Contacts of the helix formed by residues 71 - 93 (chain H) in PDB entry 1R5I
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 GLU 71 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LYS* 5.2 12.8 + - + +
69H LEU* 2.9 30.5 + - + +
70H LEU* 1.3 93.0 - - + +
72H TYR* 1.3 66.1 + - - +
73H LYS 3.1 2.9 - - - -
74H GLU* 3.0 21.3 + - + +
75H ILE* 3.3 13.9 + - + +
121H PHE* 3.6 59.2 - - + +
125H ASN* 4.2 7.1 + - - +
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Residues in contact with TYR 72 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ILE* 5.0 10.0 - - + +
63H VAL* 3.6 39.4 - - + +
66H TYR* 3.3 22.2 - - + +
67H ASN* 3.7 30.4 - - + +
69H LEU* 2.7 34.7 + - + +
70H LEU* 3.2 3.6 - - - -
71H GLU* 1.3 71.2 - - - +
73H LYS* 1.3 98.0 + - + +
75H ILE* 3.5 9.4 + - - +
76H PHE* 3.0 29.7 + + + +
118H LEU* 5.6 1.1 - - - -
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Residues in contact with LYS 73 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLN* 3.7 36.6 - - + +
70H LEU 3.9 7.1 + - - +
71H GLU 3.0 1.0 + - - -
72H TYR* 1.3 117.3 + - + +
74H GLU* 1.3 60.2 + - - +
76H PHE* 3.7 4.9 - - + +
77H ASN* 2.8 38.4 + - - +
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Residues in contact with GLU 74 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H GLN 4.2 4.5 - - - +
13H LYS* 3.4 27.5 - - + +
14H HIS* 2.4 36.2 + - - +
15H PHE 2.9 9.0 + - - -
16H VAL* 3.5 15.8 + - - +
17H GLN* 4.1 23.2 - - + +
71H GLU* 3.0 19.5 + - + +
73H LYS* 1.3 77.8 - - - +
75H ILE* 1.3 60.3 + - + +
77H ASN* 3.9 1.0 - - - +
78H MET* 2.8 52.1 + - - +
121H PHE* 4.9 7.9 - - + -
214H PO4 5.7 0.2 + - - -
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Residues in contact with ILE 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H ILE* 4.0 21.3 - - + -
69H LEU* 5.7 0.2 - - + -
71H GLU* 3.3 12.9 + - + +
72H TYR* 3.8 6.7 - - - +
74H GLU* 1.3 74.6 - - - +
76H PHE* 1.3 66.8 + - - +
78H MET* 3.8 5.4 - - - +
79H MET* 3.1 24.6 + - + +
114H ALA* 4.0 29.2 - - + +
117H ASP* 4.4 7.0 - - + -
118H LEU* 3.1 49.8 - - + +
121H PHE* 3.7 26.9 - - + -
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Residues in contact with PHE 76 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H VAL* 4.2 10.8 - - + -
23H VAL* 4.7 7.9 - - + -
59H ALA* 3.4 33.9 - - + -
60H PHE* 3.7 29.8 - + - -
62H ILE* 5.6 2.2 - - + +
63H VAL* 3.5 33.4 - - + -
72H TYR* 3.0 23.4 + + + +
73H LYS* 3.7 7.4 - - + +
75H ILE* 1.3 79.8 - - - +
77H ASN* 1.3 77.8 + - - +
79H MET* 3.1 22.5 + - - +
80H PHE* 3.4 30.6 + + - -
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Residues in contact with ASN 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H VAL* 2.7 35.5 + - + +
17H GLN* 3.4 21.0 + - - +
19H LEU* 3.4 19.5 + - - +
22H VAL* 3.5 31.7 - - + +
73H LYS* 2.8 22.2 + - - +
76H PHE* 1.3 83.5 - - - +
78H MET* 1.3 62.8 + - - +
80H PHE* 3.1 4.0 + - - +
81H LEU* 2.9 27.0 + - - +
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Residues in contact with MET 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E ALA* 3.9 19.1 - - + +
64E ALA* 4.7 3.8 - - + -
65E VAL* 4.0 10.5 - - + -
14H HIS* 3.4 33.7 - - + +
16H VAL* 3.8 16.4 - - + -
74H GLU* 2.8 41.8 + - - +
75H ILE* 3.8 6.1 - - - +
77H ASN* 1.3 70.9 - - - +
79H MET* 1.3 64.9 + - - +
81H LEU* 3.1 7.8 + - - +
82H LYS* 2.9 59.7 + - + +
