Contacts of the helix formed by residues 82 - 107 (chain B) in PDB entry 1T0R
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 VAL 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TYR* 5.6 2.7 - - - +
139A GLN* 2.9 27.1 - - + +
27B GLU* 4.3 18.4 - - - +
28B TYR* 3.8 34.3 - - + +
31B VAL* 3.8 16.8 - - + -
32B SER* 4.3 1.1 - - - +
80B GLN 4.1 3.6 - - - +
81B LEU* 1.3 80.0 - - - +
83B TYR* 1.3 65.2 + - - +
84B ARG* 3.1 16.6 - - + +
85B THR* 3.0 13.2 + - + +
86B TYR* 2.8 20.4 + - - +
157B TYR* 3.5 10.1 - - - -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 2.8 23.1 + + - -
62A GLN* 2.9 33.2 + - + +
66A ASP* 3.3 20.2 - - - -
132A MET* 3.1 48.5 - - + -
133A ASP* 4.4 0.2 + - - -
135A ASN* 3.1 21.1 - - - +
136A ARG* 3.6 34.3 - - + -
139A GLN* 2.9 17.0 - - - +
82B VAL* 1.3 71.0 - - - +
84B ARG* 1.3 62.3 + - - +
86B TYR* 3.3 2.8 + - - +
87B ASN* 3.1 41.2 + - - +
157B TYR* 3.1 9.8 + - - -
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 6.0 0.5 - - - -
66A ASP* 3.7 28.5 - - + +
70A TYR* 3.8 36.6 - - + +
27B GLU* 3.1 35.8 + - - +
82B VAL* 3.1 11.6 - - + +
83B TYR* 1.3 82.8 - - - +
85B THR* 1.3 75.7 + - + +
87B ASN* 3.7 4.5 + - - +
88B LEU* 3.5 44.1 + - + +
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLU* 4.4 9.6 - - - +
80B GLN 4.2 3.8 + - - +
81B LEU* 3.9 13.2 - - - +
82B VAL* 3.0 26.2 + - + +
84B ARG* 1.3 104.2 - - - +
86B TYR* 1.3 65.1 + - - +
88B LEU* 3.7 11.3 - - + +
89B LEU* 3.2 24.1 + - - +
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Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 2.8 28.5 + + - -
59A VAL* 4.7 0.7 - - + -
132A MET* 3.7 26.5 - - + -
81B LEU* 3.9 22.2 - - + -
82B VAL 2.8 17.4 + - - +
83B TYR* 3.3 4.9 + - - +
85B THR* 1.3 79.0 + - - +
87B ASN* 1.3 70.6 + - - +
89B LEU* 3.9 2.5 - - + +
90B GLN* 3.0 42.2 + - + +
157B TYR* 3.7 39.7 - + + -
160B ALA* 3.3 18.1 - - + +
161B ASP* 2.6 32.8 + - - -
263B ARG* 4.3 5.6 - - - -
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 4.5 8.7 - - - -
59A VAL* 3.6 44.1 - - - +
62A GLN* 3.7 7.0 - - - +
63A ARG* 4.2 12.3 - - - -
132A MET* 4.8 1.0 - - - +
83B TYR* 3.1 48.0 + - - +
84B ARG* 3.7 4.9 + - - +
86B TYR* 1.3 89.6 - - - +
88B LEU* 1.3 58.6 + - - +
91B ASP* 2.8 34.1 + - - +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 3.5 44.9 + - + +
67A SER* 5.5 3.1 - - - +
84B ARG* 3.5 36.6 + - + +
85B THR* 3.7 15.0 - - + +
86B TYR 3.3 0.4 - - - -
87B ASN* 1.3 76.7 - - - +
89B LEU* 1.3 67.3 + - - +
91B ASP* 3.8 3.7 - - - +
92B GLY* 3.0 18.9 + - - -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP* 6.0 0.7 - - - +
81B LEU* 4.5 18.2 - - + -
85B THR 3.2 13.3 + - - +
86B TYR* 3.9 4.3 - - + +
88B LEU* 1.3 78.9 - - - +
90B GLN* 1.3 74.6 + - + +
92B GLY* 3.0 6.1 + - - -
93B GLN* 3.0 40.2 + - + +
259B ARG* 6.1 0.7 - - - +
