Contacts of the helix formed by residues 96 - 116 (chain H) in PDB entry 1TKK
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 96 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C LEU* 4.8 2.4 - - - +
56C GLY* 2.8 30.9 + - - +
61C SER* 5.7 0.9 - - - -
55H THR 5.8 1.2 + - - -
57H ASP* 3.4 20.1 + - - +
61H SER* 4.0 17.2 + - - +
62H ILE* 6.1 0.2 - - - +
65H ALA* 4.0 12.0 - - - +
93H LEU* 3.5 29.1 - - + +
94H THR 3.0 19.4 + - - -
95H GLY* 1.3 70.3 - - - +
97H MET* 1.3 62.8 + - - +
98H SER 3.3 2.9 - - - -
99H ALA* 3.3 9.3 + - + +
100H LYS* 3.2 22.5 + - - +
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Residues in contact with MET 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H THR* 5.4 4.0 - - + -
57H ASP* 3.6 6.0 + - - +
90H GLN* 4.0 10.1 - - - +
95H GLY* 3.8 23.1 - - - +
96H ASN* 1.3 73.8 - - - +
98H SER* 1.3 63.5 + - - +
100H LYS* 3.5 14.1 + - - -
101H ALA* 3.1 25.3 + - - +
248H PHE* 4.9 9.6 - - + -
249H THR* 4.3 18.4 - - + -
270H MET 3.1 19.2 - - - +
271H LYS* 3.3 23.8 - - - +
272H ALA* 3.5 9.2 - - - +
273H GLY* 3.3 25.0 - - - +
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Residues in contact with SER 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H ALA* 3.2 19.5 - - - +
49H PRO 4.2 3.7 + - - -
51H THR* 4.2 3.1 + - - -
55H THR* 3.3 20.6 + - - +
57H ASP* 2.5 33.2 + - - +
62H ILE* 4.0 11.4 - - - -
97H MET* 1.3 75.0 - - - +
99H ALA* 1.3 65.3 + - - +
101H ALA* 3.4 2.1 + - - +
102H ALA 3.2 12.1 + - - -
270H MET* 3.6 27.1 + - - +
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Residues in contact with ALA 99 (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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62H ILE* 4.0 32.1 - - + +
65H ALA* 3.8 28.3 - - + -
66H ILE* 4.3 6.5 - - + +
70H LEU* 4.5 5.6 - - + -
93H LEU* 5.5 0.2 - - + -
96H ASN* 3.3 14.2 + - + +
97H MET 3.3 0.4 - - - -
98H SER* 1.3 76.7 - - - +
100H LYS* 1.3 65.5 + - + +
101H ALA 3.1 1.0 + - - -
102H ALA* 3.2 4.9 + - - +
103H VAL* 3.2 24.4 + - - +
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Residues in contact with LYS 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H LEU* 4.3 6.1 - - + -
89H ILE* 3.3 42.6 - - + +
90H GLN* 3.3 29.7 + - - +
93H LEU* 2.6 43.2 + - + -
94H THR* 3.9 1.2 - - - +
95H GLY 2.7 31.3 + - - +
96H ASN 3.2 9.8 + - - +
97H MET* 3.8 19.7 - - - +
98H SER 3.4 0.2 - - - -
99H ALA* 1.3 75.1 - - + +
101H ALA* 1.3 56.8 + - - +
103H VAL* 3.5 1.2 + - - +
104H GLU* 3.0 27.2 + - - +
273H GLY* 3.4 16.0 - - - +
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Residues in contact with ALA 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H MET 3.1 14.8 + - - +
98H SER 3.7 5.2 - - - +
99H ALA 3.1 0.6 - - - -
100H LYS* 1.3 75.8 - - - +
102H ALA* 1.3 64.4 + - - +
104H GLU* 3.9 1.4 - - - +
105H MET* 3.0 30.5 + - - +
269H LEU* 3.2 29.2 - - + +
270H MET* 3.7 15.7 - - + -
273H GLY 3.4 8.9 + - - -
274H GLY* 3.4 9.4 - - - +
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Residues in contact with ALA 102 (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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32H VAL 5.3 0.2 - - - +
34H VAL* 4.0 20.6 - - + +
46H GLY* 3.6 7.8 - - - -
47H GLU 3.4 38.0 + - - +
48H ALA* 3.8 5.8 - - + +
66H ILE* 4.5 4.3 - - + -
98H SER 3.2 11.6 + - - +
99H ALA 3.6 8.1 - - - +
101H ALA* 1.3 76.7 - - - +
103H VAL* 1.3 62.4 + - - +
105H MET* 3.2 13.4 + - - +
106H ALA* 3.4 10.0 + - - +
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Residues in contact with VAL 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ILE* 5.4 5.4 - - + -
