Contacts of the helix formed by residues 67 - 90 (chain X) in PDB entry 6JM9
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 SER 67 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22X TRP* 4.2 11.3 - - - -
64X ASP* 4.0 4.3 - - - -
66X LYS* 1.4 76.3 - - - +
68X PHE* 1.4 63.7 + - - +
69X GLU* 4.0 16.5 + - - +
70X SER* 3.4 29.9 + - - -
71X MET* 3.5 14.9 + - - +
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Residues in contact with PHE 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X LEU* 3.3 39.3 - - + -
6X GLU 3.7 16.4 - - - -
7X LEU* 4.7 5.3 - - + +
22X TRP* 3.5 57.3 - + + +
67X SER* 1.4 70.6 + - - +
69X GLU* 1.3 64.3 + - + +
71X MET* 3.9 2.5 - - - +
72X GLN* 2.9 66.7 + - + +
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Residues in contact with GLU 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67X SER* 4.3 10.3 + - - +
68X PHE* 1.3 84.5 - - + +
70X SER* 1.3 57.5 + - - +
72X GLN* 3.5 6.6 + - - +
73X ARG* 3.2 30.5 + - - +
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Residues in contact with SER 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62X ASP 4.9 1.1 + - - -
63X TYR* 3.5 17.1 - - - +
64X ASP* 3.0 36.5 + - - -
67X SER* 3.4 18.7 + - - -
69X GLU* 1.3 74.7 - - - +
71X MET* 1.3 64.0 + - - +
73X ARG* 3.5 34.8 + - - +
74X LEU* 4.2 2.4 + - - +
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Residues in contact with MET 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X LEU* 3.9 16.8 - - + -
22X TRP* 6.3 1.6 - - + -
24X LEU* 5.5 3.8 - - + -
34X ALA* 3.8 18.8 - - - +
37X ILE* 3.4 39.7 - - + -
38X ILE* 4.0 14.8 - - + -
63X TYR* 4.7 7.4 - - - -
64X ASP 3.1 32.8 - - - +
65X THR* 3.5 19.1 - - - +
67X SER 3.5 12.7 + - - +
68X PHE* 4.2 1.3 - - - +
70X SER* 1.3 79.9 - - - +
72X GLN* 1.4 58.8 + - - +
73X ARG 3.4 0.2 - - - -
74X LEU* 3.3 11.1 + - + +
75X CYS* 2.9 32.8 + - - -
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Residues in contact with GLN 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X GLU 3.1 21.3 + - - +
7X LEU* 3.6 24.0 - - + +
8X ARG* 4.4 11.5 + - - +
68X PHE* 2.9 58.7 + - + +
69X GLU* 3.5 6.9 + - - +
71X MET* 1.4 74.5 - - - +
73X ARG* 1.3 55.8 + - - +
75X CYS* 4.4 7.9 - - - +
76X ASP* 2.9 53.4 + - - +
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Residues in contact with ARG 73 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X TYR* 5.6 4.8 - - + +
59X VAL* 3.7 46.0 + - - +
60X LEU 4.6 0.2 - - - +
62X ASP* 3.0 39.0 + - - +
63X TYR* 3.3 19.4 - - - +
69X GLU 3.2 12.7 + - - +
70X SER* 3.5 30.7 + - - +
72X GLN* 1.3 73.6 - - - +
74X LEU* 1.3 57.6 - - - +
76X ASP* 4.1 7.2 - - - +
77X LYS* 3.3 33.1 + - - +
80X ARG* 4.2 4.5 + - - +
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Residues in contact with LEU 74 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X ILE* 5.2 0.2 - - + -
38X ILE* 4.9 12.8 - - + -
41X ILE* 4.0 25.6 - - + -
55X MET* 3.9 16.6 - - + +
59X VAL 5.1 1.3 - - - +
60X LEU* 4.2 9.9 - - + -
63X TYR* 3.5 52.5 - - + +
70X SER 4.3 7.9 - - - +
71X MET* 3.3 17.6 + - + +
73X ARG* 1.3 78.6 - - - +
75X CYS* 1.4 64.6 + - - +
77X LYS* 3.4 23.1 + - - +
