Contacts of the helix formed by residues 90 - 112 (chain C) in PDB entry 3ER8
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 ASN 90 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C THR* 3.6 3.0 - - + +
89C TYR* 1.3 76.8 - - - +
91C ILE* 1.3 86.4 + - - +
92C GLY* 2.6 14.6 - - - +
93C LYS* 3.1 38.8 - - + +
94C LEU* 3.1 24.7 + - - +
900H C 4.1 11.7 - - - -
901H U 3.4 16.0 + - - +
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Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASN* 3.3 24.5 - - - +
30C GLU* 3.3 46.7 - - + +
33C MET* 3.7 26.9 - - + -
34C LEU* 5.3 2.4 - - + +
89C TYR 3.4 5.3 + - - +
90C ASN* 1.3 77.6 - - - +
92C GLY* 1.3 59.6 + - - +
94C LEU* 3.5 11.7 - - + +
95C PHE* 3.4 36.0 + - + -
900H C 3.9 20.2 - - - +
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Residues in contact with GLY 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ASN* 2.6 16.6 - - - +
91C ILE* 1.3 70.5 - - - +
93C LYS* 1.3 61.0 + - - -
94C LEU 3.1 1.7 + - - -
95C PHE* 3.4 6.1 + - - +
96C THR* 2.9 25.3 + - - -
900H C 3.1 32.9 + - - +
901H U 3.3 14.3 - - - +
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Residues in contact with LYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C THR* 4.1 19.5 - - + +
90C ASN* 3.1 26.3 + - + +
92C GLY* 1.3 71.7 - - - +
94C LEU* 1.3 65.0 + - - +
96C THR* 3.4 7.7 + - - -
97C ILE* 2.9 27.2 + - - +
474C LYS* 3.3 37.9 + - - +
475C ASP* 3.4 29.5 + - + +
901H U 3.4 28.7 - - - +
902H U 3.7 12.1 + - - -
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 5.3 1.6 - - + -
22C LEU* 3.6 18.6 - - + -
24C ARG* 4.2 1.6 - - - +
30C GLU* 3.9 18.2 - - - +
34C LEU* 3.8 35.4 - - + -
85C GLN* 4.0 15.7 - - + -
88C THR* 3.5 29.2 - - + +
90C ASN 3.1 24.9 + - - +
91C ILE* 3.5 18.8 - - + +
92C GLY 3.1 0.6 - - - -
93C LYS* 1.3 74.9 - - - +
95C PHE* 1.3 52.1 + - - +
97C ILE* 2.5 30.8 + - + +
98C ILE* 2.7 22.5 + - + +
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Residues in contact with PHE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLY* 3.9 32.3 - - - -
107B ARG* 4.0 17.4 - - + +
33C MET* 3.5 38.1 - - + -
34C LEU* 3.9 22.4 - - + -
37C GLN* 4.4 12.6 - - + -
91C ILE* 3.4 32.4 + - + -
92C GLY 3.4 6.8 + - - +
94C LEU* 1.3 76.9 - - - +
96C THR* 1.3 56.4 + - - +
98C ILE* 3.8 7.5 - - + +
99C GLU* 3.2 28.8 + - - +
900H C 3.3 41.5 - + - +
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Residues in contact with THR 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 4.2 7.6 - - - +
81C TYR* 4.4 0.2 + - - -
92C GLY 2.9 9.2 + - - -
93C LYS 3.5 9.2 - - - -
94C LEU 2.8 4.4 + - - -
95C PHE* 1.3 74.2 - - - +
97C ILE* 1.3 57.7 + - - +
98C ILE 3.4 0.2 - - - -
99C GLU 4.2 0.7 - - - -
100C LEU* 3.3 30.1 + - + +
475C ASP* 3.5 25.0 + - - +
477C ILE* 3.3 25.6 - - + +
901H U 2.4 44.9 + - - +
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Residues in contact with ILE 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 4.4 2.5 - - - +
81C TYR* 4.0 18.6 + - + +
84C LYS* 3.2 39.3 - - + +
85C GLN* 4.2 10.1 - - + +
88C THR* 4.2 14.4 - - + +
93C LYS 2.9 17.6 + - - +
94C LEU* 2.5 15.8 + - + +
