Contacts of the helix formed by residues 60 - 83 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K TYR* 3.7 27.4 - - + +
7K TYR* 5.3 2.9 - - - +
53K ILE* 5.1 4.7 - - - +
58K HIS 3.5 7.5 - - - +
59K THR* 1.3 99.0 - - + +
61K GLY* 1.3 62.5 + - - +
63K ASP 4.7 0.3 + - - -
64K TYR* 3.5 28.0 + - + -
65K ASN* 3.8 20.9 - - - +
154K TYR 6.0 1.3 - - - +
158K PHE* 4.1 16.6 - - + -
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Residues in contact with GLY 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59K THR 3.5 2.5 + - - -
60K PRO* 1.3 71.7 - - - +
62K ASN* 1.3 81.2 + - - +
63K ASP 3.3 1.8 - - - -
65K ASN* 2.9 21.8 + - - +
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Residues in contact with ASN 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61K GLY* 1.3 74.1 - - - +
63K ASP* 1.3 79.7 + - - +
65K ASN* 2.9 27.0 + - - +
66K PHE* 3.5 5.4 + - - +
67K ASN* 5.0 8.0 + - - +
154K TYR* 5.0 4.2 + - - -
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Residues in contact with ASP 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K ILE* 3.6 17.1 - - + +
42K GLY 5.1 8.6 - - - +
44K VAL* 3.6 24.4 - - - +
47K ARG* 4.9 6.1 + - - -
60K PRO 4.7 0.8 + - - -
61K GLY 3.3 0.8 - - - -
62K ASN* 1.3 81.9 - - - +
64K TYR* 1.3 76.9 + - - +
66K PHE* 2.9 20.4 + - + +
67K ASN* 5.9 1.0 + - - -
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Residues in contact with TYR 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K TYR* 3.6 17.7 - + - -
7K TYR* 2.7 35.9 + - + +
21K PHE* 3.2 33.4 - + + -
23K ASP* 2.8 30.1 + - - -
31K THR* 3.0 34.2 + - + -
33K ILE* 3.8 6.1 - - + -
44K VAL* 6.3 0.2 - - + -
47K ARG* 3.5 11.0 + - - -
51K PHE* 4.1 4.5 - - - -
53K ILE* 4.1 13.8 - - + +
59K THR* 3.4 27.3 - - + +
60K PRO* 3.5 19.0 + - + -
61K GLY 3.3 5.9 + - - -
62K ASN 3.2 0.6 - - - -
63K ASP* 1.3 80.9 - - - +
65K ASN* 1.3 74.1 + - - +
66K PHE 3.0 0.9 + - - -
170K TYR* 4.0 1.0 + - - -
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Residues in contact with ASN 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60K PRO* 3.8 17.8 - - - +
61K GLY 2.9 21.9 + - - +
62K ASN* 2.9 27.2 + - - +
64K TYR* 1.3 75.8 - - - +
66K PHE* 1.3 65.5 + - - +
67K ASN 3.4 2.2 - - - -
68K PHE* 3.2 15.0 + - + +
69K TRP* 3.0 34.5 + - + +
154K TYR* 3.5 44.1 + - + +
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Residues in contact with PHE 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K TYR* 4.5 13.5 - + + -
19K GLY* 3.9 12.6 - - - -
20K VAL 3.9 13.5 - - - -
21K PHE* 3.7 26.9 - + + -
33K ILE* 3.6 21.3 - - + -
34K SER 4.1 1.6 - - - -
35K TYR* 3.8 29.2 - + + -
42K GLY* 3.7 30.5 - - - -
62K ASN 3.5 2.9 + - - +
63K ASP* 2.9 19.8 + - + +
64K TYR* 3.0 3.1 + - + -
65K ASN* 1.3 74.6 - - - +
67K ASN* 1.3 68.7 + - - +
69K TRP* 3.2 1.2 + - - +
70K TYR* 2.7 52.7 + + + +
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Residues in contact with ASN 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K TYR* 5.4 2.0 - - - -
40K ARG 5.7 0.2 - - - -
41K HIS* 3.6 18.5 + - - +
42K GLY 3.0 28.9 + - - -
62K ASN* 5.0 8.2 + - - +
63K ASP* 5.9 1.0 + - - -
65K ASN 3.4 0.6 - - - -
66K PHE* 1.3 80.7 - - - +
68K PHE* 1.3 63.8 + - - +
70K TYR* 3.9 4.4 - - - +
71K SER* 3.1 26.3 + - - -
