Contacts of the helix formed by residues 54 - 77 (chain C) in PDB entry 2I2X
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 SER 54 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA 3.4 4.7 + - - +
52C GLY 4.3 0.9 - - - -
53C ALA* 1.3 79.2 - - - +
55C LYS* 1.3 63.2 + - - +
56C GLU* 3.3 13.4 + - - +
57C LYS* 3.0 34.4 + - - +
58C LEU* 3.1 19.2 + - - +
97C TRP* 4.1 10.3 - - - -
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Residues in contact with LYS 55 (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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54C SER* 1.3 72.6 - - - +
56C GLU* 1.3 82.0 + - - +
58C LEU* 3.2 5.1 + - - +
59C ILE* 2.9 43.1 + - + +
96C SER* 5.1 3.0 + - - -
97C TRP* 3.6 66.6 - - + +
100C GLU* 2.6 40.8 + - - +
101C VAL* 6.3 0.2 - - + -
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C SER* 3.2 11.0 + - - +
55C LYS* 1.3 106.7 + - - +
57C LYS* 1.3 66.1 + - + +
59C ILE* 3.9 12.9 - - + +
60C LYS* 3.1 25.1 + - - +
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Residues in contact with LYS 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C GLU 4.3 5.4 - - - +
51C ALA* 3.3 24.2 - - - +
53C ALA* 4.3 20.9 - - + +
54C SER* 3.0 23.0 + - - +
56C GLU* 1.3 78.4 - - + +
58C LEU* 1.3 56.8 + - - +
60C LYS* 3.4 6.0 + - - +
61C GLU* 3.0 28.4 + - - +
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO* 4.1 26.5 - - + -
51C ALA 3.0 25.7 + - - +
52C GLY* 3.7 7.6 - - - +
54C SER 3.1 6.9 + - - +
55C LYS* 3.4 8.5 - - + +
57C LYS* 1.3 73.2 - - - +
59C ILE* 1.3 65.2 + - - +
61C GLU* 3.2 3.0 + - - +
62C TYR* 3.1 43.6 + - + -
88C VAL* 4.2 7.2 - - + -
90C GLN* 4.1 12.8 - - + +
91C MET* 4.0 24.0 - - + -
97C TRP* 4.0 26.5 - - + -
101C VAL* 4.6 5.4 - - + -
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Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LYS* 2.9 34.1 + - + +
56C GLU* 3.9 10.8 - - + +
58C LEU* 1.3 76.2 - - - +
60C LYS* 1.3 62.8 + - - +
62C TYR* 3.3 3.6 + - - +
63C GLU* 3.0 38.7 + - - +
100C GLU* 4.0 31.9 - - + +
101C VAL* 4.2 26.7 - - + +
104C ALA* 3.7 26.3 - - + +
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Residues in contact with LYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LYS* 3.3 34.9 + - - +
258B HIS* 2.8 38.8 + - - -
56C GLU 3.1 18.4 + - - +
57C LYS* 3.6 7.2 - - - +
58C LEU 3.2 0.2 - - - -
59C ILE* 1.3 75.3 - - - +
61C GLU* 1.3 65.5 + - - +
63C GLU* 3.1 23.2 + - + +
64C ARG* 3.0 43.2 + - - +
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Residues in contact with GLU 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C PRO* 3.6 24.6 - - + +
48C ARG* 2.7 64.0 + - - +
51C ALA* 3.6 17.6 - - + +
57C LYS 3.0 17.5 + - - +
58C LEU 3.2 5.1 + - - +
60C LYS* 1.3 74.6 - - - +
62C TYR* 1.3 58.1 + - + +
64C ARG* 3.2 14.4 + - - +
65C ILE* 3.0 33.8 + - + +
317C TYR* 3.7 10.4 - - - -
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Residues in contact with TYR 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 3.6 37.6 + + - -
47C PRO* 3.4 35.0 - - + +
58C LEU* 3.1 34.5 + - + +
59C ILE 3.8 4.3 - - - +
61C GLU* 1.3 78.7 - - + +
63C GLU* 1.3 56.2 + - - +
65C ILE* 3.7 11.6 - - + +
66C THR* 2.6 37.6 + - - -
85C THR* 3.9 13.7 - - + -
86C GLU 4.0 12.8 + - - -
88C VAL* 4.5 2.3 + - - +
91C MET* 3.5 33.8 - - + +
101C VAL* 3.5 26.5 - - + -
104C ALA* 6.4 0.7 - - + -
