Contacts of the helix formed by residues 60 - 83 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F TYR* 3.7 27.1 - - + +
7F TYR* 5.2 2.2 - - - +
53F ILE* 5.1 4.9 - - - +
58F HIS 3.6 6.2 - - - +
59F THR* 1.3 98.0 - - + +
61F GLY* 1.3 63.8 + - - +
63F ASP* 4.7 0.3 + - - -
64F TYR* 3.4 30.6 + - + +
65F ASN* 3.8 16.6 - - - +
154F TYR 5.9 1.3 - - - +
158F PHE* 4.1 17.0 - - + -
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Residues in contact with GLY 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59F THR 3.5 3.4 + - - -
60F PRO* 1.3 71.4 - - - +
62F ASN* 1.3 80.6 + - - +
63F ASP 3.2 2.2 - - - -
64F TYR 3.3 0.2 + - - -
65F ASN* 2.9 21.2 + - - +
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Residues in contact with ASN 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F GLY* 1.3 74.3 - - - +
63F ASP* 1.3 79.2 + - - +
65F ASN* 2.9 27.1 + - - +
66F PHE* 3.4 5.2 + - - +
67F ASN* 5.0 7.6 + - - +
154F TYR* 5.0 4.6 + - - -
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Residues in contact with ASP 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F ILE* 3.6 17.6 - - + +
42F GLY 5.2 8.5 - - - +
43F ASN 6.3 0.2 - - - -
44F VAL* 3.6 23.4 - - - +
47F ARG* 4.9 6.5 + - - +
53F ILE* 6.2 1.8 - - - -
60F PRO 4.9 0.4 - - - -
61F GLY* 3.2 1.0 - - - -
62F ASN* 1.3 82.1 - - - +
64F TYR* 1.3 77.3 + - - +
66F PHE* 3.0 20.7 + - + +
67F ASN* 5.9 0.7 + - - -
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Residues in contact with TYR 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F TYR* 3.6 17.5 - + - -
7F TYR* 2.6 37.3 + - + +
21F PHE* 3.2 33.7 - + + -
23F ASP* 2.9 30.0 + - - -
31F THR* 3.0 34.6 + - + -
33F ILE* 3.8 5.6 - - + -
47F ARG* 3.5 12.0 + - - -
51F PHE* 4.1 4.5 - - - -
53F ILE* 4.0 12.2 - - + +
59F THR* 3.5 27.0 - - + +
60F PRO* 3.4 18.1 + - + -
61F GLY 3.3 5.9 + - - -
62F ASN 3.3 0.6 - - - -
63F ASP* 1.3 81.3 - - - +
65F ASN* 1.3 74.8 + - - +
66F PHE 3.0 0.7 + - - -
170F TYR* 4.0 1.0 + - - -
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Residues in contact with ASN 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F PRO* 3.8 17.5 - - - +
61F GLY 2.9 18.4 + - - +
62F ASN* 2.9 31.8 + - - +
64F TYR* 1.3 75.6 - - - +
66F PHE* 1.3 65.1 + - - +
67F ASN 3.5 2.2 - - - -
68F PHE* 3.3 14.2 + - + +
69F TRP* 3.0 35.6 + - + +
154F TYR* 3.5 43.7 + - + +
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Residues in contact with PHE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F TYR* 4.5 12.6 - + + -
19F GLY* 3.8 12.3 - - - -
20F VAL 3.9 12.8 - - - -
21F PHE* 3.7 27.1 - + + -
33F ILE* 3.6 20.9 - - + -
34F SER 4.1 1.6 - - - -
35F TYR* 3.8 30.5 - + + -
42F GLY* 3.7 30.5 - - - -
62F ASN 3.4 3.1 + - - +
63F ASP* 3.0 20.5 + - + +
64F TYR* 3.0 3.1 - - + -
65F ASN* 1.3 74.7 - - - +
67F ASN* 1.3 65.8 + - - +
69F TRP* 3.2 1.4 + - - +
70F TYR* 2.7 54.9 + + + +
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Residues in contact with ASN 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35F TYR* 5.4 1.6 - - - -
41F HIS* 3.6 19.0 - - - +
42F GLY* 3.0 29.0 + - - +
62F ASN* 5.0 7.2 + - - +
63F ASP* 5.9 0.6 + - - -
65F ASN 3.5 0.6 - - - -
66F PHE* 1.3 79.8 - - - +
68F PHE* 1.3 63.4 + - - +
70F TYR* 3.9 4.7 - - - +
71F SER* 3.1 27.0 + - - -