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Residues in contact with PHE 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65K ASN* 3.2 16.0 + - + +
66K PHE 3.1 0.4 - - - -
67K ASN* 1.3 80.3 - - - +
69K TRP* 1.3 102.3 + + - +
71K SER* 3.7 2.9 - - - -
72K LEU* 3.0 42.6 + - + +
147K LEU* 4.2 22.0 - - + -
150K ASP* 3.5 37.0 - - + -
151K VAL* 4.2 6.1 - - + -
154K TYR* 3.6 29.2 - + + -
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Residues in contact with TRP 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K TYR* 3.5 47.3 + + + -
64K TYR 3.8 1.6 - - - -
65K ASN* 3.0 31.8 + - + +
66K PHE 3.9 0.7 - - - +
68K PHE* 1.3 100.5 - + - +
70K TYR* 1.3 58.7 + - - +
72K LEU* 4.3 11.7 - - + +
73K MET* 2.7 54.9 + - + +
93K LEU* 3.7 26.9 - - + -
140K MET* 4.2 17.0 - - - -
151K VAL* 4.2 15.5 - - + -
154K TYR* 3.7 26.3 - - + +
155K LEU* 3.9 25.6 - - + -
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Residues in contact with TYR 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K TYR* 5.6 0.2 - - - -
9K VAL* 3.9 16.9 - - + +
17K TYR* 2.7 37.1 + - + +
18K ASP 3.9 3.4 - - - -
19K GLY* 3.7 26.0 - - - -
35K TYR* 3.4 55.7 - + + -
37K HIS* 4.3 1.4 - - - -
66K PHE* 2.7 37.7 + + + +
67K ASN* 3.9 5.2 - - - +
69K TRP* 1.3 71.2 - - - +
71K SER* 1.3 64.2 + - - +
73K MET* 3.3 2.1 + - - +
74K LYS* 2.8 56.8 + - + +
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Residues in contact with SER 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67K ASN 3.1 16.3 + - - -
68K PHE* 3.7 3.8 - - - -
70K TYR* 1.3 89.4 - - - +
72K LEU* 1.3 57.0 + - - +
74K LYS* 3.3 8.1 + - - +
75K GLU* 3.0 27.0 + - - +
147K LEU* 6.1 0.7 - - - +
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Residues in contact with LEU 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K PHE* 3.0 40.3 + - + +
69K TRP* 4.0 7.4 - - + +
71K SER* 1.3 73.7 - - - +
73K MET* 1.3 61.7 + - - +
75K GLU* 3.5 15.6 + - - +
76K THR* 2.9 29.5 + - - -
140K MET* 3.5 31.0 - - + +
145K ASN* 3.9 25.4 - - - +
147K LEU* 4.3 21.7 - - + +
151K VAL* 3.6 22.0 - - + -
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Residues in contact with MET 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K TYR* 3.7 36.3 - - - +
9K VAL* 3.7 20.6 - - + +
69K TRP* 2.7 41.6 + - + +
70K TYR* 5.3 0.2 - - - -
72K LEU* 1.3 70.8 - - - +
74K LYS* 1.3 61.0 + - - +
76K THR* 3.2 1.8 + - - -
77K LEU* 2.8 31.4 + - - +
91K LEU* 3.4 37.6 - - + +
92K SER* 3.8 2.2 - - - +
93K LEU* 3.7 18.4 - - - +
140K MET* 3.2 30.1 - - + -
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Residues in contact with LYS 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K VAL* 4.4 9.6 - - - +
17K TYR* 3.9 33.1 - - + +
35K TYR* 5.9 0.8 + - - -
70K TYR* 2.8 47.5 + - + +
71K SER* 3.4 8.5 - - - +
73K MET* 1.3 77.2 - - - +
75K GLU* 1.3 62.4 + - - +
77K LEU* 3.3 3.4 + - - +
78K GLU* 3.1 47.5 + - - +
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Residues in contact with GLU 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K SER 3.0 13.4 + - - +
72K LEU* 3.5 20.0 - - - +
74K LYS* 1.3 76.6 - - - +
76K THR* 1.3 62.7 + - - +
78K GLU* 3.2 13.4 + - - +
79K GLU* 3.1 39.5 + - + +
139K GLY* 3.9 8.6 + - - -
145K ASN* 3.3 25.7 + - - -
146K THR* 6.0 1.9 - - - +
147K LEU* 5.3 4.3 - - - +
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Residues in contact with THR 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K LEU 2.9 14.0 + - - -