96C THR* 1.3 73.3 - - - +
98C ILE* 1.3 55.9 + - + +
99C GLU 3.4 0.4 - - - -
100C LEU* 4.0 1.4 - - - +
101C GLN* 3.1 48.6 + - + +
475C ASP* 3.3 32.8 - - + +
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 3.6 28.3 - - + +
34C LEU* 3.4 33.7 - - + -
37C GLN* 4.4 17.5 - - + +
40C ASN* 4.8 6.3 - - + -
41C ILE* 3.7 30.5 - - + -
44C ILE* 3.9 3.6 - - + +
94C LEU* 2.7 23.1 + - + +
95C PHE* 3.9 12.3 - - + +
97C ILE* 1.3 78.2 - - + +
99C GLU* 1.3 58.0 + - - +
100C LEU 3.3 0.4 - - - -
102C SER* 2.7 36.7 + - - +
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Residues in contact with GLU 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TYR* 2.7 34.7 + - + +
107B ARG* 3.2 33.9 + - + +
95C PHE 3.2 17.5 + - - +
96C THR 4.1 2.0 + - - +
98C ILE* 1.3 77.6 - - - +
100C LEU* 1.3 64.4 + - - +
102C SER* 3.9 7.1 + - - -
103C VAL* 3.2 25.4 + - - +
211C ARG* 3.7 14.9 + - - -
477C ILE* 3.7 12.0 - - - +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C TYR* 3.5 22.9 - - - +
96C THR* 3.3 24.7 + - + +
97C ILE 3.8 0.6 + - - +
98C ILE 3.3 0.4 - - - -
99C GLU* 1.3 83.1 - - - +
101C GLN* 1.3 66.3 + - - +
102C SER 3.1 1.3 - - - -
103C VAL* 3.2 16.4 + - - +
104C LEU* 3.8 1.9 + - - +
215C ILE* 3.7 39.3 - - + -
219C PHE* 3.6 20.2 - - + -
470C ILE* 4.0 29.4 - - + -
471C ASN 5.8 0.2 - - - -
472C ILE* 4.5 15.9 - - + -
475C ASP* 6.1 0.9 - - - -
476C ILE 6.2 0.2 - - - +
477C ILE* 4.0 13.9 - - + -
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Residues in contact with GLN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 2.6 40.5 + - - -
44C ILE* 3.2 26.7 - - + +
49C LYS* 4.8 0.7 - - - -
81C TYR* 3.5 24.3 - - + +
82C PHE* 3.5 25.3 + - + -
85C GLN* 2.7 27.9 + - - +
97C ILE* 3.1 25.6 + - - +
100C LEU* 1.3 75.8 - - - +
102C SER* 1.3 57.9 + - - +
104C LEU* 3.0 27.3 + - - +
105C VAL* 3.3 14.0 + - + +
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Residues in contact with SER 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ASN* 4.2 19.7 - - - +
44C ILE* 3.3 18.2 - - - +
98C ILE 2.7 22.7 + - - -
99C GLU* 4.0 9.0 - - - -
100C LEU 3.1 0.4 - - - -
101C GLN* 1.3 79.6 - - - +
103C VAL* 1.3 60.3 + - - +
104C LEU 3.2 0.5 + - - -
105C VAL* 3.4 6.0 + - - -
106C THR* 3.3 32.9 + - - +
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B TYR* 6.1 0.4 - - - +
99C GLU* 3.2 20.4 - - - +
100C LEU* 3.2 10.2 + - + +
102C SER* 1.3 76.7 - - - +
104C LEU* 1.3 60.6 + - + +
106C THR* 4.8 2.7 - - - -
107C THR* 2.5 38.8 + - + +
211C ARG* 5.1 7.6 - - - +
212C THR* 4.2 9.9 - - + +
215C ILE* 3.5 46.7 - - + -
216C ASP* 3.2 20.0 - - - +
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PHE* 4.3 6.4 - - - -
52C PHE* 4.1 26.9 - - + -
81C TYR* 5.2 0.9 - - + -
82C PHE* 3.7 31.9 - - + -
100C LEU 3.9 6.7 - - - +
101C GLN* 3.0 13.2 + - - +
103C VAL* 1.3 76.3 - - + +
105C VAL* 1.3 59.6 + - - +
106C THR 2.9 11.3 + - - -
107C THR 3.4 0.2 + - - -
108C TYR* 3.4 28.3 + - + +
109C THR 4.9 0.7 + - - -
216C ASP* 3.3 23.6 - - + +
219C PHE* 3.7 51.4 - - + -
223C PHE* 4.4 0.7 - - + -
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LYS* 3.3 46.2 - - + +