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Residues in contact with PHE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F ASN* 3.3 17.3 + - + +
66F PHE 3.1 0.4 - - - -
67F ASN* 1.3 80.0 - - - +
69F TRP* 1.3 100.7 + + - +
71F SER* 3.8 3.2 - - - -
72F LEU* 3.0 48.9 + - + +
147F LEU* 4.2 22.2 - - + +
150F ASP* 3.5 37.0 - - + -
151F VAL* 4.2 5.6 - - + -
154F TYR* 3.6 25.4 - + + -
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Residues in contact with TRP 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F TYR* 3.5 48.7 + + + -
64F TYR 3.8 1.6 - - - -
65F ASN* 3.0 31.9 + - + +
66F PHE 3.9 0.4 - - - +
68F PHE* 1.3 101.3 - + - +
70F TYR* 1.3 67.9 + - - +
72F LEU* 4.3 11.2 - - + +
73F MET* 2.7 46.3 + - + +
93F LEU* 3.7 29.4 - - + -
140F MET* 4.1 17.0 - - - -
151F VAL* 4.2 16.2 - - + -
154F TYR* 3.6 27.8 - - + +
155F LEU* 3.9 23.1 - - + -
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Residues in contact with TYR 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F TYR* 5.6 0.4 - - - -
9F VAL* 3.8 15.2 - - + +
17F TYR* 2.6 37.6 + - + +
18F ASP 4.0 3.1 - - - -
19F GLY* 3.8 26.2 - - - -
35F TYR* 3.4 57.5 - + + -
37F HIS* 4.3 1.4 - - - -
66F PHE* 2.7 36.8 + + + +
67F ASN* 3.9 4.7 - - - +
69F TRP* 1.3 72.3 - - - +
71F SER* 1.3 65.5 + - - +
73F MET* 3.7 2.2 - - - +
74F LYS* 2.8 56.5 + - + +
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Residues in contact with SER 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F ASN 3.1 16.8 + - - -
68F PHE* 3.8 3.6 - - - -
70F TYR* 1.3 89.0 - - - +
72F LEU* 1.3 58.2 + - - +
74F LYS* 3.2 9.0 + - - +
75F GLU* 3.0 26.5 + - - +
147F LEU* 6.2 0.2 - - - +
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F PHE* 3.0 47.7 + - + +
69F TRP* 4.0 8.3 - - + +
71F SER* 1.3 78.2 + - - +
73F MET* 1.3 58.7 + - - +
75F GLU* 3.5 15.1 + - - +
76F THR* 2.8 29.9 + - - -
140F MET* 3.6 31.0 - - + +
145F ASN* 3.8 26.0 - - - +
147F LEU* 4.3 21.5 - - + -
151F VAL* 3.6 13.7 - - + -
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Residues in contact with MET 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F TYR* 3.7 36.8 - - - +
9F VAL* 3.8 20.4 - - + +
69F TRP* 2.7 40.8 + - + +
70F TYR* 5.3 0.2 - - - -
72F LEU* 1.3 69.7 - - - +
74F LYS* 1.3 61.4 + - - +
76F THR* 3.5 1.7 - - - -
77F LEU* 2.8 31.5 + - - +
91F LEU* 3.4 40.3 - - + +
92F SER* 3.9 1.3 - - - -
93F LEU* 3.7 15.9 - - - +
140F MET* 3.2 31.6 - - + -
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Residues in contact with LYS 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F VAL* 4.4 9.8 - - - +
17F TYR* 3.9 34.5 - - + -
35F TYR* 6.0 0.2 + - - -
70F TYR* 2.8 47.8 + - + +
71F SER* 3.2 8.0 + - - +
73F MET* 1.3 79.0 - - - +
75F GLU* 1.3 61.6 + - - +
77F LEU* 3.2 3.1 + - - +
78F GLU* 3.0 47.5 + - - +
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Residues in contact with GLU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F SER 3.0 12.5 + - - +
72F LEU* 3.5 20.2 - - - +
74F LYS* 1.3 78.2 - - - +
76F THR* 1.3 61.9 + - - +
78F GLU* 3.2 12.8 + - - +
79F GLU* 3.1 39.1 + - + +
139F GLY* 3.9 8.4 + - - -
145F ASN* 3.2 25.7 + - - -
146F THR* 6.0 1.7 - - - +
147F LEU* 5.3 4.5 - - - +