34H VAL* 4.8 12.3 - - + -
36H ILE* 4.0 7.9 - - + +
66H ILE* 4.1 24.2 - - + -
70H LEU* 3.7 27.8 - - + -
74H LEU* 3.7 29.4 - - + -
89H ILE* 3.8 16.8 - - + -
99H ALA 3.2 7.1 + - - +
100H LYS 3.8 7.0 - - - +
102H ALA* 1.3 78.4 - - - +
104H GLU* 1.3 57.2 + - - +
105H MET 3.3 0.2 + - - -
106H ALA* 3.4 4.4 + - - +
107H LEU* 3.0 25.7 + - + +
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Residues in contact with GLU 104 (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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86H LEU* 3.3 26.9 - - + +
89H ILE* 4.2 9.8 - - + +
90H GLN* 2.7 27.6 + - - +
100H LYS 3.0 19.5 + - - +
101H ALA 3.9 0.2 - - - +
102H ALA 3.3 0.2 - - - -
103H VAL* 1.3 73.8 - - - +
105H MET* 1.3 59.5 + - - +
107H LEU* 3.6 6.0 - - - +
108H TYR* 2.9 42.9 + - + -
273H GLY 3.2 8.0 - - - +
274H GLY* 3.9 12.8 - - - -
275H ILE* 3.0 6.4 + - - +
276H SER* 2.8 42.5 + - - -
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Residues in contact with MET 105 (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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45H TRP 3.3 10.2 - - - +
46H GLY* 3.9 2.5 - - - -
47H GLU* 3.4 24.7 - - - +
101H ALA 3.0 14.7 + - - +
102H ALA 3.2 6.7 + - - +
104H GLU* 1.3 77.4 - - - +
106H ALA* 1.3 60.1 + - - +
108H TYR* 3.4 2.3 + - - +
109H ASP* 3.0 28.1 + - - +
269H LEU* 4.0 24.2 - - + -
270H MET* 3.3 35.0 - - + -
274H GLY* 6.0 0.4 - - - -
275H ILE* 4.1 9.2 - - + +
299H GLU* 4.3 2.5 - - - +
302H LEU* 5.0 2.7 - - - +
303H GLY* 4.1 21.5 - - - +
306H ALA* 3.5 30.3 - - + -
352H LEU* 4.0 5.4 - - + +
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Residues in contact with ALA 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H VAL* 4.4 5.6 - - + -
36H ILE* 3.4 30.7 - - + +
38H TYR* 3.0 8.6 + - - -
44H GLY* 3.6 19.0 - - - +
45H TRP 3.0 21.9 + - - +
46H GLY 4.2 1.1 - - - +
102H ALA 3.4 6.1 + - - +
103H VAL 3.4 3.7 + - - +
104H GLU 3.4 0.2 - - - -
105H MET* 1.3 76.4 - - - +
107H LEU* 1.3 62.7 + - - +
109H ASP* 3.2 3.3 + - - +
110H GLY 3.0 19.6 + - - -
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Residues in contact with LEU 107 (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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3H ILE* 3.9 19.5 - - + -
36H ILE* 4.0 3.3 - - + +
38H TYR* 3.3 9.0 + - - +
74H LEU* 5.0 2.7 - - + -
79H LEU* 3.3 31.8 - - + +
82H TYR* 4.5 14.1 - - + -
85H ILE* 4.2 23.1 - - + -
86H LEU* 3.9 31.4 - - + -
89H ILE* 4.4 4.3 - - + -
103H VAL* 3.0 18.6 + - + +
104H GLU* 3.6 7.4 - - - +
106H ALA* 1.3 77.3 - - - +
108H TYR* 1.3 61.3 + - + +
110H GLY 3.4 0.5 + - - -
111H TRP* 3.0 28.9 + - + +
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Residues in contact with TYR 108 (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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82H TYR* 4.5 12.7 - + - -
86H LEU* 3.6 22.5 - - + +
104H GLU* 2.9 48.4 + - + +
105H MET 4.0 0.7 - - - +
107H LEU* 1.3 77.9 - - + +
109H ASP* 1.3 65.7 + - - +
111H TRP* 3.7 20.7 - + + +
112H ALA* 3.1 25.3 + - - +
119H LEU* 3.6 28.9 - - + +
123H LEU* 4.2 19.3 - - + -
275H ILE* 3.7 36.5 - - + +
276H SER* 3.4 23.6 - - - -
279H GLU* 4.6 7.1 + - - -
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Residues in contact with ASP 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H GLY* 3.5 7.5 - - - -
45H TRP* 3.1 27.9 + - - -
105H MET 3.0 13.3 + - - +
106H ALA 3.2 9.9 - - - +
108H TYR* 1.3 77.9 - - - +
110H GLY* 1.3 57.9 + - - +
113H GLN* 2.7 51.3 + - - +
119H LEU* 4.7 0.6 - - - +
351H GLY* 3.3 4.1 - - - -
352H LEU* 2.9 49.5 + - + +
353H GLY 4.5 1.9 + - - -