214H PO4 4.7 5.8 - - - +
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Residues in contact with MET 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H PHE* 3.4 28.8 - - + +
58H HIS* 4.4 10.5 - - - -
59H ALA* 3.2 44.6 - - + +
62H ILE* 3.6 21.1 - - + -
75H ILE* 3.1 14.0 + - + +
76H PHE* 3.1 26.2 + - - +
78H MET* 1.3 78.5 - - - +
80H PHE* 1.3 60.7 + - + +
82H LYS* 3.2 3.3 + - - +
83H LEU 3.0 21.7 + - - -
110H ILE* 4.1 17.7 - - + +
111H MET* 5.0 3.1 - - - -
114H ALA* 3.8 24.5 - - + -
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Residues in contact with PHE 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H VAL* 3.6 30.2 - - + +
23H VAL* 3.5 29.8 - - + -
24H PHE* 4.1 14.2 - + - -
55H PHE* 4.6 7.2 - + - -
56H TYR* 3.5 47.8 - + - -
59H ALA* 3.7 20.2 - - + -
60H PHE* 4.8 1.8 - + - -
76H PHE* 3.4 45.4 + + - -
77H ASN 3.1 2.8 + - - +
79H MET* 1.3 79.9 - - + +
81H LEU* 1.3 67.4 + - - +
83H LEU* 3.5 11.5 - - + +
84H SER* 2.9 23.4 + - - -
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Residues in contact with LEU 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E ALA* 3.5 26.6 - - + +
65E VAL* 4.4 14.6 - - + -
67E LYS* 5.5 0.3 - - - +
68E ALA* 4.3 16.8 - - + -
16H VAL* 3.4 31.4 - - + -
19H LEU* 3.9 18.8 - - + -
22H VAL* 4.1 12.3 - - + -
77H ASN 2.9 19.6 + - - +
78H MET* 3.1 10.5 + - - +
80H PHE* 1.3 77.5 - - - +
82H LYS* 1.3 60.8 + - - +
84H SER* 3.4 9.8 + - - -
85H VAL* 3.4 23.7 + - - +
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Residues in contact with LYS 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E GLN* 3.2 23.3 + - - +
60E LEU* 4.1 14.5 - - + +
61E ALA* 4.0 17.1 - - - +
64E ALA* 4.0 17.3 - - + -
78H MET* 2.9 44.4 + - - +
79H MET* 3.6 4.0 - - - +
81H LEU* 1.3 75.2 - - - +
83H LEU* 1.3 67.5 + - - +
85H VAL* 2.9 16.4 + - - +
86H VAL* 2.9 14.9 + - - +
110H ILE* 3.4 38.4 + - + -
113H LYS* 3.4 22.2 - - - +
114H ALA* 5.6 0.4 - - - +
214H PO4 4.0 9.1 + - - -
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Residues in contact with LEU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H PHE* 3.9 13.9 - - + -
52H VAL* 5.1 3.1 - - + -
55H PHE* 3.9 29.4 - - + -
56H TYR* 4.5 9.6 - - + -
79H MET 3.0 14.2 + - - +
80H PHE* 3.5 16.4 - - + +
82H LYS* 1.3 74.8 - - - +
84H SER* 1.3 64.9 + - - +
86H VAL* 3.0 4.8 + - + +
87H PHE* 2.8 73.1 + - + -
107H LEU* 3.5 27.4 - - + -
110H ILE* 4.0 6.5 - - - +
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Residues in contact with SER 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E LYS* 2.9 32.9 + - - +
24H PHE* 3.6 29.5 - - - -
80H PHE 2.9 11.3 + - - -
81H LEU* 3.4 16.4 - - - -
82H LYS 3.1 0.2 - - - -
83H LEU* 1.3 76.2 - - - +
85H VAL* 1.3 62.0 + - - +
87H PHE* 3.2 7.2 + - - +
88H ASP* 3.2 22.3 + - - +
91H ARG* 4.0 1.0 + - - -
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Residues in contact with VAL 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 5.3 1.6 - - + -
36E MSE 5.3 10.8 - - + -
60E LEU* 3.9 20.4 - - + -
63E ILE* 4.3 19.7 - - + +
64E ALA* 3.4 37.0 - - + +
67E LYS* 4.4 13.5 - - + -
81H LEU 3.5 6.1 - - - +
82H LYS 2.9 7.8 + - - +
84H SER* 1.3 75.7 - - - +
86H VAL* 1.3 66.3 + - - +
88H ASP* 3.0 31.1 + - + +
89H THR* 3.7 6.0 + - - +
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Residues in contact with VAL 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E LEU* 4.9 8.1 - - + -