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Residues in contact with THR 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F LEU 2.8 17.9 + - - -
73F MET* 3.2 9.4 + - - -
75F GLU* 1.3 76.6 - - - +
77F LEU* 1.3 60.4 + - - +
79F GLU* 3.5 3.3 + - - +
80F ILE* 3.0 43.0 + - + +
91F LEU* 3.6 20.2 - - + -
138F VAL* 4.2 16.4 - - + +
139F GLY* 3.4 7.4 - - - -
140F MET* 2.8 37.2 + - + +
141F LEU* 4.5 7.4 - - + -
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.6 34.5 - - + +
11F LEU* 4.5 0.9 - - + +
17F TYR* 3.8 22.0 - - + -
73F MET 2.8 20.3 + - - +
74F LYS 3.6 4.9 - - - +
76F THR* 1.3 73.1 - - - +
78F GLU* 1.3 63.3 + - - +
80F ILE* 3.3 10.0 + - + +
81F ASN* 3.0 49.1 + - - +
88F THR* 3.8 17.5 - - - +
89F THR 4.0 14.1 - - - +
90F SER* 4.1 13.7 - - - +
91F LEU* 4.1 10.7 - - + +
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Residues in contact with GLU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17F TYR* 3.3 32.1 - - + +
74F LYS* 3.0 45.7 + - - +
75F GLU* 3.5 11.4 - - - +
77F LEU* 1.3 76.1 - - - +
79F GLU* 1.3 68.2 + - - +
81F ASN* 3.2 15.2 + - - +
82F LYS* 3.4 18.4 + - - +
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Residues in contact with GLU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F GLU* 3.1 28.7 + - + +
76F THR 3.8 1.3 - - - +
78F GLU* 1.3 78.2 - - - +
80F ILE* 1.3 64.6 + - - +
82F LYS* 3.1 51.6 + - - +
83F ASN* 4.2 2.6 + - - +
138F VAL* 3.6 36.1 - - + +
139F GLY 4.4 7.4 - - - +
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Residues in contact with ILE 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F THR* 3.0 39.6 + - + +
77F LEU* 3.5 11.0 - - + +
78F GLU 3.3 0.2 - - - -
79F GLU* 1.3 76.1 - - - +
81F ASN* 1.3 65.6 + - - +
82F LYS 3.4 0.5 + - - -
83F ASN* 3.6 6.6 + - - +
86F THR* 3.3 49.6 - - + +
87F LYS 3.9 0.2 + - - -
88F THR* 4.4 7.0 - - - +
91F LEU* 4.1 16.6 - - + -
112F THR* 4.7 2.9 - - - +
117F LEU* 4.1 25.8 - - + -
136F PRO* 4.1 13.5 - - + -
138F VAL* 4.0 15.3 - - + -
141F LEU* 4.9 1.6 - - + -
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Residues in contact with ASN 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F LEU* 4.0 18.7 - - - +
17F TYR* 4.5 5.8 + - - +
77F LEU* 3.0 40.3 + - - +
78F GLU* 3.2 6.7 + - - +
79F GLU 3.1 0.6 - - - -
80F ILE* 1.3 77.9 - - - +
82F LYS* 1.3 63.6 + - - +
83F ASN 3.4 4.6 - - - -
84F ASP* 4.2 0.7 + - - -
87F LYS* 3.0 32.4 - - + +
88F THR 2.6 40.1 + - - +
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Residues in contact with LYS 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F GLU* 3.4 15.0 + - - +
79F GLU* 3.1 38.2 + - - +
81F ASN* 1.3 76.4 - - - +
83F ASN* 1.3 60.5 + - - +
84F ASP* 3.0 9.7 + - - +
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Residues in contact with ASN 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F GLU 4.2 2.3 + - - +
80F ILE 3.6 4.6 + - - +
81F ASN 4.0 0.6 - - - +
82F LYS* 1.3 74.6 - - - +
84F ASP* 1.3 55.2 + - - +
85F SER* 2.7 36.4 + - - -
86F THR* 2.8 26.8 + - - +
87F LYS 3.5 6.8 + - - -
136F PRO* 6.6 0.2 - - + -
327F NAG 1.5 65.2 + - - +
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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
------------------------------------------------------------
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