Contacts of the helix formed by residues 54 - 77 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51K ALA 3.3 6.7 + - - +
52K GLY 4.3 1.2 - - - -
53K ALA* 1.3 80.2 - - - +
55K LYS* 1.3 63.4 + - - +
56K GLU* 3.6 17.8 + - - +
57K LYS* 3.2 32.5 + - - +
58K LEU* 3.3 19.9 + - - +
97K TRP* 4.4 5.8 - - - -
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Residues in contact with LYS 55 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54K SER* 1.3 73.4 - - - +
56K GLU* 1.3 74.4 + - - +
58K LEU* 3.4 5.1 + - + +
59K ILE* 3.0 40.9 + - + +
96K SER* 5.4 1.0 + - - -
97K TRP* 3.5 70.5 - - + +
100K GLU* 2.8 40.4 + - - +
101K VAL* 6.1 0.9 - - + -
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Residues in contact with GLU 56 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K SER* 3.2 19.0 - - - +
55K LYS* 1.3 96.3 + - - +
57K LYS* 1.3 57.1 + - + +
59K ILE* 3.6 11.2 + - + +
60K LYS* 3.1 29.9 + - - +
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Residues in contact with LYS 57 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50K GLU* 4.0 7.7 + - + +
51K ALA* 3.5 20.9 - - + +
53K ALA* 4.0 23.9 - - + +
54K SER* 3.2 19.6 + - - +
56K GLU* 1.3 74.7 - - + +
58K LEU* 1.3 59.4 + - - +
60K LYS* 3.6 6.0 + - - +
61K GLU* 3.0 29.5 + - - +
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Residues in contact with LEU 58 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47K PRO* 4.1 27.8 - - + -
51K ALA* 3.1 29.0 + - + +
52K GLY* 4.0 5.6 - - - -
54K SER 3.3 6.1 + - - +
55K LYS* 3.5 9.0 - - + +
57K LYS* 1.3 73.0 - - - +
59K ILE* 1.3 67.3 + - - +
61K GLU* 3.2 3.5 + - - +
62K TYR* 3.0 44.6 + - + -
88K VAL* 4.1 13.0 - - + -
90K GLN* 4.2 5.8 - - + +
91K MET* 4.0 18.2 - - + -
97K TRP* 4.0 31.2 - - + -
101K VAL* 5.0 4.3 - - + -
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Residues in contact with ILE 59 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K LYS* 3.0 43.5 + - + +
56K GLU* 3.9 10.3 - - + +
58K LEU* 1.3 73.4 - - - +
60K LYS* 1.3 58.8 + - - +
62K TYR* 3.1 4.4 + - - +
63K GLU* 2.8 40.4 + - - +
100K GLU* 4.0 22.2 - - + +
101K VAL* 4.1 30.0 - - + +
104K ALA* 3.8 24.7 - - + +
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Residues in contact with LYS 60 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257J LYS* 3.2 38.5 - - - +
258J HIS* 3.4 26.8 + - - +
56K GLU 3.1 16.6 + - - +
57K LYS* 3.6 7.9 - - - +
58K LEU 3.2 0.2 - - - -
59K ILE* 1.3 78.3 - - - +
61K GLU* 1.3 63.3 + - - +
63K GLU* 3.0 34.3 + - - +
64K ARG* 3.0 57.7 + - - +
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Residues in contact with GLU 61 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K PRO* 3.6 20.5 - - + +
48K ARG* 2.6 66.9 + - - +
51K ALA* 3.7 19.4 - - + +
57K LYS 3.0 18.0 + - - +
58K LEU* 3.2 5.4 + - - +
60K LYS* 1.3 74.1 - - - +
62K TYR* 1.3 58.7 + - - +
64K ARG* 3.3 12.2 + - - +
65K ILE* 3.0 38.3 + - + +
317K TYR* 3.9 8.7 - - + -
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Residues in contact with TYR 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K TYR* 3.7 37.2 + + - -
47K PRO* 3.2 32.4 - - + +
58K LEU* 3.0 37.8 + - + +
59K ILE* 3.1 4.9 + - - +
61K GLU* 1.3 76.8 - - + +
63K GLU* 1.3 53.9 + - - +
65K ILE* 3.5 11.5 + - + +
66K THR* 2.6 37.9 + - - -
85K THR* 4.0 11.4 - - + -
86K GLU 4.0 12.5 + - - -
88K VAL* 4.3 1.7 - - - +
91K MET* 3.6 33.6 - - + -
