 67.1 - - - +
69J TRP 3.2 0.5 + - - -
70J TYR* 2.8 52.1 + - + +
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Residues in contact with ASN 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35J TYR* 5.4 1.4 - - - -
41J HIS* 3.6 18.3 + - - +
42J GLY* 3.0 28.9 + - - -
62J ASN* 5.0 7.7 + - - +
63J ASP* 5.9 1.0 + - - -
65J ASN 3.5 0.4 - - - -
66J PHE* 1.3 80.1 - - - +
68J PHE* 1.3 63.8 + - - +
70J TYR* 3.9 4.8 - - - +
71J SER* 3.1 26.9 + - - -
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Residues in contact with PHE 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65J ASN* 3.3 15.8 + - + +
66J PHE 3.2 0.2 - - - -
67J ASN* 1.3 80.0 - - - +
69J TRP* 1.3 103.9 + + - +
71J SER* 3.8 3.3 - - - -
72J LEU* 3.0 43.0 + - + +
147J LEU* 4.2 22.2 - - + +
150J ASP* 3.5 37.2 - - + -
151J VAL* 4.2 5.8 - - + -
154J TYR* 3.7 28.9 - + + -
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Residues in contact with TRP 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J TYR* 3.5 48.6 + + + -
64J TYR 3.8 1.3 - - - -
65J ASN* 3.1 32.3 + - + +
66J PHE 3.9 0.7 - - - +
68J PHE* 1.3 101.1 - + - +
70J TYR* 1.3 68.6 + - - +
72J LEU* 4.3 10.8 - - + +
73J MET* 2.7 45.6 + - + +
93J LEU* 3.7 30.5 - - + -
140J MET* 4.1 17.0 - - - -
151J VAL* 4.2 16.2 - - + -
154J TYR* 3.7 26.0 - - + +
155J LEU* 3.9 24.2 - - + -
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Residues in contact with TYR 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J TYR* 5.6 0.2 - - - -
9J VAL* 3.9 16.5 - - + +
17J TYR* 2.6 37.4 + - + +
18J ASP 4.0 3.1 - - - -
19J GLY* 3.8 26.7 - - - -
35J TYR* 3.4 58.7 - + + -
37J HIS* 4.2 1.4 - - - -
66J PHE* 2.8 37.9 + + + +
67J ASN* 3.9 4.0 - - - +
69J TRP* 1.3 71.8 - - - +
71J SER* 1.3 64.1 + - - +
73J MET* 3.7 2.1 - - - +
74J LYS* 2.8 57.8 + - + +
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Residues in contact with SER 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J ASN 3.1 16.3 + - - -
68J PHE* 3.8 3.6 - - - -
70J TYR* 1.3 89.6 - - - +
72J LEU* 1.3 57.4 + - - +
74J LYS* 3.2 8.0 + - - +
75J GLU* 3.0 27.2 + - - +
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Residues in contact with LEU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68J PHE* 3.0 48.6 + - + +
69J TRP* 4.0 9.0 - - + +
71J SER* 1.3 76.9 + - - +
73J MET* 1.3 57.8 + - - +
75J GLU* 3.5 16.2 + - - +
76J THR* 2.8 29.5 + - - -
140J MET* 3.5 30.3 - - + +
145J ASN* 3.8 25.8 - - - +
147J LEU* 4.3 20.6 - - + -
151J VAL* 3.7 14.1 - - + -
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Residues in contact with MET 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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7J TYR* 3.7 36.1 - - - +
9J VAL* 3.8 21.2 - - + +
69J TRP* 2.7 38.5 + - + +
70J TYR* 5.3 0.2 - - - -
72J LEU* 1.3 71.4 - - - +
74J LYS* 1.3 61.8 + - - +
76J THR* 3.5 1.7 - - - -
77J LEU* 2.8 31.7 + - - +
91J LEU* 3.4 40.2 - - + +
92J SER* 3.9 2.0 - - - +
93J LEU* 3.7 15.7 - - - +
140J MET* 3.2 29.6 - - + -
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Residues in contact with LYS 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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9J VAL* 4.4 9.8 - - + +
17J TYR* 3.9 34.5 - - + +
35J TYR* 6.0 0.2 + - - -
70J TYR* 2.8 46.0 + - + +
71J SER* 3.3 8.5 - - - +
73J MET* 1.3 78.7 - - - +
75J GLU* 1.3 63.3 + - - +
77J LEU* 3.2 3.6 + - - +
78J GLU* 3.0 46.3 + - - +
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Residues in contact with GLU 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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71J SER 3.0 12.9 + - - +
72J LEU* 3.6 20.5 - - - +
73J MET 3.2 0.2 - - - -
74J LYS* 1.3 76.4 - - - +
76J THR* 1.3 61.4 + - - +
78J GLU* 3.2 13.1 + - - +