105C GLN* 4.2 9.1 - - + +
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C ILE* 3.0 29.9 + - - +
60C LYS* 3.5 33.3 + - + +
62C TYR* 1.3 75.4 - - + +
64C ARG* 1.3 59.6 + - + +
66C THR* 4.4 0.2 - - - -
67C THR* 2.8 35.8 + - - -
104C ALA* 3.8 25.1 - - + +
105C GLN* 5.8 0.7 - - - -
108C ILE* 3.7 24.8 - - + +
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Residues in contact with ARG 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B GLN* 4.2 16.8 + - - +
217B ASP* 4.7 10.9 + - - -
257B LYS* 4.6 1.6 - - - +
258B HIS* 2.8 46.7 + - - +
48C ARG* 4.0 15.4 - - - +
60C LYS* 3.0 38.9 + - - +
61C GLU* 3.2 20.8 + - - +
63C GLU* 1.3 72.1 - - - +
65C ILE* 1.3 65.9 + - - +
67C THR* 4.6 3.1 - - - -
68C ASP* 3.0 32.6 + - - +
317C TYR* 3.4 22.9 - - + +
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C TYR* 3.5 49.6 - - + -
47C PRO* 4.7 5.2 - - + -
61C GLU* 3.0 29.6 + - + +
62C TYR* 3.7 28.3 - - + +
63C GLU 3.3 0.2 - - - -
64C ARG* 1.3 77.4 - - - +
66C THR* 1.3 65.8 + - - +
68C ASP* 3.2 1.7 + - - +
69C VAL* 3.0 30.2 + - + +
83C LEU* 4.9 0.9 - - + -
317C TYR* 3.3 44.0 - - + -
326C VAL* 4.3 7.2 - - + -
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Residues in contact with THR 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C TYR 2.6 23.9 + - - -
63C GLU 4.1 3.1 - - - -
65C ILE* 1.3 76.8 - - - +
67C THR* 1.3 62.8 + - - +
69C VAL* 3.5 1.2 + - - +
70C MET* 3.1 26.6 + - + +
83C LEU* 3.9 19.1 - - + -
105C GLN* 3.0 34.2 + - - +
108C ILE* 4.1 16.4 - - + -
109C MET* 3.7 32.5 - - + -
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Residues in contact with THR 67 (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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63C GLU 2.8 23.2 + - - -
64C ARG* 4.2 3.8 - - - -
66C THR* 1.3 76.9 - - - +
68C ASP* 1.3 61.7 + - - +
71C GLU* 2.9 35.3 + - + +
108C ILE* 3.4 26.3 - - + +
112C TYR* 3.9 19.2 + - + +
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Residues in contact with ASP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ARG* 3.0 22.4 + - - +
65C ILE 3.6 3.1 - - - +
67C THR* 1.3 82.8 - - - +
69C VAL* 1.3 60.6 + - - +
71C GLU* 3.9 2.6 - - - +
72C ARG* 3.2 11.1 + - - +
317C TYR* 2.4 24.2 + - - -
324C THR* 3.0 34.9 + - + +
326C VAL* 3.9 1.1 - - + -
327C GLN* 2.9 34.2 + - + +
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Residues in contact with VAL 69 (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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43C ILE* 3.9 14.6 - - + -
65C ILE* 3.0 22.9 + - + +
66C THR 3.8 3.1 - - - +
68C ASP* 1.3 74.9 - - - +
70C MET* 1.3 68.3 + - - +
72C ARG* 3.1 15.6 + - - +
73C MET* 3.1 16.0 + - + +
81C ILE* 3.3 34.5 - - + -
83C LEU* 3.9 20.0 - - + -
326C VAL* 3.7 34.1 - - + +
330C SER* 4.7 5.6 + - - +
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Residues in contact with MET 70 (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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66C THR* 3.1 25.6 + - + +
69C VAL* 1.3 72.5 - - - +
71C GLU* 1.3 69.0 + - - +
73C MET* 3.4 5.1 + - - +
74C VAL* 3.2 25.8 + - - +
81C ILE* 4.0 9.4 - - + -
83C LEU* 3.8 27.6 - - - -
108C ILE* 4.7 0.7 - - + -
109C MET* 4.2 13.5 - - + +
112C TYR* 3.5 38.9 - - + -
118C ILE* 3.8 37.9 - - + -
120C CYS* 3.9 22.0 - - - -
