Contacts of the helix formed by residues 60 - 83 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L TYR* 3.7 26.9 - - + +
7L TYR* 5.3 2.7 - - - +
53L ILE* 5.1 4.9 - - - +
58L HIS 3.5 7.5 - - - +
59L THR* 1.3 100.1 - - + +
61L GLY* 1.3 62.9 + - - +
63L ASP* 4.7 0.5 + - - -
64L TYR* 3.5 27.0 + - + +
65L ASN* 3.7 20.0 - - - +
154L TYR 6.0 0.9 - - - +
158L PHE* 4.1 16.8 - - + -
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Residues in contact with GLY 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59L THR 3.5 3.1 + - - -
60L PRO* 1.3 70.8 - - - +
62L ASN* 1.3 81.6 + - - +
63L ASP 3.2 2.7 - - - -
64L TYR 3.2 0.2 + - - -
65L ASN* 2.9 21.5 + - - +
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Residues in contact with ASN 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61L GLY* 1.3 74.1 - - - +
63L ASP* 1.3 77.9 + - - +
65L ASN* 2.9 27.5 + - - +
66L PHE* 3.4 5.5 + - - +
67L ASN* 5.0 6.8 + - - +
154L TYR* 4.9 4.8 + - - -
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Residues in contact with ASP 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L ILE* 3.6 17.3 - - + +
42L GLY* 5.1 8.9 - - - +
43L ASN 6.3 0.2 - - - -
44L VAL* 3.6 23.5 - - - +
47L ARG* 4.9 6.7 + - - +
53L ILE* 6.2 1.8 - - - -
60L PRO 4.9 0.4 - - - -
61L GLY* 3.2 1.2 - - - -
62L ASN* 1.3 80.4 - - - +
64L TYR* 1.3 77.7 + - - +
66L PHE* 3.0 20.5 + - + +
67L ASN* 5.9 0.7 + - - -
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Residues in contact with TYR 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5L TYR* 3.7 15.9 - + - -
7L TYR* 2.6 37.0 + - + +
21L PHE* 3.2 33.0 - + + -
23L ASP* 2.9 30.5 + - - -
31L THR* 3.0 35.9 + - + -
33L ILE* 3.8 6.1 - - + -
47L ARG* 3.5 11.8 + - - -
51L PHE* 4.1 5.0 - - - -
53L ILE* 4.0 12.7 - - + +
59L THR* 3.4 27.0 - - + +
60L PRO* 3.5 17.9 + - + -
61L GLY 3.2 6.1 + - - -
63L ASP* 1.3 81.9 - - - +
65L ASN* 1.3 73.6 + - - +
66L PHE 3.0 1.0 + - - -
170L TYR* 4.0 1.4 + - - -
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Residues in contact with ASN 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L PRO* 3.7 18.2 - - - +
61L GLY 2.9 22.2 + - - +
62L ASN* 2.9 28.1 + - - +
64L TYR* 1.3 76.1 - - - +
66L PHE* 1.3 64.3 + - - +
67L ASN 3.5 2.0 - - - -
68L PHE* 3.3 13.8 + - + +
69L TRP* 3.0 35.3 + - + +
154L TYR* 3.6 44.7 + - + +
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Residues in contact with PHE 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L TYR* 4.5 12.3 - + + -
19L GLY* 3.8 24.5 - - - -
20L VAL 3.9 12.6 - - - -
21L PHE* 3.7 28.0 - + + -
33L ILE* 3.6 21.3 - - + -
34L SER 4.1 1.6 - - - -
35L TYR* 3.8 17.9 - + + -
42L GLY* 3.7 29.8 - - - -
62L ASN 3.4 3.9 + - - +
63L ASP* 3.0 21.7 + - + +
64L TYR 3.0 3.3 - - - -
65L ASN* 1.3 73.6 - - - +
67L ASN* 1.3 72.7 + - - +
69L TRP* 3.2 1.2 + - - +
70L TYR* 2.8 46.1 + + + +
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Residues in contact with ASN 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L TYR* 5.4 1.9 - - - -
40L ARG 5.7 0.2 - - - -
41L HIS* 3.6 19.1 - - - +
42L GLY* 3.0 28.1 + - - -
62L ASN* 5.0 7.4 + - - +
63L ASP* 5.9 0.6 + - - -
65L ASN 3.5 0.4 - - - -
66L PHE* 1.3 80.7 - - - +
68L PHE* 1.3 64.6 + - - +
70L TYR* 3.9 4.2 - - - +
71L SER* 3.1 26.7 + - - -