354H ILE* 5.3 0.7 + - - +
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Residues in contact with GLY 110 (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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1H MET* 3.8 4.7 - - - +
38H TYR* 3.7 28.7 - - - -
79H LEU* 3.4 8.6 - - - +
106H ALA 3.0 10.9 + - - -
107H LEU 3.9 1.1 - - - -
109H ASP* 1.3 74.4 - - - +
111H TRP* 1.3 55.7 + - - +
113H GLN* 3.5 12.2 - - - +
114H MET* 2.8 33.1 + - - +
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Residues in contact with TRP 111 (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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82G TYR* 5.7 0.2 - - - -
111G TRP* 4.5 6.5 - + - -
117G LEU* 6.1 0.2 - - - +
121G GLN 5.0 1.4 + - - -
122G MET* 3.8 30.1 + - + -
79H LEU* 3.3 24.8 + - + +
82H TYR* 3.5 35.0 - + + -
107H LEU* 3.0 18.9 + - + +
108H TYR* 3.7 29.4 - + + +
109H ASP 3.2 0.2 - - - -
110H GLY* 1.3 77.1 - - - +
112H ALA* 1.3 69.7 + - - +
114H MET* 3.3 28.4 - - + +
115H CYS* 3.0 39.2 + - - -
119H LEU* 4.3 7.2 - - + -
122H MET* 3.7 48.7 - - + -
123H LEU* 4.6 8.7 - - + -
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Residues in contact with ALA 112 (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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108H TYR 3.1 17.2 + - - +
111H TRP* 1.3 74.1 - - + +
113H GLN* 1.3 56.6 + - - +
115H CYS 3.1 1.4 + - - +
116H GLY 2.7 29.3 + - - -
117H LEU 3.1 28.6 + - - +
119H LEU* 3.7 19.1 - - + -
122H MET* 3.5 24.5 - - + -
351H GLY* 3.9 7.0 - - - -
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Residues in contact with GLN 113 (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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1H MET* 4.5 4.4 - - - +
42H ALA* 3.2 32.3 - - + +
43H VAL 3.3 19.7 + - - +
109H ASP* 2.7 50.5 + - - +
110H GLY* 3.5 9.8 - - - +
112H ALA* 1.3 73.1 - - - +
114H MET* 1.3 64.7 + - - +
116H GLY* 3.1 13.7 + - - -
350H PRO* 3.6 31.1 + - + +
351H GLY 4.1 0.6 - - - +
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Residues in contact with MET 114 (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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115G CYS 4.8 4.7 - - - +
117G LEU* 3.9 32.5 - - + -
1H MET* 3.6 46.1 - - + +
79H LEU* 3.9 22.4 - - + +
80H ALA* 4.7 1.6 - - - -
110H GLY 2.8 21.2 + - - +
111H TRP* 3.3 35.4 - - + +
113H GLN* 1.3 74.9 - - - +
115H CYS* 1.3 65.7 + - - +
116H GLY* 4.6 0.3 - - - -
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Residues in contact with CYS 115 (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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114G MET* 4.7 2.9 - - - +
115G CYS* 3.5 32.3 - - - -
117G LEU* 5.6 0.2 - - - -
122G MET* 3.7 25.1 - - - -
111H TRP* 3.0 26.2 + - - +
112H ALA 3.1 1.7 + - - +
114H MET* 1.3 88.8 - - - +
116H GLY* 1.3 61.2 + - - +
117H LEU* 3.5 5.2 + - - +
122H MET* 3.5 38.8 - - + -
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Residues in contact with GLY 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H ALA 2.7 8.1 + - - -
113H GLN 3.1 12.5 + - - -
114H MET 3.3 1.0 - - - -
115H CYS* 1.3 79.5 - - - +
117H LEU* 1.3 63.2 + - - +
118H PRO* 4.8 0.3 - - - +
350H PRO* 3.8 21.2 - - - +
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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
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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) + - + + + + + -
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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