Contacts of the helix formed by residues 65 - 89 (chain I) in PDB entry 1U8R
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 THR 65 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I GLY* 2.9 27.6 + - - +
53I LEU 3.1 5.4 + - - -
54I LEU* 3.3 33.7 - - - +
55I ARG* 3.9 21.8 - - + +
64I LEU* 1.3 75.8 - - - +
66I GLU* 1.3 67.2 + - - +
67I LYS* 3.3 3.3 + - - +
68I GLY 3.1 10.9 + - - -
69I ARG* 2.9 21.5 + - - +
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Residues in contact with GLU 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I THR* 1.3 76.6 - - - +
67I LYS* 1.3 62.0 + - - +
69I ARG* 3.6 3.9 + - - +
70I ALA* 3.3 19.1 + - - +
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Residues in contact with LYS 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51I ASP* 3.7 16.7 + - - +
52I GLY 3.7 14.4 - - - +
53I LEU* 3.9 15.7 - - + +
65I THR* 3.2 7.1 + - - +
66I GLU* 1.3 79.5 - - - +
68I GLY* 1.3 66.6 + - - +
70I ALA* 3.0 17.8 + - - +
71I LEU* 3.2 14.0 + - + +
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Residues in contact with GLY 68 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I LEU* 3.8 11.8 - - - +
53I LEU* 3.2 38.5 - - - +
64I LEU* 4.5 2.2 - - - -
65I THR* 3.1 8.5 + - - -
67I LYS* 1.3 80.1 - - - +
69I ARG* 1.3 61.8 + - - +
71I LEU* 3.4 2.6 + - - +
72I ALA* 3.0 24.2 + - - +
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Residues in contact with ARG 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I TYR* 4.3 17.1 - - + -
19I GLU* 3.2 40.0 + - - -
63I GLU* 5.7 2.6 + - - -
64I LEU* 3.9 36.3 + - + +
65I THR 2.9 16.3 + - - +
66I GLU* 4.0 4.3 - - - +
68I GLY* 1.3 72.6 - - - +
70I ALA* 1.3 67.3 - - - +
72I ALA* 3.2 1.5 + - + +
73I ILE* 2.9 46.1 + - + +
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Residues in contact with ALA 70 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I GLU* 3.3 11.3 + - - +
67I LYS* 3.0 12.2 + - - +
69I ARG* 1.3 79.6 - - - +
71I LEU* 1.3 57.4 + - - +
73I ILE* 3.5 11.8 - - - +
74I ALA* 3.1 25.5 + - - +
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Residues in contact with LEU 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I THR* 5.1 6.1 - - + -
9I GLU* 3.9 18.8 - - + +
12I LEU* 3.5 20.2 - - + -
53I LEU* 4.7 13.9 - - + -
67I LYS* 3.2 9.2 + - + +
68I GLY* 3.6 7.9 - - - +
70I ALA* 1.3 76.6 - - - +
72I ALA* 1.3 67.2 + - - +
74I ALA* 2.8 22.8 + - + +
75I VAL* 2.9 30.1 + - + +
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Residues in contact with ALA 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I LEU* 4.1 28.8 - - + +
13I ARG* 4.6 3.6 - - - +
16I TYR* 4.3 14.0 - - + -
64I LEU* 4.0 20.2 - - + -
68I GLY 3.0 14.5 + - - +
69I ARG* 3.4 7.9 - - - +
71I LEU* 1.3 76.4 - - - +
73I ILE* 1.3 64.2 + - - +
75I VAL* 3.1 7.6 + - - +
76I MET* 3.0 22.2 + - - +
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Residues in contact with ILE 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I TYR* 4.1 22.9 - - + +
69I ARG* 2.9 37.9 + - + +
70I ALA* 3.5 11.2 - - - +
72I ALA* 1.3 73.8 - - - +
74I ALA* 1.3 66.2 + - - +
76I MET* 3.0 9.3 + - - +
77I ARG* 2.8 22.8 + - + +
133I PRO* 3.7 8.7 - - + -
134I GLY* 3.3 37.0 - - - +
137I GLU* 4.9 12.8 - - + +
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Residues in contact with ALA 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I ALA 3.1 11.0 + - - +
71I LEU* 2.8 21.7 + - + +
73I ILE* 1.3 81.2 - - - +
75I VAL* 1.3 59.2 + - - +
77I ARG* 3.5 28.3 + - - +
