Contacts of the helix formed by residues 70 - 91 (chain o) in PDB entry 3J9X
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 GLY 70 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2558 A 3.4 25.9 + - - +
2568 T 4.1 2.3 + - - -
69o THR* 1.3 76.3 - - - +
71o PRO* 1.3 70.0 - - - +
73o ARG* 2.9 32.0 + - - +
90q ILE* 5.5 0.8 - - - +
99q MET* 5.3 0.2 - - - +
111r PHE* 3.6 19.2 - - - -
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Residues in contact with PRO 71 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2558 A 3.7 29.8 - - + +
2568 T 3.6 26.5 - - - +
69o THR 4.4 0.4 - - - +
70o GLY* 1.3 82.3 - - - +
72o ASN* 1.3 64.5 + - - +
73o ARG 3.1 0.4 - - - -
74o ALA* 3.0 5.6 + - + +
75o ILE* 3.0 24.8 + - - +
71r PRO* 3.6 19.4 - - + +
74r ALA 4.8 0.7 - - - -
75r ILE* 3.6 37.7 - - + +
107r TYR* 6.5 0.9 - - + -
111r PHE* 4.6 5.8 - - + -
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Residues in contact with ASN 72 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68o ILE* 3.5 16.2 - - + -
69o THR 3.3 14.0 + - - +
70o GLY 3.0 0.6 - - - -
71o PRO* 1.3 75.8 - - - +
73o ARG* 1.3 65.5 + - - +
75o ILE* 3.3 18.1 + - + +
76o TYR* 3.1 26.7 - - + -
72r ASN* 3.1 24.4 - - - +
75r ILE* 3.5 11.5 - - - +
111r PHE 3.2 25.7 + - - -
112r ASN* 4.6 11.1 + - - +
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Residues in contact with ARG 73 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2558 A 2.9 38.9 + - - +
60o SER* 2.7 45.1 + - - +
63o LEU* 3.5 17.4 - - + +
64o THR* 3.0 32.3 + - - +
68o ILE* 2.8 54.5 + - + +
69o THR* 3.9 8.3 - - - +
70o GLY 2.9 13.8 + - - +
72o ASN* 1.3 75.8 - - - +
74o ALA* 1.3 58.6 + - - +
76o TYR 3.1 3.5 + - - -
77o GLN* 2.8 32.4 + - - +
89q ARG 4.6 0.6 + - - -
90q ILE* 3.7 26.9 + - - +
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Residues in contact with ALA 74 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957 A 4.1 25.8 - - + +
2548 T 4.3 5.1 - - - +
2558 A 3.8 38.0 + - + +
70o GLY 3.7 1.2 + - - -
71o PRO* 3.0 11.3 + - + +
73o ARG* 1.3 79.6 - - - +
75o ILE* 1.3 61.2 - - - +
77o GLN* 3.6 9.0 - - - +
78o GLY* 2.9 21.1 + - - -
71r PRO* 4.8 4.0 - - + -
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Residues in contact with ILE 75 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71o PRO 3.0 14.0 + - - +
72o ASN* 3.4 23.3 - - - +
74o ALA* 1.3 79.1 - - - +
76o TYR* 1.3 70.7 + - + +
78o GLY* 3.3 0.5 + - - -
79o PHE* 3.2 17.2 + - - +
107o TYR* 3.5 30.5 - - + -
111o PHE* 4.8 10.8 - - + +
113o ALA* 4.2 19.7 - - + -
71r PRO* 3.5 28.7 - - + +
72r ASN* 3.5 34.8 - - - +
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Residues in contact with TYR 76 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59o VAL* 4.3 5.3 - - - +
63o LEU* 3.6 34.1 - - + -
68o ILE* 4.0 18.8 - - + +
72o ASN* 3.1 26.4 + - + -
73o ARG 3.1 2.7 + - - +
75o ILE* 1.3 80.5 - - + +
77o GLN* 1.3 60.1 + - - +
79o PHE* 3.2 7.0 + - - +
80o GLY* 2.9 26.0 + - - -
112o ASN 5.2 0.2 + - - -
113o ALA* 4.0 8.4 - - + -
114o ASN* 2.9 37.9 + - - +
117o VAL* 3.7 28.8 - - + +
118o LEU* 3.6 30.3 - - + -
121o VAL* 4.4 9.1 - - + +
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Residues in contact with GLN 77 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2548 T 3.2 31.6 + - + +