263B ARG* 4.1 30.3 - - - +
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.1 26.0 + - + +
59A VAL* 4.3 11.7 - - + -
86B TYR* 3.0 35.2 + - + +
87B ASN 4.4 0.2 - - - +
89B LEU* 1.3 92.4 - - + +
91B ASP* 1.3 56.8 + - - +
92B GLY 2.9 2.2 - - - -
93B GLN* 3.1 11.7 + - - +
94B GLU* 2.7 38.4 + - - +
161B ASP* 3.0 25.0 + - - -
164B ARG* 3.7 15.8 - - - +
260B ASP* 3.2 18.4 + - - +
263B ARG* 3.9 5.8 + - - -
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Residues in contact with ASP 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A PRO 4.7 0.2 - - - +
59A VAL* 3.9 16.5 - - + +
60A SER* 3.4 33.8 + - - -
63A ARG* 2.9 40.0 + - - +
87B ASN 2.8 25.4 + - - +
88B LEU 3.8 3.1 - - - +
90B GLN* 1.3 72.7 - - - +
92B GLY* 1.3 62.1 + - - +
94B GLU* 3.9 3.6 - - - +
95B SER* 3.1 31.3 + - - -
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Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ARG* 4.9 3.3 - - - +
88B LEU 3.0 8.7 + - - -
89B LEU 3.0 8.7 + - - -
90B GLN 2.9 0.8 - - - -
91B ASP* 1.3 78.4 - - - +
93B GLN* 1.3 65.8 - - - +
95B SER* 3.1 17.8 + - - -
96B TYR* 3.2 11.6 + - - +
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 3.0 28.6 + - + +
90B GLN* 3.6 22.0 - - - +
92B GLY* 1.3 77.7 - - - +
94B GLU* 1.3 57.2 + - - +
96B TYR* 3.0 19.5 + - - +
97B VAL* 2.9 28.9 + - - +
164B ARG* 3.4 22.1 + - - +
256B ALA* 5.0 3.3 - - - +
259B ARG* 3.2 45.0 + - + +
260B ASP* 5.6 1.1 - - - +
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.7 27.4 - - + -
56A PRO* 3.6 16.7 - - + +
59A VAL* 4.2 10.3 - - + -
90B GLN 2.7 22.2 + - - +
91B ASP* 4.1 8.7 - - - +
93B GLN* 1.3 70.0 - - - +
95B SER* 1.3 59.3 + - - +
97B VAL* 4.2 2.0 - - - +
98B GLN* 2.6 68.0 + - + +
164B ARG* 2.7 39.0 + - - +
167B THR* 5.8 0.7 - - - +
168B HIS* 3.0 15.3 - - - -
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP* 3.1 20.2 + - - -
92B GLY* 3.1 13.3 + - - -
94B GLU* 1.3 75.8 - - - +
96B TYR* 1.3 57.3 + - - +
98B GLN* 4.0 4.1 - - - +
99B GLY* 3.0 24.8 + - - -
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLY 3.2 7.7 + - - +
93B GLN* 3.0 22.6 + - - +
94B GLU 3.0 0.6 - - - -
95B SER* 1.3 77.2 - - - +
97B VAL* 1.3 75.9 + - + +
99B GLY* 3.0 10.6 + - - -
100B LEU* 3.1 46.1 + - + +
252B LEU* 3.9 24.1 + - - +
256B ALA* 4.3 20.0 - - + -
259B ARG* 6.4 1.1 - - - -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLN 2.9 13.8 + - - +
94B GLU* 4.1 8.5 - - - +
96B TYR* 1.3 78.8 - - + +
98B GLN* 1.3 59.1 + - - +
100B LEU* 3.1 9.6 + - + +
101B PHE* 3.0 56.7 + - + -
164B ARG* 3.6 24.9 - - - +
168B HIS* 3.8 17.3 - - + +
253B LEU* 3.9 11.4 - - + -
256B ALA* 3.8 24.9 - - + -
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 3.4 29.9 - - + +
56A PRO* 4.0 22.1 - - + +
94B GLU* 2.6 63.7 + - + +
95B SER* 4.3 4.5 - - - +
97B VAL* 1.3 72.7 - - - +