78I LYS* 3.1 36.2 + - - +
110I GLU* 5.8 0.4 - - - +
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Residues in contact with VAL 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLU* 3.5 37.9 - - + +
12I LEU* 5.8 0.4 - - + -
13I ARG* 3.9 16.6 - - + -
71I LEU* 2.9 26.2 + - + +
72I ALA* 3.4 9.0 - - - +
74I ALA* 1.3 72.8 - - + +
76I MET* 1.3 68.3 + - - +
78I LYS* 3.2 12.7 + - - +
79I HIS* 2.9 21.0 + - - +
105I GLU* 3.6 36.4 - - + +
106I HIS* 4.4 6.7 - - + -
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Residues in contact with MET 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ARG* 3.6 24.4 - - + +
16I TYR* 3.6 29.4 - - + -
17I ASP* 3.5 21.8 - - - +
20I GLU* 4.0 0.4 - - - +
72I ALA 3.0 9.1 + - - +
73I ILE* 3.0 10.6 + - - +
75I VAL* 1.3 80.3 - - - +
77I ARG* 1.3 62.7 - - - +
79I HIS* 3.3 14.5 + - - +
80I ARG* 3.0 69.0 + - - +
133I PRO* 3.7 20.0 - - + -
172I GLU* 4.0 1.6 - - + +
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Residues in contact with ARG 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I ILE* 2.8 15.6 + - - +
74I ALA* 3.6 24.3 + - - +
76I MET* 1.3 75.3 - - - +
78I LYS* 1.3 63.8 + - - +
80I ARG* 3.9 1.6 - - - +
81I LEU* 3.0 32.8 + - + +
110I GLU* 3.5 23.4 + - - +
113I GLU* 2.6 34.5 + - - +
132I ILE* 3.8 15.6 - - + +
133I PRO* 3.5 22.6 - - - +
134I GLY* 2.6 40.2 + - - -
135I LEU* 4.4 1.8 - - - +
137I GLU* 4.3 8.3 - - - +
138I LEU* 3.2 36.3 - - - +
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Residues in contact with LYS 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLU* 6.5 0.7 - - - -
74I ALA* 3.1 26.2 - - - +
75I VAL* 3.2 7.1 + - - +
77I ARG* 1.3 76.4 - - - +
79I HIS* 1.3 66.7 + - - +
81I LEU* 3.2 3.5 + - - +
82I ALA* 2.9 26.9 + - - +
105I GLU* 3.3 27.4 - - - +
106I HIS 6.4 0.2 - - - -
107I VAL 5.5 0.2 - - - +
108I MET* 3.0 47.2 + - + +
109I SER* 4.6 0.2 - - - +
110I GLU* 3.9 15.0 + - - +
113I GLU* 2.6 41.5 + - + +
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Residues in contact with HIS 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ARG* 4.4 3.8 - - - -
75I VAL 2.9 8.4 + - - +
76I MET* 3.4 16.8 - - - +
78I LYS* 1.3 78.6 - - - +
80I ARG* 1.3 63.4 + - + +
82I ALA* 3.3 5.2 + - - +
83I GLU* 3.1 34.4 + - - +
98I HIS* 3.2 20.6 - + - -
101I ALA* 3.3 36.7 + - + +
102I CYS* 3.8 4.3 - - - -
105I GLU* 3.1 31.3 + - - +
172I GLU* 2.7 23.2 + - + +
7001I CO 2.2 31.3 + - - -
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Residues in contact with ARG 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I TYR* 5.5 0.2 + - - -
20I GLU* 2.8 39.6 + - - -
76I MET* 3.0 46.8 + - - +
77I ARG 4.1 1.1 - - - +
79I HIS* 1.3 74.0 - - + +
81I LEU* 1.3 65.6 + - - +
82I ALA 3.0 1.8 - - - -
83I GLU* 3.3 14.8 + - - +
84I ARG* 3.0 24.3 + - - +
126I SER* 3.8 20.5 - - - -
130I ASN* 3.3 33.1 - - - +
131I PRO* 3.0 29.7 + - - +
132I ILE* 4.1 15.7 - - + -
133I PRO* 4.3 3.0 - - - +
172I GLU* 3.0 25.5 + - - +
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Residues in contact with LEU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I ARG* 3.0 24.6 + - + +
78I LYS* 3.8 4.3 - - - +
80I ARG* 1.3 77.0 - - - +
82I ALA* 1.3 57.0 + - - +
84I ARG* 3.2 6.7 - - - +
85I LEU* 3.0 26.2 + - - +
108I MET* 4.9 1.1 - - + -
113I GLU* 3.6 48.0 - - + +
116I LEU* 4.6 13.1 - - + +
117I VAL* 4.4 22.9 - - + +
120I LEU* 4.0 8.3 - - + +
123I PRO* 4.1 17.7 - - + -
132I ILE* 3.7 26.7 - - + -
135I LEU* 5.2 1.6 - - + -
138I LEU* 4.6 2.2 - - + -