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Residues in contact with PHE 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65L ASN* 3.3 16.4 + - + +
66L PHE 3.1 0.2 - - - -
67L ASN* 1.3 80.4 - - - +
69L TRP* 1.3 98.0 + + - +
71L SER* 3.8 3.2 - - - -
72L LEU* 3.0 47.2 + - + +
147L LEU* 4.2 23.3 - - + +
150L ASP* 3.5 36.8 - - + -
151L VAL* 4.2 5.2 - - + -
154L TYR* 3.7 28.5 - + + -
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Residues in contact with TRP 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7L TYR* 3.5 45.8 + + + -
64L TYR 3.8 1.3 - - - -
65L ASN* 3.0 32.1 + - + +
66L PHE 3.9 0.4 - - - +
68L PHE* 1.3 100.7 - + - +
70L TYR* 1.3 57.9 + - - +
72L LEU* 4.3 11.0 - - + +
73L MET* 2.7 57.6 + - + +
93L LEU* 3.7 28.3 - - + -
140L MET* 4.2 17.9 - - - -
151L VAL* 4.2 15.5 - - + -
154L TYR* 3.7 26.9 - - + +
155L LEU* 3.9 24.5 - - + -
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Residues in contact with TYR 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L TYR* 5.6 0.4 - - - -
9L VAL* 3.8 16.7 - - + +
17L TYR* 2.7 38.2 + - + +
18L ASP 4.0 2.7 - - - -
19L GLY* 3.8 26.9 - - - -
35L TYR* 3.5 57.2 - + + -
37L HIS* 4.3 1.4 - - - -
66L PHE* 2.8 37.0 + + + +
67L ASN* 3.9 4.7 - - - +
69L TRP* 1.3 72.1 - - - +
71L SER* 1.3 65.2 + - - +
73L MET* 3.7 2.3 - - - +
74L LYS* 2.8 56.0 + - + +
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Residues in contact with SER 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67L ASN 3.1 16.6 + - - -
68L PHE* 3.8 3.1 - - - -
70L TYR* 1.3 88.7 - - - +
72L LEU* 1.3 58.4 + - - +
74L LYS* 3.2 8.6 + - - +
75L GLU* 3.0 26.7 + - - +
147L LEU* 6.2 0.2 - - - +
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Residues in contact with LEU 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L PHE* 3.0 40.0 + - + +
69L TRP* 4.0 8.7 - - + +
71L SER* 1.3 77.1 - - - +
73L MET* 1.3 57.2 + - - +
75L GLU* 3.5 15.4 + - - +
76L THR* 2.9 30.0 + - - -
140L MET* 3.6 30.7 - - + +
145L ASN* 3.8 26.5 - - - +
147L LEU* 4.3 20.9 - - + -
151L VAL* 3.6 22.7 - - + -
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Residues in contact with MET 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L TYR* 3.7 38.1 - - - +
9L VAL* 3.8 20.8 - - + +
69L TRP* 2.7 42.1 + - + +
70L TYR* 5.0 0.4 - - - -
72L LEU* 1.3 71.4 - - - +
74L LYS* 1.3 59.8 + - - +
76L THR* 3.2 1.6 + - - -
77L LEU* 2.8 31.4 + - - +
91L LEU* 3.4 39.8 - - + +
92L SER 3.9 1.3 - - - -
93L LEU* 3.7 15.5 - - - +
140L MET* 3.2 30.5 - - + -
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Residues in contact with LYS 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9L VAL* 4.3 9.6 - - - +
17L TYR* 3.9 34.9 - - + -
70L TYR* 2.8 47.4 + - + +
71L SER* 3.4 7.6 - - - +
73L MET* 1.3 78.0 - - - +
75L GLU* 1.3 62.3 + - - +
77L LEU* 3.2 3.8 + - - +
78L GLU* 3.1 47.2 + - - +
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Residues in contact with GLU 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L SER 3.0 13.2 + - - +
72L LEU* 3.5 20.4 - - - +
74L LYS* 1.3 77.7 - - - +
76L THR* 1.3 62.5 + - - +
78L GLU* 3.3 12.4 + - - +
79L GLU* 3.1 39.6 + - + +
139L GLY* 3.9 8.6 + - - -
145L ASN* 3.3 25.2 + - - +
146L THR* 6.0 2.1 - - - +
147L LEU* 5.3 4.7 - - - +
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Residues in contact with THR 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L LEU 2.9 15.6 + - - -