79J GLU* 3.1 39.3 + - + +
139J GLY* 3.9 8.2 + - - -
145J ASN* 3.2 25.7 + - - +
146J THR* 6.0 2.3 - - - +
147J LEU* 5.3 4.2 - - - +
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Residues in contact with THR 76 (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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72J LEU 2.8 19.3 + - - -
73J MET* 3.2 6.0 + - - -
75J GLU* 1.3 77.4 - - - +
77J LEU* 1.3 62.1 + - - +
79J GLU* 3.4 3.3 + - - +
80J ILE* 3.0 35.5 + - + +
91J LEU* 3.6 20.6 - - + -
110J VAL* 6.1 0.2 - - + -
138J VAL* 4.2 16.8 - - + +
139J GLY* 3.3 8.1 - - - -
140J MET* 2.8 37.0 + - + +
141J LEU* 4.5 7.2 - - + -
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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
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9J VAL* 3.7 35.2 - - + +
11J LEU* 4.5 1.6 - - + +
17J TYR* 3.8 22.7 - - + -
73J MET 2.8 20.3 + - - +
74J LYS 3.2 4.9 + - - +
76J THR* 1.3 73.1 - - - +
78J GLU* 1.3 62.2 + - - +
80J ILE* 3.3 9.1 + - + +
81J ASN* 3.0 47.5 + - - +
88J THR* 3.9 16.6 - - - +
89J THR 4.0 14.1 - - - +
90J SER* 4.1 14.8 - - - +
91J LEU* 4.0 10.1 - - + +
112J THR* 6.1 0.4 - - - +
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Residues in contact with GLU 78 (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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17J TYR* 3.3 32.5 - - + +
74J LYS* 3.0 45.8 + - - +
75J GLU* 3.5 11.6 - - - +
77J LEU* 1.3 76.7 - - - +
79J GLU* 1.3 69.0 + - - +
81J ASN* 3.1 14.5 + - - +
82J LYS* 3.4 17.9 + - - +
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Residues in contact with GLU 79 (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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75J GLU* 3.1 29.7 + - + +
76J THR 3.8 1.8 - - - +
77J LEU 3.3 0.2 - - - -
78J GLU* 1.3 78.5 - - - +
80J ILE* 1.3 63.9 + - - +
82J LYS* 3.0 52.2 + - - +
83J ASN* 4.2 2.8 + - - +
138J VAL* 3.6 35.8 - - + +
139J GLY* 4.4 6.7 - - - +
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Residues in contact with ILE 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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76J THR* 3.0 36.4 + - + +
77J LEU* 3.5 10.5 - - + +
78J GLU 3.3 0.2 - - - -
79J GLU* 1.3 75.3 - - - +
81J ASN* 1.3 65.0 + - - +
82J LYS 3.4 0.7 + - - -
83J ASN* 3.6 6.6 + - - +
86J THR* 3.3 49.5 - - + +
87J LYS 3.9 0.2 + - - -
88J THR* 4.4 7.6 - - - +
91J LEU* 4.1 17.5 - - + -
112J THR* 4.7 2.7 - - - +
117J LEU* 4.1 25.8 - - + -
136J PRO* 4.0 12.3 - - + -
138J VAL* 4.0 15.0 - - + -
141J LEU* 4.9 1.3 - - + -
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Residues in contact with ASN 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J LEU* 4.0 18.3 - - - +
17J TYR* 4.5 6.0 + - - +
77J LEU* 3.0 34.5 + - - +
78J GLU* 3.7 7.0 - - - +
79J GLU 3.1 1.0 - - - -
80J ILE* 1.3 76.6 - - - +
82J LYS* 1.3 63.2 + - - +
83J ASN 3.4 5.0 - - - -
84J ASP* 4.2 0.9 + - - -
87J LYS* 3.0 32.4 - - + +
88J THR* 2.6 45.6 + - - +
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Residues in contact with LYS 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J GLU* 3.4 15.0 + - - +
79J GLU* 3.0 39.8 + - - +
81J ASN* 1.3 77.3 - - - +
83J ASN* 1.3 61.1 + - - +
84J ASP* 3.0 9.7 + - - +
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Residues in contact with ASN 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J GLU 4.2 2.7 + - - +
80J ILE 3.6 5.3 + - - +
81J ASN 3.4 0.6 - - - -
82J LYS* 1.3 75.5 - - - +
84J ASP* 1.3 53.8 + - - +
85J SER* 2.7 38.7 + - - -
86J THR* 2.8 25.9 + - - +
87J LYS 3.5 6.6 + - - -
136J PRO* 6.6 0.2 - - + -
327J NAG 1.4 69.5 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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