99B GLY* 1.3 55.8 + - - +
101B PHE* 3.8 23.9 - - - -
102B ASP* 3.0 30.0 + - - +
167B THR* 6.1 1.4 - - - +
168B HIS* 4.3 6.7 + - - -
171B TYR* 5.6 3.3 - - - -
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER 3.0 17.4 + - - -
96B TYR* 3.0 5.1 + - - -
98B GLN* 1.3 76.0 - - - +
100B LEU* 1.3 64.9 + - - +
102B ASP* 3.5 3.7 + - - +
103B GLN* 3.0 38.5 + - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 3.1 43.2 + - + +
97B VAL* 3.1 11.2 + - + +
99B GLY* 1.3 74.3 - - - +
101B PHE* 1.3 71.3 + - + +
103B GLN* 5.2 1.1 - - - -
104B LEU* 2.8 47.8 + - + +
249B LEU* 4.8 5.2 - - + +
252B LEU* 3.5 45.5 - - + -
253B LEU* 4.6 8.7 - - + +
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 4.6 1.1 - - - -
3A MET* 4.2 4.0 - - - -
97B VAL* 3.0 39.4 + - + -
98B GLN* 3.6 28.7 - - - +
100B LEU* 1.3 82.0 - - + +
102B ASP* 1.3 64.4 + - - +
104B LEU* 4.5 0.5 - - - +
105B ASN* 3.2 23.0 + - - +
168B HIS* 4.3 18.8 - - + -
171B TYR* 3.3 48.9 - + + -
172B ARG* 3.9 31.6 - - + -
175B GLU* 4.6 5.3 - - - +
249B LEU* 4.2 21.9 - - + +
253B LEU* 4.4 7.0 - - + -
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.7 54.3 + - - -
3A MET* 3.4 23.5 - - - -
98B GLN 3.0 15.0 + - - +
99B GLY* 3.8 5.4 - - - +
100B LEU 3.3 0.2 - - - -
101B PHE* 1.3 81.1 - - - +
103B GLN* 1.3 67.5 + - + +
106B ASP* 3.2 18.8 + - - +
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Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY* 3.0 22.1 + - - +
100B LEU* 4.5 1.6 - - - +
102B ASP* 1.3 83.0 + - - +
104B LEU* 1.3 67.5 + - + +
105B ASN 3.1 1.8 - - - -
106B ASP* 3.0 28.7 + - + +
107B ARG* 3.3 10.4 + - - +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B LEU* 2.8 41.2 + - + +
103B GLN* 1.3 74.8 - - + +
105B ASN* 1.3 59.9 + - - +
107B ARG* 3.4 47.4 + - + +
109B HIS* 3.1 42.3 + - + +
248B THR* 4.3 5.6 - - - +
249B LEU* 3.6 48.5 - - + +
252B LEU* 5.3 2.9 - - + -
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.7 50.2 + - - +
101B PHE 3.2 20.1 + - - +
102B ASP 3.4 3.1 - - - +
103B GLN 3.1 0.4 - - - -
104B LEU* 1.3 78.4 - - - +
106B ASP* 1.3 62.9 + - - +
108B GLY* 3.0 15.9 + - - -
109B HIS* 4.9 1.6 - - - +
110B ASP* 6.1 1.3 - - - +
175B GLU* 3.7 17.4 - - - +
249B LEU* 5.8 0.4 - - - +
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.8 32.8 + - - -
102B ASP* 3.2 16.5 + - - +
103B GLN* 3.0 23.3 + - + +
105B ASN* 1.3 82.6 + - - +
107B ARG* 1.3 55.8 + - + +
108B GLY 3.6 1.4 + - - -
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLN 3.3 10.2 + - - +
104B LEU* 3.5 35.5 - - + +
105B ASN 3.2 1.2 - - - -
106B ASP* 1.3 77.6 - - - +
108B GLY* 1.3 64.4 + - - +
109B HIS* 3.4 11.3 + - - +
112B MET* 4.7 22.6 - - - +
248B THR* 4.7 8.7 + - - +
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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