48H PHE* 5.6 2.0 - - + -
82H LYS 2.9 16.4 + - - +
83H LEU* 3.6 6.5 - - + +
85H VAL* 1.3 75.9 - - - +
87H PHE* 1.3 67.7 + - + +
89H THR* 3.0 10.5 + - - -
90H GLN* 3.0 18.4 + - + +
103H ASN* 3.7 38.1 - - + +
106H ILE* 3.7 29.2 - - + -
107H LEU* 4.2 17.3 - - + -
110H ILE* 4.2 11.0 - - + -
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Residues in contact with PHE 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H PHE* 3.7 28.0 - + - -
29H LEU* 3.5 31.6 - - + -
32H ILE* 3.4 21.9 - - + +
33H TYR* 5.8 0.2 - + - -
48H PHE* 3.9 30.3 - + - -
52H VAL* 4.3 9.0 - - + -
83H LEU* 2.8 54.2 + - + -
84H SER 3.4 9.4 - - - +
85H VAL 3.2 0.2 - - - -
86H VAL* 1.3 79.5 - - + +
88H ASP* 1.3 53.2 + - - +
90H GLN* 3.5 6.8 - - + +
91H ARG* 2.7 53.5 + - - +
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Residues in contact with ASP 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E TYR* 2.5 36.2 + - - -
18E GLN* 2.9 35.4 + - - +
67E LYS* 3.0 9.6 + - - +
84H SER 3.2 7.7 + - - -
85H VAL* 3.0 17.4 + - + +
87H PHE* 1.3 79.3 - - - +
89H THR* 1.3 60.7 + - - +
91H ARG* 2.8 31.5 + - - +
92H LYS* 3.0 23.5 + - - +
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Residues in contact with THR 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E MSE 4.9 3.6 + - - +
37E ALA* 3.8 27.9 + - + +
85H VAL* 4.0 6.2 + - - +
86H VAL* 3.0 10.6 + - - -
88H ASP* 1.3 77.2 - - - +
90H GLN* 1.3 66.4 + - - +
92H LYS* 3.0 12.0 + - + +
93H GLU* 2.9 33.5 + - + +
99H GLN* 3.6 36.8 - - + +
103H ASN* 4.2 6.3 - - - +
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Residues in contact with GLN 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H ILE* 3.8 21.9 + - + +
33H TYR* 6.1 0.2 - - - +
35H LEU* 4.9 0.2 - - - +
36H SER* 3.6 22.2 + - - -
45H LEU* 5.5 0.4 - - - +
48H PHE* 3.6 42.6 - - + -
86H VAL* 3.0 12.6 + - + +
87H PHE* 3.5 14.1 - - + +
89H THR* 1.3 77.4 - - - +
91H ARG* 1.3 57.0 + - - +
93H GLU* 4.6 2.6 - - - +
94H ALA* 3.0 37.1 + - - +
100H ILE* 3.8 23.7 - - - +
103H ASN* 2.9 26.8 + - - +
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Residues in contact with ARG 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E GLN* 3.0 28.4 + - - +
67E LYS* 3.8 7.5 - - - +
24H PHE* 5.5 5.7 - - - -
32H ILE* 3.5 39.9 - - + +
35H LEU* 3.7 34.2 - - + +
84H SER* 4.0 1.0 + - - -
87H PHE* 2.7 26.2 + - - +
88H ASP* 2.8 37.9 + - - +
89H THR 3.1 0.2 - - - -
90H GLN* 1.3 74.9 - - - +
92H LYS* 1.3 58.8 + - + +
94H ALA* 4.5 3.7 - - - +
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Residues in contact with LYS 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E ASP 3.0 27.0 + - - -
18E GLN* 3.3 17.4 + - - +
19E SER* 3.9 8.3 + - - +
88H ASP 3.0 22.4 - - - +
89H THR* 3.0 15.6 + - + +
91H ARG* 1.3 78.7 - - + +
93H GLU* 1.3 80.9 + - + +
94H ALA 3.6 1.3 - - - -
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Residues in contact with GLU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E ALA* 6.2 0.4 - - + -
89H THR* 2.9 22.6 + - + +
90H GLN* 3.5 5.5 - - - +
92H LYS* 1.3 98.4 - - + +
94H ALA* 1.3 57.3 + - - +
95H ASN 3.0 11.8 + - - -
96H ASN* 3.2 41.9 + - + +
99H GLN* 3.6 27.2 - - + +
100H ILE* 4.2 6.4 - - - +
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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