73K MET* 3.2 8.5 + - - -
75K GLU* 1.3 76.2 - - - +
77K LEU* 1.3 58.7 + - - +
79K GLU* 3.4 3.1 + - - +
80K ILE* 3.0 40.4 + - + +
91K LEU* 3.6 20.9 - - + -
110K VAL* 6.1 0.2 - - + -
138K VAL* 4.2 15.5 - - + +
139K GLY* 3.4 7.3 - - - -
140K MET* 2.8 38.0 + - + +
141K LEU* 4.5 7.4 - - + -
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Residues in contact with LEU 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K VAL* 3.6 35.0 - - + +
11K LEU* 4.5 0.9 - - + +
17K TYR* 3.8 22.2 - - + -
73K MET 2.8 19.7 + - - +
74K LYS 3.6 4.5 - - - +
76K THR* 1.3 74.5 - - - +
78K GLU* 1.3 63.0 + - - +
80K ILE* 3.3 9.5 + - + +
81K ASN* 3.0 49.4 + - - +
88K THR* 3.8 16.2 - - - +
89K THR 4.1 13.9 - - - +
90K SER* 4.1 14.6 - - - +
91K LEU* 4.1 10.9 - - + +
112K THR* 6.1 0.2 - - - +
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Residues in contact with GLU 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17K TYR* 3.3 31.2 - - + +
74K LYS* 3.1 43.6 + - - +
75K GLU* 3.5 10.8 - - + +
77K LEU* 1.3 75.9 - - - +
79K GLU* 1.3 68.3 + - - +
81K ASN* 3.2 14.7 + - - +
82K LYS* 3.4 18.3 + - - +
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Residues in contact with GLU 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75K GLU* 3.1 28.8 + - + +
76K THR 3.8 1.3 - - - +
77K LEU 3.4 0.2 - - - -
78K GLU* 1.3 77.9 - - - +
80K ILE* 1.3 64.1 + - - +
82K LYS* 3.0 52.2 + - - +
83K ASN* 4.2 2.3 + - - +
138K VAL* 3.6 35.6 - - + +
139K GLY 4.4 7.2 - - - +
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Residues in contact with ILE 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76K THR* 3.0 38.7 + - + +
77K LEU* 3.5 10.8 - - + +
79K GLU* 1.3 75.1 - - - +
81K ASN* 1.3 66.9 + - - +
82K LYS 3.4 0.7 + - - -
83K ASN* 3.6 6.6 + - - +
86K THR* 3.3 49.4 - - + +
88K THR* 4.4 7.0 - - - +
91K LEU* 4.1 17.5 - - + -
112K THR* 4.7 3.4 - - - +
117K LEU* 4.0 26.5 - - + -
136K PRO* 4.1 12.6 - - + -
138K VAL* 4.0 14.8 - - + -
141K LEU* 4.9 1.1 - - + -
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Residues in contact with ASN 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K LEU* 4.0 18.7 - - - +
17K TYR* 4.6 5.8 + - - +
77K LEU* 3.0 39.1 + - - +
78K GLU* 3.2 6.3 + - - +
79K GLU 3.1 0.6 - - - -
80K ILE* 1.3 77.0 - - - +
82K LYS* 1.3 63.2 + - - +
83K ASN 3.4 4.6 + - - +
84K ASP* 4.2 0.7 + - - +
87K LYS* 3.0 31.7 - - + +
88K THR* 2.6 40.1 + - - +
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Residues in contact with LYS 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K GLU* 3.4 13.9 + - - +
79K GLU* 3.0 38.2 + - - +
81K ASN* 1.3 76.5 - - - +
83K ASN* 1.3 60.4 + - - +
84K ASP* 3.0 9.7 + - - +
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Residues in contact with ASN 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79K GLU 4.2 1.9 + - - +
80K ILE 3.6 5.1 + - - +
81K ASN 3.4 0.9 - - - -
82K LYS* 1.3 74.4 - - - +
84K ASP* 1.3 54.5 + - - +
85K SER* 2.7 34.8 + - - -
86K THR* 2.8 26.8 + - - +
87K LYS 3.5 6.4 + - - -
327K NAG 1.5 66.8 + - - +
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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) + - + + + + + -
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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