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Residues in contact with ALA 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I LYS 2.9 18.1 + - - +
79I HIS* 3.3 6.7 - - - +
81I LEU* 1.3 74.5 - - - +
83I GLU* 1.3 59.7 + - - +
84I ARG 3.1 1.3 - - - -
85I LEU* 3.2 7.4 + - - +
86I LEU* 2.8 36.2 + - + +
101I ALA* 4.1 12.6 - - + -
104I TRP* 4.5 21.8 - - + -
108I MET* 4.0 17.7 - - - -
116I LEU* 5.3 1.1 - - - -
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Residues in contact with GLU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I HIS* 3.1 24.8 + - - +
80I ARG* 3.3 7.3 + - - +
82I ALA* 1.3 75.6 - - - +
84I ARG* 1.3 62.5 + - - +
86I LEU* 3.8 8.8 - - - +
87I VAL* 3.1 21.5 + - - +
97I VAL* 4.3 9.6 - - + +
98I HIS* 3.2 13.1 + - - +
101I ALA* 3.5 14.1 - - + +
126I SER* 3.7 19.8 - - - -
127I PRO* 3.5 21.9 - - + +
128I PHE* 3.9 7.2 - - - -
172I GLU* 3.8 4.0 - - - +
175I GLN* 2.6 12.0 + - - +
7001I CO 2.1 32.5 + - - -
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Residues in contact with ARG 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I ARG 3.0 13.5 + - - +
81I LEU* 3.2 13.2 - - - +
82I ALA 3.1 0.2 - - - -
83I GLU* 1.3 79.0 - - - +
85I LEU* 1.3 65.4 + - - +
87I VAL* 3.8 1.1 - - - +
88I ASP* 2.7 61.4 + - - +
120I LEU* 3.4 15.5 - - + -
123I PRO* 3.6 30.8 - - + +
125I THR* 2.5 52.3 + - - +
126I SER 3.3 9.1 + - - -
127I PRO* 3.7 31.4 - - + +
132I ILE* 4.7 0.9 - - + -
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Residues in contact with LEU 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I LEU 3.0 10.0 + - - +
82I ALA* 3.2 9.4 + - - +
84I ARG* 1.3 78.9 - - - +
86I LEU* 1.3 62.0 + - + +
89I VAL* 3.1 36.0 + - + +
90I ILE* 3.0 36.8 + - + -
104I TRP* 4.4 22.0 - - + -
116I LEU* 3.5 31.6 - - + -
119I VAL* 5.6 1.6 - - + -
120I LEU* 3.8 9.5 - - + +
85J LEU* 4.8 2.5 - - + -
89J VAL* 5.3 2.2 - - + -
90J ILE* 3.5 29.6 - - + -
104J TRP* 5.0 2.5 - - + -
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Residues in contact with LEU 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82I ALA* 2.8 33.6 + - + +
83I GLU* 3.8 1.8 - - - +
85I LEU* 1.3 72.4 - - + +
87I VAL* 1.3 57.9 + - - +
90I ILE* 3.4 13.9 - - + +
91I GLY 2.8 26.5 + - - -
92I LEU* 2.9 27.7 + - + -
97I VAL* 3.4 42.8 - - + +
100I GLU* 4.0 15.0 - - + -
101I ALA* 4.1 7.2 - - + +
104I TRP* 3.9 35.2 - - + -
112J VAL* 4.3 4.9 - - + -
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Residues in contact with VAL 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83I GLU 3.1 17.0 + - - +
84I ARG* 3.9 2.5 - - - +
86I LEU* 1.3 80.0 - - - +
88I ASP* 1.3 76.6 + - - +
91I GLY* 3.4 14.4 - - - -
92I LEU 3.9 9.9 - - - +
94I TRP* 4.2 16.6 - - + -
97I VAL* 3.4 28.5 - - + -
127I PRO* 3.9 25.1 - - + -
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Residues in contact with ASP 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I ARG* 2.7 60.9 + - - +
87I VAL* 1.3 85.6 - - - +
89I VAL* 1.3 68.5 + - + +
91I GLY* 4.4 1.7 + - - -
120I LEU* 4.4 10.2 - - + +
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Residues in contact with VAL 89 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I LEU* 3.1 29.0 + - + -
88I ASP* 1.3 76.3 - - + +
90I ILE* 1.3 72.9 + - + +
91I GLY* 3.1 2.7 + - - -
119I VAL* 4.8 9.9 - - + +
120I LEU* 3.8 21.8 - - + -
89J VAL* 3.6 28.5 - - + -
115J ARG* 5.4 0.3 + - - -
119J VAL* 4.0 22.7 - - + +
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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