2558 A 3.2 19.7 + - - +
55o VAL* 4.8 1.0 - - - +
56o ASN* 3.1 41.6 + - - +
59o VAL* 3.3 23.9 - - - +
60o SER* 3.4 12.3 - - - +
63o LEU* 4.0 3.5 - - + +
73o ARG 2.8 24.0 + - - +
74o ALA* 3.6 7.4 - - - +
76o TYR* 1.3 76.5 - - - +
78o GLY* 1.3 56.3 + - - +
80o GLY* 3.2 1.7 + - - -
81o LEU* 2.9 36.6 + - + +
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Residues in contact with GLY 78 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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957 A 5.6 1.3 - - - -
967 T 3.7 31.2 + - - +
74o ALA 2.9 14.3 + - - -
75o ILE 3.8 2.9 - - - -
77o GLN* 1.3 77.3 - - - +
79o PHE* 1.3 61.9 + - - +
81o LEU* 3.3 5.4 + - - +
82o LYS* 3.0 24.3 + - - +
107o TYR* 3.5 11.1 + - - -
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Residues in contact with PHE 79 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75o ILE 3.2 12.3 + - - +
76o TYR 3.2 7.6 + - - +
78o GLY* 1.3 76.8 - - - +
80o GLY* 1.3 64.3 + - - +
82o LYS* 3.2 6.0 + - - +
83o VAL* 3.1 29.3 + - + +
100o ILE* 5.0 0.7 - - + -
103o LEU* 3.6 32.1 - - + -
104o LYS* 3.8 28.5 - - + -
107o TYR* 3.5 27.2 + + + -
118o LEU* 3.3 51.1 - - + -
121o VAL* 3.8 17.0 - - + -
122o VAL* 3.6 24.9 - - + -
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Residues in contact with GLY 80 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55o VAL* 4.1 6.7 - - - -
59o VAL* 4.7 2.2 - - - -
76o TYR 2.9 12.4 + - - -
77o GLN 3.2 2.9 + - - -
79o PHE* 1.3 76.2 - - - +
81o LEU* 1.3 61.7 - - - +
83o VAL* 3.1 2.9 + - - -
84o ALA* 3.1 18.9 + - - +
121o VAL* 3.6 13.9 - - - -
125o ILE* 3.2 30.0 - - - +
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Residues in contact with LEU 81 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967 T 3.6 21.3 - - + +
977 A 3.4 32.6 - - - +
2538 A 4.9 6.5 - - + -
2548 T 5.2 2.7 - - - +
52o PHE* 3.7 37.6 - - + +
55o VAL* 4.3 7.2 - - + +
56o ASN* 3.3 29.6 - - - +
77o GLN* 2.9 25.8 + - + +
78o GLY* 3.6 4.9 - - - +
80o GLY* 1.3 75.4 - - - +
82o LYS* 1.3 57.1 + - - +
84o ALA* 3.3 7.0 + - - +
85o ARG* 2.9 27.9 + - - +
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Residues in contact with LYS 82 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967 T 4.0 14.3 + - - +
977 A 2.9 31.9 + - - +
2448 T 5.6 1.3 - - - -
2458 A 3.8 12.5 + - - -
78o GLY 3.0 13.0 + - - +
79o PHE* 3.2 10.3 + - - +
81o LEU* 1.3 74.0 - - - +
83o VAL* 1.3 65.7 + - - +
85o ARG* 3.2 10.7 + - + +
86o ALA* 3.1 24.6 + - + +
99o MET* 4.8 16.6 - - + -
103o LEU* 3.5 28.7 - - + +
106o TYR* 5.5 4.0 - - - -
107o TYR* 5.2 1.8 - - + -
106p TYR* 2.7 36.5 + - - -
111p PHE* 6.1 0.2 - - - -
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Residues in contact with VAL 83 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79o PHE* 3.1 34.7 + - + +
80o GLY* 3.1 8.7 + - - +
82o LYS* 1.3 77.1 - - - +
84o ALA* 1.3 62.1 + - - +
86o ALA* 3.4 6.1 + - - +
87o LEU* 3.0 20.4 + - + +
96o LEU* 4.3 4.1 - - + +
99o MET* 6.3 0.7 - - - -
100o ILE* 4.3 19.3 - - + -
103o LEU* 3.6 19.1 - - + -
122o VAL* 4.5 8.5 - - + -
125o ILE* 3.7 27.4 - - + -
126o THR* 4.3 15.9 - - + -
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Residues in contact with ALA 84 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51o LYS 5.5 1.1 - - - +