73L MET* 3.6 6.1 - - - -
75L GLU* 1.3 78.0 - - - +
77L LEU* 1.3 62.5 + - - +
79L GLU* 3.4 3.6 + - - +
80L ILE* 3.0 41.9 + - + +
91L LEU* 3.6 21.1 - - + -
138L VAL* 4.2 16.4 - - + +
139L GLY* 3.3 7.2 - - - -
140L MET* 2.8 38.4 + - + +
141L LEU* 4.5 7.0 - - + -
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Residues in contact with LEU 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L VAL* 3.6 35.2 - - + +
11L LEU* 4.5 1.3 - - + +
17L TYR* 3.8 23.1 - - + -
73L MET 2.8 20.1 + - - +
74L LYS 3.6 4.7 - - - +
76L THR* 1.3 73.5 - - - +
78L GLU* 1.3 63.3 + - - +
80L ILE* 3.3 10.1 + - + +
81L ASN* 3.0 48.1 + - - +
88L THR* 3.9 16.4 - - - +
89L THR 4.1 13.5 - - - +
90L SER* 4.1 14.4 - - - +
91L LEU* 4.1 11.2 - - + +
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Residues in contact with GLU 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17L TYR* 3.3 32.1 - - + +
74L LYS* 3.1 46.5 + - - +
75L GLU* 3.3 10.6 + - - +
77L LEU* 1.3 76.3 - - - +
79L GLU* 1.3 67.5 + - + +
81L ASN* 3.2 15.3 + - - +
82L LYS* 3.4 18.2 + - - +
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Residues in contact with GLU 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L GLU* 3.1 29.0 + - + +
76L THR 3.8 1.8 - - - +
78L GLU* 1.3 77.5 - - - +
80L ILE* 1.3 64.5 + - - +
82L LYS* 3.1 52.0 + - - +
83L ASN* 4.2 2.3 + - - +
138L VAL* 3.6 35.9 - - + +
139L GLY 4.4 7.2 - - - +
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Residues in contact with ILE 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L THR* 3.0 37.8 + - + +
77L LEU* 3.3 11.0 + - + +
79L GLU* 1.3 76.0 - - - +
81L ASN* 1.3 65.2 + - - +
82L LYS 3.4 1.0 + - - -
83L ASN* 3.6 7.1 + - - +
86L THR* 3.3 48.6 - - + +
87L LYS 3.9 0.2 + - - -
88L THR* 4.4 7.0 - - - +
91L LEU* 4.1 16.4 - - + -
112L THR* 4.7 3.1 - - - +
117L LEU* 4.1 25.8 - - + -
136L PRO* 4.0 13.0 - - + -
138L VAL* 4.0 15.5 - - + -
141L LEU* 4.9 0.9 - - + -
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Residues in contact with ASN 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L LEU* 4.0 17.8 - - - +
17L TYR* 4.5 6.4 + - - +
77L LEU* 3.0 40.8 + - - +
78L GLU* 3.7 6.7 - - - +
79L GLU 3.1 0.8 - - - -
80L ILE* 1.3 77.3 - - - +
82L LYS* 1.3 63.4 + - - +
83L ASN 3.4 4.6 - - - +
84L ASP* 4.2 0.5 + - - -
87L LYS* 3.0 32.2 - - + +
88L THR* 2.6 40.7 + - - +
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Residues in contact with LYS 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78L GLU* 3.4 14.3 + - - +
79L GLU* 3.1 37.6 + - - +
81L ASN* 1.3 75.9 - - - +
83L ASN* 1.3 61.7 + - - +
84L ASP* 3.0 10.6 + - - +
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Residues in contact with ASN 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L GLU 4.2 2.0 + - - +
80L ILE 3.6 5.4 + - - +
81L ASN 4.1 0.4 - - - +
82L LYS* 1.3 74.0 - - - +
84L ASP* 1.3 55.2 + - - +
85L SER* 2.7 37.8 + - - -
86L THR* 2.8 26.5 + - - +
87L LYS 3.5 6.4 + - - -
136L PRO* 6.6 0.2 - - + -
327L NAG 1.5 68.3 + - - +
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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
------------------------------------------------------------
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