Contacts of the helix formed by residues 96 - 116 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C THR 5.8 0.8 + - - -
57C ASP* 3.5 15.4 + - - +
61C SER* 3.9 30.1 + - - +
65C ALA* 4.0 2.3 - - - +
93C LEU* 3.6 29.8 - - + +
94C THR 3.0 20.4 + - - -
95C GLY* 1.3 72.0 - - - +
97C MET* 1.3 59.7 + - - +
98C SER 3.2 3.4 - - - -
99C ALA* 3.0 13.6 + - + +
100C LYS* 2.9 27.0 + - - +
52H LEU* 5.2 1.5 - - - +
56H GLY* 2.8 31.0 + - - +
61H SER* 5.6 0.3 - - - -
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Residues in contact with MET 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C THR* 5.5 5.6 + - + +
57C ASP* 3.6 5.6 + - - +
90C GLN* 4.0 9.6 - - - +
95C GLY* 3.8 23.8 - - - +
96C ASN* 1.3 77.7 - - - +
98C SER* 1.3 56.7 + - - +
100C LYS* 3.9 15.0 - - - -
101C ALA* 3.0 23.7 + - - +
248C PHE* 4.9 10.1 - - + -
249C THR* 4.1 21.1 - - + -
250C PRO* 6.5 0.2 - - + -
270C MET 3.2 17.6 - - - +
271C LYS* 3.4 23.8 - - - +
272C ALA 3.6 7.2 - - - +
273C GLY* 3.1 30.4 - - - +
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ALA* 3.2 22.6 - - - +
49C PRO 4.4 3.9 + - - -
51C THR* 4.4 0.3 + - - -
55C THR* 3.3 20.3 + - - +
57C ASP* 2.4 35.4 + - - +
62C ILE* 4.1 4.3 - - - -
97C MET* 1.3 75.7 - - - +
99C ALA* 1.3 61.9 + - - +
101C ALA* 3.4 1.7 + - - +
102C ALA 3.2 17.8 + - - -
270C MET* 3.5 27.8 - - - +
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Residues in contact with ALA 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C ASP* 4.5 0.4 + - - +
62C ILE* 3.9 31.3 - - + +
65C ALA* 3.8 28.9 - - + -
66C ILE* 4.3 6.2 - - + +
70C LEU* 4.5 5.2 - - + -
96C ASN* 3.0 13.9 + - + +
98C SER* 1.3 77.1 - - - +
100C LYS* 1.3 63.3 + - - +
101C ALA 3.4 0.5 + - - -
102C ALA* 3.5 2.2 + - - +
103C VAL* 3.4 27.9 + - - +
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Residues in contact with LYS 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C LEU* 4.4 4.7 - - + -
89C ILE* 3.4 39.3 - - + +
90C GLN* 3.3 33.5 + - - +
93C LEU* 2.6 39.5 + - + -
94C THR* 3.9 1.2 - - - +
95C GLY 2.5 37.1 + - - +
96C ASN* 2.9 15.1 + - + +
97C MET* 3.8 18.8 - - - +
98C SER 3.3 0.2 - - - -
99C ALA* 1.3 75.6 - - - +
101C ALA* 1.3 57.3 + - - +
103C VAL* 3.7 0.7 + - - +
104C GLU* 3.1 23.9 + - - +
273C GLY* 3.2 18.4 - - - +
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C MET 3.0 15.5 + - - +
98C SER 3.7 4.9 - - - +
99C ALA 3.2 0.6 - - - -
100C LYS* 1.3 76.3 - - - +
102C ALA* 1.3 60.3 + - - +
104C GLU* 3.2 1.9 + - - +
105C MET* 2.9 35.0 + - - +
269C LEU* 3.3 34.1 - - + +
270C MET* 3.8 12.6 - - + -
273C GLY 3.3 8.9 + - - -
274C GLY* 3.4 8.4 - - - +
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Residues in contact with ALA 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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32C VAL* 5.2 0.4 - - + +
34C VAL* 3.6 22.7 - - + +
46C GLY* 3.4 8.1 - - - -
47C GLU 3.3 36.3 - - - +
48C ALA* 3.8 4.7 - - + -
62C ILE* 5.5 0.2 - - + -
66C ILE* 4.9 3.1 - - + -
98C SER 3.2 14.6 + - - +
99C ALA* 4.0 3.8 - - - +
100C LYS 3.4 0.4 - - - -
101C ALA* 1.3 76.4 - - - +
103C VAL* 1.3 63.5 + - - +
105C MET* 3.3 18.1 + - - +
106C ALA* 3.4 6.4 + - - +
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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
----------------------------------------------------------
6C ILE* 5.5 3.4 - - + -
34C VAL* 4.5 14.4 - - + -
36C ILE* 3.8 7.0 - - + +
66C ILE* 3.6 34.5 - - + -
70C LEU* 4.0 16.6 - - + -
74C LEU* 3.7 30.5 - - + -