52o PHE* 3.6 20.6 - - + -
55o VAL* 4.0 20.9 - - + -
80o GLY 3.1 9.5 + - - +
81o LEU* 3.5 8.3 - - - +
82o LYS 3.2 0.2 - - - -
83o VAL* 1.3 78.2 - - - +
85o ARG* 1.3 65.0 + - - +
87o LEU* 3.1 12.1 + - + +
88o ASN* 2.9 27.0 + - - +
125o ILE* 4.5 7.6 - - + +
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Residues in contact with ARG 85 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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977 A 3.0 36.3 + - - +
987 T 3.1 34.6 + - - +
2448 T 3.8 34.1 + - - +
2458 A 3.9 21.1 + - - -
52o PHE* 3.6 10.5 - - - -
81o LEU 2.9 14.0 + - - +
82o LYS* 3.2 15.7 + - + +
84o ALA* 1.3 75.4 - - - +
86o ALA* 1.3 64.5 + - - +
88o ASN* 3.1 5.4 + - - +
89o ARG* 3.0 52.5 + - - +
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Residues in contact with ALA 86 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2448 T 5.4 3.1 - - - -
82o LYS* 3.1 11.1 + - - +
83o VAL* 3.7 9.0 - - - +
85o ARG* 1.3 76.7 - - - +
87o LEU* 1.3 58.5 + - - +
89o ARG* 4.5 2.9 - - - +
90o ILE* 2.7 51.1 + - + +
96o LEU* 3.9 9.6 - - + -
99o MET* 3.8 33.9 - - + -
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Residues in contact with LEU 87 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83o VAL* 3.0 14.4 + - + +
84o ALA* 3.1 12.3 + - + +
86o ALA* 1.3 76.6 - - - +
88o ASN* 1.3 63.5 + - - +
91o GLY* 2.7 31.2 + - - +
92o SER* 3.6 33.0 - - - +
96o LEU* 3.8 23.9 - - + +
125o ILE* 4.8 22.9 - - + +
126o THR* 6.1 2.5 - - + -
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Residues in contact with ASN 88 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987 T 5.9 1.3 - - - +
7n SER* 3.8 17.4 + - - +
48o ASN* 4.9 5.6 + - - -
51o LYS* 3.9 30.1 + - - +
52o PHE* 3.3 34.5 - - + -
84o ALA* 2.9 12.7 + - - +
85o ARG* 3.1 7.8 + - - +
87o LEU* 1.3 86.8 - - - +
89o ARG* 1.3 63.5 + - + +
90o ILE 3.7 0.5 + - - -
91o GLY* 4.8 0.7 + - - -
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Residues in contact with ARG 89 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987 T 3.8 18.6 + - - +
997 A 4.3 14.5 + - - -
2428 T 4.7 4.2 + - - -
2438 A 3.6 26.0 + - - +
2448 T 3.5 36.2 + - - +
60m SER* 4.7 2.6 + - - -
73m ARG* 4.6 3.8 + - - -
7n SER* 3.6 35.4 - - - +
8n ARG* 5.5 3.2 - - - +
85o ARG* 3.0 55.3 + - + +
86o ALA* 4.2 1.6 - - - +
88o ASN* 1.3 80.2 - - + +
90o ILE* 1.3 62.2 + - + +
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Residues in contact with ILE 90 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2438 A 5.4 1.1 - - - +
2448 T 4.4 10.5 - - - +
60m SER* 4.7 2.8 + - - -
64m THR* 2.6 36.0 + - + +
69m THR* 4.4 17.5 - - + -
70m GLY 5.5 0.7 - - - +
73m ARG* 3.7 19.8 + - - +
86o ALA* 2.7 27.2 + - + +
88o ASN 5.0 0.7 - - - -
89o ARG* 1.3 80.0 - - - +
91o GLY* 1.3 67.7 + - - +
95o ALA* 3.5 26.2 - - + +
96o LEU* 4.2 3.6 - - - +
99o MET* 3.7 31.0 - - + -
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Residues in contact with GLY 91 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64m THR* 3.8 1.7 - - - +
86o ALA 3.6 0.4 + - - -
87o LEU* 2.7 29.7 + - - -
88o ASN 4.6 0.6 + - - -
90o ILE* 1.3 89.8 - - - +
92o SER* 1.3 68.5 + - - +
96o LEU* 3.6 10.2 - - - +
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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