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Residues in contact with GLU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU* 4.9 2.3 - - - +
67C THR* 2.9 21.4 + - + +
68C ASP* 3.9 6.5 - - - +
70C MET* 1.3 79.7 - - - +
72C ARG* 1.3 62.1 + - - +
74C VAL* 3.4 6.7 + - - +
75C GLN* 3.0 55.8 + - + +
112C TYR* 2.9 34.7 + - - +
116C TYR* 4.8 4.3 + - - -
327C GLN* 4.7 6.1 - - - +
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Residues in contact with ARG 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A THR* 4.5 6.3 + - - -
296A SER* 3.4 26.7 + - - +
68C ASP 3.2 11.4 + - - +
69C VAL 3.1 9.7 + - - +
71C GLU* 1.3 80.8 - - - +
73C MET* 1.3 65.4 + - - +
75C GLN* 3.2 7.0 + - - -
76C VAL* 3.1 28.4 + - + +
78C PHE* 4.7 0.6 - - + -
322C GLY 3.2 28.1 + - - -
323C GLY* 4.8 0.4 - - - -
327C GLN* 3.6 63.8 + - + +
328C CYS* 4.3 3.0 - - - +
330C SER* 4.5 4.7 - - - +
331C GLU* 2.9 34.0 + - + +
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Residues in contact with MET 73 (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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41C PRO* 3.8 2.0 - - + -
69C VAL 3.1 18.4 + - - +
70C MET* 3.8 3.6 - - - +
71C GLU 3.3 0.2 - - - -
72C ARG* 1.3 78.0 - - - +
74C VAL* 1.3 57.4 + - - +
76C VAL 3.4 0.7 + - - -
77C GLY 3.0 23.0 + - - -
78C PHE* 3.0 52.4 + - + +
80C ALA 3.5 21.3 - - - +
81C ILE* 3.7 36.8 - - + -
118C ILE* 3.5 20.6 - - + -
330C SER* 4.3 20.2 - - - +
331C GLU* 5.1 0.4 - - - -
334C ALA* 3.6 19.3 - - + -
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Residues in contact with VAL 74 (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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233A LEU* 4.1 4.0 - - - +
234A LEU* 3.7 26.8 - - + +
16B TYR* 3.5 40.0 - - + +
70C MET 3.2 12.7 + - - +
71C GLU* 3.4 16.4 - - - +
73C MET* 1.3 77.2 - - - +
75C GLN* 1.3 61.1 + - - +
76C VAL 3.3 0.5 + - - -
77C GLY 3.5 2.1 + - - -
112C TYR* 4.1 7.2 - - + -
116C TYR* 3.7 46.9 - - + -
118C ILE* 4.1 16.6 - - + -
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Residues in contact with GLN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A GLY* 3.2 21.0 - - - -
233A LEU* 2.9 29.7 + - - +
234A LEU* 3.0 45.3 + - + +
235A ASN* 3.4 16.4 + - - +
296A SER* 5.9 0.4 - - - +
298A VAL* 5.1 1.6 - - - +
71C GLU* 3.0 49.7 + - + +
72C ARG* 3.2 11.1 + - - +
74C VAL* 1.3 77.8 - - - +
76C VAL* 1.3 62.3 + - + +
77C GLY 3.5 0.2 - - - -
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Residues in contact with VAL 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A GLY* 6.0 1.1 - - - -
233A LEU* 3.8 4.5 - - - -
296A SER* 3.5 24.2 - - - +
297A ASP 3.5 9.6 - - - +
298A VAL* 4.5 5.6 - - + -
363A ARG* 3.0 32.9 + - - +
72C ARG* 3.1 19.8 + - - +
75C GLN* 1.3 83.0 - - + +
77C GLY* 1.3 59.1 + - - +
78C PHE* 3.4 30.1 - - + -
331C GLU* 3.7 9.4 - - - +
335C TYR* 3.5 27.1 - - + +
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Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.6 9.2 - - - +
363A ARG* 3.9 3.6 - - - -
13B LEU* 3.4 10.8 - - - +
14B THR 3.0 45.3 + - - -
16B TYR* 3.8 6.5 - - - -
73C MET 3.0 5.1 + - - -
74C VAL 3.5 1.4 + - - -
75C GLN 3.5 2.8 - - - -
76C VAL* 1.3 82.6 - - - +
78C PHE* 1.3 63.3 + - - +
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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