78X TYR* 3.2 22.0 + - - +
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Residues in contact with CYS 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X LEU* 3.9 31.2 - - + -
8X ARG 4.1 13.2 - - - +
9X LEU* 4.1 17.0 - - + -
37X ILE* 4.3 17.5 - - - -
41X ILE* 5.0 0.4 - - - -
71X MET 2.9 23.0 + - - +
72X GLN* 4.1 13.7 - - - +
74X LEU* 1.4 74.2 - - - +
76X ASP* 1.4 58.3 - - - +
78X TYR* 3.2 9.2 - - - +
79X ASN* 3.0 35.2 + - - +
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Residues in contact with ASP 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X ARG* 5.1 4.9 + - - -
72X GLN* 2.9 49.3 + - - +
73X ARG* 4.1 4.9 + - - +
74X LEU 3.4 0.2 - - - -
75X CYS* 1.4 73.2 - - - +
77X LYS* 1.3 58.0 + - - +
79X ASN* 3.5 14.8 + - - +
80X ARG* 3.1 51.6 + - - +
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Residues in contact with LYS 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X ALA 3.6 19.1 - - - +
55X MET* 3.2 37.0 - - - +
57X ASN* 3.0 32.5 + - + +
58X TYR* 4.1 13.6 - - + +
59X VAL 3.3 21.0 + - - -
60X LEU* 4.5 1.1 - - - -
73X ARG* 3.3 24.8 + - - +
74X LEU* 3.4 20.9 + - - +
76X ASP* 1.3 74.1 - - - +
78X TYR* 1.3 57.2 + - - +
80X ARG* 3.4 18.5 + - - +
81X ALA* 3.1 24.9 + - - +
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Residues in contact with TYR 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X LEU* 3.7 25.8 - - + -
10X LYS 3.3 33.6 + - - -
12X PRO* 4.4 0.7 - - - +
40X THR* 4.5 3.4 - - + +
41X ILE* 3.7 32.8 - - + -
44X VAL* 3.6 34.2 - - + +
51X LEU* 3.9 16.4 - - + -
55X MET* 3.7 12.6 - - + -
74X LEU 3.2 12.0 + - - +
75X CYS* 3.2 11.9 - - - +
77X LYS* 1.3 73.8 - - - +
79X ASN* 1.4 61.7 + - - +
81X ALA* 3.0 4.0 + - - +
82X ILE* 2.9 53.0 + - + +
208X TRP* 3.8 14.0 - - - -
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Residues in contact with ASN 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X ARG* 2.6 42.5 + - - +
9X LEU* 3.8 1.9 - - - -
10X LYS* 4.0 29.4 + - - +
75X CYS* 3.0 25.9 + - - +
76X ASP* 3.7 17.0 + - - +
78X TYR* 1.4 79.6 - - - +
80X ARG* 1.4 65.0 + - + +
82X ILE* 3.6 6.2 + - - +
83X ASP* 3.3 28.7 + - - +
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Residues in contact with ARG 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X TYR* 3.9 33.8 + - - -
73X ARG* 4.2 4.8 + - - +
76X ASP* 3.1 31.0 + - - +
77X LYS* 3.4 30.2 - - - +
79X ASN* 1.4 77.5 - - + +
81X ALA* 1.3 61.9 + - - +
83X ASP* 3.3 8.5 + - - +
84X SER* 3.1 21.5 + - - -
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Residues in contact with ALA 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X LEU* 4.2 20.2 - - + +
54X ALA* 3.8 26.0 - - + -
55X MET* 4.6 2.2 - - - -
77X LYS 3.1 15.8 + - - +
78X TYR* 3.2 12.6 - - - +
80X ARG* 1.3 75.7 - - - +
82X ILE* 1.3 57.1 + - - +
84X SER* 3.2 9.9 + - - -
85X ILE* 3.0 33.0 + - - +
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Residues in contact with ILE 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X LYS* 3.6 24.2 - - + +
11X SER 3.4 21.1 - - - +
12X PRO* 4.1 15.3 - - + -
51X LEU* 3.6 23.8 - - + -
78X TYR* 2.9 61.1 + - + +
79X ASN 3.8 5.4 - - - +