44C ILE* 3.7 26.7 - - + -
47C PHE* 3.3 51.7 - - + -
82C PHE* 5.0 3.6 - - + -
101C GLN 3.3 15.2 + - - +
102C SER* 3.4 7.8 + - - +
104C LEU* 1.3 74.3 - - + +
106C THR* 1.3 59.6 + - + +
703F U 4.3 4.4 + - - +
704F C 5.7 2.9 + - - -
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Residues in contact with THR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C LYS* 3.8 30.5 - - + +
102C SER* 3.3 22.7 + - - +
103C VAL* 4.5 1.4 + - - -
104C LEU 3.0 1.0 - - - -
105C VAL* 1.3 86.0 - - + +
107C THR* 1.3 75.4 + - - +
109C THR* 5.4 2.8 - - - -
110C ASP* 3.9 13.7 - - - +
704F C 4.5 13.1 + - - +
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Residues in contact with THR 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C VAL* 2.5 26.0 + - + +
104C LEU 3.4 0.2 + - - -
106C THR* 1.3 94.5 + - - +
108C TYR* 1.3 66.8 + - - +
109C THR 2.9 4.4 + - - -
110C ASP* 2.9 8.1 + - + +
111C ILE* 2.7 29.6 + - + +
212C THR* 3.3 31.5 - - + +
216C ASP* 2.9 15.4 + - - -
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Residues in contact with TYR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C PHE* 6.3 0.2 - - + -
52C PHE* 3.4 35.9 - + + -
55C LEU* 3.6 53.9 + - + -
56C VAL* 3.9 12.4 - - + -
59C ASN* 4.4 6.8 - - - +
103C VAL 3.8 1.2 + - - -
104C LEU* 3.4 23.0 + - + +
107C THR* 1.3 77.6 + - - +
109C THR* 1.3 54.8 + - - +
112C LEU* 2.8 57.3 + - + +
113C GLY* 2.5 38.1 + - - -
216C ASP* 3.9 17.0 + - + +
220C LEU* 4.2 12.8 - - + +
703F U 6.2 1.3 - + - -
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Residues in contact with THR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C LEU* 4.9 0.9 - - - +
104C LEU 4.9 0.8 + - - -
106C THR 5.7 2.2 - - - -
107C THR 2.9 5.3 + - - +
108C TYR* 1.3 78.9 - - - +
110C ASP* 1.3 78.7 + - - +
113C GLY* 3.1 1.1 + - - -
114C VAL* 2.9 33.5 + - + +
702F U 2.5 45.2 + - - +
703F U 2.9 35.4 + - - +
704F C 5.7 1.3 - - - +
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C THR 3.9 16.1 - - - +
107C THR* 2.9 9.9 + - + +
109C THR* 1.3 89.7 - - - +
111C ILE* 1.3 58.2 + - + +
114C VAL* 3.7 10.6 - - - +
179C HIS* 2.7 33.3 - - - -
704F C 4.2 13.2 + - - -
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C THR* 2.7 34.7 + - + +
108C TYR* 4.0 0.4 - - - +
109C THR 3.1 0.8 - - - -
110C ASP* 1.3 81.9 - - + +
112C LEU* 1.3 72.3 + - + +
113C GLY 3.6 0.2 - - - -
114C VAL* 4.7 2.3 + - - +
115C LEU* 4.3 2.6 - - - +
175C TYR* 2.9 41.8 - - + +
179C HIS* 2.8 24.2 + - + -
182C SER* 6.0 1.1 - - - +
209C ASN* 3.3 27.1 - - - +
212C THR* 3.7 5.4 - - + -
213C PHE* 4.3 11.7 - - + -
216C ASP* 3.5 27.1 - - + +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ASN* 5.0 3.7 - - - +
108C TYR* 2.8 39.0 + - + +
111C ILE* 1.3 85.8 - - + +
113C GLY* 1.3 62.9 + - - +
114C VAL 3.4 0.7 - - - -
115C LEU* 2.9 43.4 - - + +
116C THR* 5.2 0.7 + - - +
171C LEU* 4.7 5.6 - - + -
175C TYR* 4.0 16.8 - - + -
213C PHE* 4.7 10.5 - - + -
216C ASP* 3.6 34.8 - - + +
217C LEU* 3.7 9.0 - - + +
220C LEU* 3.7 22.4 - - + -
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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