89C ILE* 3.9 17.3 - - + -
99C ALA 3.4 10.6 + - - +
100C LYS 3.9 3.1 - - - +
101C ALA 3.3 0.2 - - - -
102C ALA* 1.3 78.0 - - - +
104C GLU* 1.3 56.9 + - - +
106C ALA* 3.1 5.9 + - - +
107C LEU* 3.0 25.4 + - + +
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Residues in contact with GLU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 3.5 28.4 - - + +
89C ILE* 4.1 10.5 - - + -
90C GLN* 3.2 21.7 + - - +
100C LYS 3.1 19.7 + - - +
101C ALA 3.2 5.1 + - - +
103C VAL* 1.3 73.8 - - - +
105C MET* 1.3 64.0 + - - +
107C LEU* 3.6 5.3 - - - +
108C TYR* 3.0 39.6 + - - -
272C ALA 5.2 0.2 - - - +
273C GLY 3.2 7.8 - - - +
274C GLY* 3.7 8.8 - - - -
275C ILE* 2.8 24.8 + - - -
276C SER* 2.9 27.8 + - - -
277C GLY 4.6 0.3 + - - -
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Residues in contact with MET 105 (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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45C TRP 3.4 5.0 - - - +
46C GLY* 3.7 8.1 - - - -
47C GLU 3.4 26.9 - - - +
101C ALA 2.9 17.3 + - - +
102C ALA 3.4 6.1 - - - +
103C VAL 3.2 0.2 - - - -
104C GLU* 1.3 77.0 - - - +
106C ALA* 1.3 56.7 + - - +
108C TYR* 3.6 1.9 + - - +
109C ASP* 3.1 27.0 + - - +
119C LEU* 5.3 0.2 - - - +
269C LEU* 3.9 27.1 - - + -
270C MET* 3.4 33.7 - - + -
274C GLY* 5.9 0.2 - - - -
275C ILE* 4.8 9.8 - - + +
299C GLU* 4.1 3.6 - - - +
302C LEU* 5.0 1.3 - - - +
303C GLY* 4.1 23.6 - - - +
306C ALA* 3.8 23.8 - - + -
352C LEU* 4.1 5.2 - - - +
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 4.8 3.6 - - + +
36C ILE* 3.3 26.2 - - + +
38C TYR* 2.8 14.6 + - - -
44C GLY* 3.5 26.8 - - - +
45C TRP 3.3 18.4 - - - +
46C GLY* 4.0 2.5 - - - +
102C ALA 3.4 4.6 + - - +
103C VAL* 3.1 5.4 + - - +
105C MET* 1.3 77.2 - - - +
107C LEU* 1.3 60.8 + - - +
109C ASP* 3.6 2.3 - - - +
110C GLY 3.1 15.8 + - - -
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Residues in contact with LEU 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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3C ILE* 3.8 19.3 - - + -
36C ILE* 3.9 2.4 - - + +
38C TYR* 3.3 6.6 + - - +
74C LEU* 4.6 5.6 - - + -
79C LEU* 3.6 25.3 - - + +
82C TYR* 4.4 12.1 - - + +
85C ILE* 3.5 37.5 - - + -
86C LEU* 3.8 29.8 - - + -
89C ILE* 4.2 4.0 - - + -
103C VAL 3.0 15.3 + - - +
104C GLU* 3.3 7.2 + - - +
106C ALA* 1.3 76.2 - - - +
108C TYR* 1.3 62.5 + - + +
110C GLY* 3.3 1.9 + - - -
111C TRP* 2.9 30.1 + - + +
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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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82C TYR* 4.6 12.4 - + - -
86C LEU* 3.5 25.8 - - + +
104C GLU* 3.0 50.3 + - + +
105C MET 4.0 2.2 - - - +
107C LEU* 1.3 76.7 - - + +
109C ASP* 1.3 66.6 + - - +
111C TRP* 3.8 20.4 - + + +
112C ALA* 3.0 26.2 + - - +
119C LEU* 3.6 35.2 - - + +
123C LEU* 4.1 13.5 - - + -
275C ILE* 3.8 32.5 - - + +
276C SER* 3.2 23.9 - - - -
279C GLU* 4.5 6.4 + - - -
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Residues in contact with ASP 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C VAL 3.8 1.6 - - - +
44C GLY* 3.2 6.8 - - - -
45C TRP* 3.0 27.0 + - - +
105C MET 3.1 19.7 + - - +
106C ALA 3.6 7.2 - - - +
108C TYR* 1.3 79.3 - - - +
110C GLY* 1.3 57.4 + - - +
112C ALA 3.4 0.2 + - - -
113C GLN* 3.0 48.8 + - - +
119C LEU* 4.6 1.5 - - - +
351C GLY* 3.2 4.9 - - - -
352C LEU* 2.8 48.9 + - + +
354C ILE* 5.3 1.6 + - - +