81X ALA* 1.3 70.8 - - - +
83X ASP* 1.3 60.2 - - - +
85X ILE* 3.3 6.8 + - + +
86X HIS* 3.0 41.9 + - + +
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Residues in contact with ASP 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X LYS* 4.2 19.4 - - - +
79X ASN* 3.3 16.3 + - - +
80X ARG* 3.3 10.4 + - - +
82X ILE* 1.3 72.6 - - - +
84X SER* 1.3 69.4 + - - +
86X HIS* 3.3 21.5 + - - +
87X GLN* 3.2 25.1 + - + +
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Residues in contact with SER 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X ALA* 5.3 4.0 - - - +
80X ARG 3.1 12.5 + - - -
81X ALA* 3.2 14.2 + - - -
82X ILE 3.2 0.2 - - - -
83X ASP* 1.3 78.0 - - - +
85X ILE* 1.4 67.6 + - - +
87X GLN* 3.0 23.6 + - - +
88X LEU* 3.1 14.0 + - - +
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Residues in contact with ILE 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X PRO* 4.4 7.0 - - + +
48X ILE* 4.1 19.5 - - + -
50X ASP* 3.8 28.0 - - + +
51X LEU* 4.0 24.2 - - + +
54X ALA* 5.4 1.3 - - + -
81X ALA* 3.0 22.9 + - + +
82X ILE* 3.3 8.3 + - - +
84X SER* 1.4 82.3 + - - +
86X HIS* 1.4 60.1 + - - +
88X LEU* 3.4 12.1 + - + +
89X TRP* 2.9 70.6 + - + +
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Residues in contact with HIS 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X LYS* 5.3 3.8 - - - +
11X SER 3.0 24.6 + - - -
12X PRO 3.2 21.7 + - - -
13X VAL 4.5 2.4 + - - -
14X GLY* 3.7 17.5 + - - -
82X ILE* 3.0 35.0 + - + +
83X ASP* 3.3 23.5 + - - +
85X ILE* 1.4 56.9 - - - +
87X GLN* 1.4 70.0 + - - +
89X TRP* 3.4 12.2 + - - +
90X LYS* 3.3 34.4 + - - +
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Residues in contact with GLN 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X ASP* 3.2 13.9 + - + +
84X SER* 3.0 11.0 + - - +
86X HIS* 1.4 91.3 + - - +
88X LEU* 1.3 62.1 + - - +
89X TRP 3.4 0.5 + - - -
90X LYS* 3.4 29.9 + - - +
91X GLY* 3.9 2.1 + - - -
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Residues in contact with LEU 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X ASP* 3.8 28.0 - - + +
84X SER 3.1 11.7 + - - +
85X ILE* 3.5 20.2 - - + +
87X GLN* 1.3 76.3 - - - +
89X TRP* 1.3 66.3 + - + +
91X GLY* 3.0 20.5 + - - -
92X THR* 5.9 1.8 - - - +
93X THR* 3.5 29.3 - - - +
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Residues in contact with TRP 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X PRO* 3.1 35.9 - - + -
13X VAL* 4.0 10.1 - - + -
48X ILE* 3.7 41.6 - - + +
50X ASP* 5.6 1.0 + - - -
85X ILE* 2.9 40.6 + - + +
86X HIS* 3.4 10.1 + - - +
87X GLN 3.2 1.0 - - - -
88X LEU* 1.3 81.2 - - + +
90X LYS* 1.3 58.2 + - - +
91X GLY 3.2 5.4 - - - +
93X THR* 2.8 43.3 - - + +
94X GLN* 3.8 17.5 - - - +
95X PRO* 3.9 25.5 - - + +
96X MET* 3.7 35.9 - - + -
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Residues in contact with LYS 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X HIS* 3.3 32.7 + - - +
87X GLN* 3.5 20.3 - - - +
89X TRP* 1.3 74.4 - - - +
91X GLY* 1.3 62.1 + - - +
94X GLN* 5.8 0.2 - - - -
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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