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Residues in contact with GLY 110 (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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1C MET* 3.9 3.3 - - - +
38C TYR* 3.6 30.2 - - - -
44C GLY* 4.5 0.2 - - - -
79C LEU* 3.3 13.8 - - - +
106C ALA 3.1 8.3 + - - -
107C LEU 3.3 2.4 + - - -
109C ASP* 1.3 79.4 - - - +
111C TRP* 1.3 56.0 + - - +
113C GLN* 3.5 10.5 - - - +
114C MET* 3.1 23.7 + - - +
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Residues in contact with TRP 111 (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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79C LEU* 3.4 34.6 + - + +
82C TYR* 3.4 36.6 - + + -
107C LEU* 2.9 18.2 + - + +
108C TYR* 3.8 25.4 - + + +
109C ASP 3.3 0.4 - - - -
110C GLY* 1.3 75.9 - - - +
112C ALA* 1.3 73.3 + - - +
114C MET* 3.3 15.4 - - + +
115C CYS* 3.3 31.7 + - - -
119C LEU* 4.4 7.4 - - + -
122C MET* 3.5 52.5 - - + -
123C LEU* 4.5 11.0 - - + -
111D TRP* 4.5 7.9 - + - -
121D GLN 5.0 0.2 + - - -
122D MET* 3.8 34.6 - - + +
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Residues in contact with ALA 112 (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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108C TYR 3.0 17.4 + - - +
111C TRP* 1.3 75.4 - - - +
113C GLN* 1.3 60.6 + - - +
115C CYS* 3.1 3.0 + - - +
116C GLY 2.9 23.7 + - - -
117C LEU 3.2 27.7 + - - +
119C LEU* 3.7 26.5 - - + -
122C MET* 3.9 15.9 - - + -
351C GLY* 3.8 9.0 - - - -
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Residues in contact with GLN 113 (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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1C MET* 4.3 9.1 - - - +
38C TYR* 6.2 0.2 - - - -
42C ALA* 3.2 26.7 - - + +
43C VAL 2.8 28.8 + - - +
109C ASP* 3.0 39.9 + - - +
110C GLY* 3.5 8.1 - - - +
112C ALA* 1.3 75.0 - - - +
114C MET* 1.3 64.0 + - - +
116C GLY* 3.2 13.2 + - - -
349C LYS* 6.6 0.4 - - - -
350C PRO* 3.8 31.4 + - + +
351C GLY* 3.8 2.4 - - - +
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Residues in contact with MET 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.6 42.5 - - + +
78C SER* 5.9 0.2 - - - -
79C LEU* 3.8 25.4 - - + +
80C ALA* 4.4 3.4 - - - +
110C GLY 3.1 12.9 + - - +
111C TRP* 3.3 40.4 - - + +
113C GLN* 1.3 77.5 - - - +
115C CYS* 1.3 63.1 + - - +
116C GLY* 3.2 1.7 + - - -
115D CYS 5.2 2.4 - - - +
117D LEU* 3.6 35.2 - - + -
122D MET* 4.7 0.2 - - + -
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Residues in contact with CYS 115 (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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111C TRP* 3.3 19.5 + - - -
112C ALA 3.1 5.8 + - - +
114C MET* 1.3 86.1 - - - +
116C GLY* 1.3 61.8 + - - +
117C LEU* 3.4 5.1 + - - +
122C MET* 3.4 40.6 - - + -
114D MET* 4.6 5.0 - - - +
115D CYS* 3.6 31.4 - - + +
117D LEU* 4.7 0.9 - - - -
122D MET* 3.6 26.9 - - - -
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Residues in contact with GLY 116 (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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112C ALA 2.9 4.2 + - - -
113C GLN 3.2 9.8 + - - -
114C MET 3.1 5.6 - - - -
115C CYS* 1.3 78.7 - - - +
117C LEU* 1.3 68.4 + - - +
118C PRO* 4.8 0.2 - - - +
350C PRO* 3.9 18.7 - - - +
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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) + - + + + + + -
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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