101K VAL* 3.5 31.4 - - + -
104K ALA* 6.3 0.7 - - + -
105K GLN* 4.3 10.3 - - + +
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Residues in contact with GLU 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258J HIS 5.9 2.2 - - - +
59K ILE* 2.8 27.2 + - - +
60K LYS* 3.0 35.0 + - + +
62K TYR* 1.3 73.8 - - - +
64K ARG* 1.3 59.4 + - + +
66K THR* 3.1 3.4 + - - -
67K THR* 2.8 36.0 + - - +
104K ALA* 3.6 27.3 - - + +
105K GLN* 5.7 0.7 - - - -
108K ILE* 3.6 24.5 - - + +
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Residues in contact with ARG 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216J GLN* 4.1 19.7 + - - +
217J ASP* 2.7 41.7 + - - -
257J LYS* 6.0 0.2 - - - +
258J HIS* 3.3 25.4 + - - +
48K ARG* 4.8 11.2 - - - +
60K LYS* 3.0 47.5 + - - +
61K GLU* 3.6 11.0 + - - +
63K GLU* 1.3 72.6 - - - +
65K ILE* 1.3 56.8 + - - +
67K THR* 3.3 5.2 + - - -
68K ASP* 2.8 41.4 + - - +
317K TYR* 3.5 26.2 - - + +
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Residues in contact with ILE 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45K TYR* 3.6 58.3 - - + -
47K PRO* 4.8 5.4 - - + -
61K GLU* 3.0 26.2 + - + +
62K TYR* 3.6 21.8 - - + +
64K ARG* 1.3 75.0 - - - +
66K THR* 1.3 67.5 + - - +
68K ASP* 3.4 1.9 + - - +
69K VAL* 3.1 26.8 + - + +
83K LEU* 4.9 0.2 - - + -
317K TYR* 3.5 45.5 - - + -
326K VAL* 4.3 7.6 - - + -
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Residues in contact with THR 66 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K TYR 2.6 23.1 + - - -
63K GLU 3.1 4.7 + - - -
65K ILE* 1.3 73.8 - - - +
67K THR* 1.3 65.2 + - - +
69K VAL* 3.4 1.9 + - - +
70K MET* 3.2 31.7 + - + +
83K LEU* 3.8 21.4 - - + +
105K GLN* 3.1 47.3 + - - +
108K ILE* 3.8 17.9 - - + -
109K MET* 3.9 13.2 - - + -
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Residues in contact with THR 67 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258J HIS 5.2 9.8 + - - +
63K GLU 2.8 23.1 + - - -
64K ARG* 3.8 5.8 - - - -
66K THR* 1.3 75.2 - - - +
68K ASP* 1.3 69.6 + - - +
69K VAL 3.2 0.2 + - - -
71K GLU* 3.0 30.5 + - + +
108K ILE* 3.6 23.9 - - - +
112K TYR* 4.0 18.7 + - + +
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Residues in contact with ASP 68 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K ARG* 2.8 20.7 + - - +
65K ILE 3.6 4.0 - - - +
67K THR* 1.3 82.1 - - - +
69K VAL* 1.3 62.1 + - - +
71K GLU* 3.9 1.7 - - - +
72K ARG* 3.2 12.1 + - - +
317K TYR* 2.4 33.0 + - - -
324K THR* 3.3 17.0 + - + +
326K VAL* 4.1 2.5 - - + -
327K GLN* 3.1 46.1 + - + +
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Residues in contact with VAL 69 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K ILE* 3.9 18.4 - - + -
65K ILE* 3.1 19.9 + - + +
66K THR 3.8 4.5 - - - +
67K THR 3.2 0.6 - - - -
68K ASP* 1.3 73.8 - - - +
70K MET* 1.3 62.9 + - - +
72K ARG* 3.2 6.0 + - - +
73K MET* 2.9 38.0 + - + +
81K ILE* 3.7 31.0 - - + -
83K LEU* 4.1 16.2 - - + -
326K VAL* 3.8 30.5 - - + +
327K GLN* 5.1 0.7 - - - -
330K SER* 4.7 7.7 + - - -
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Residues in contact with MET 70 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K THR* 3.2 24.5 + - + +
67K THR 4.1 0.2 - - - +
69K VAL* 1.3 75.3 - - - +
71K GLU* 1.3 62.4 + - - +
73K MET* 3.3 4.9 + - - +
74K VAL* 3.1 28.9 + - - +
81K ILE* 4.0 15.7 - - + -
83K LEU* 3.9 27.1 - - - -
108K ILE* 4.6 2.2 - - + -
109K MET* 4.6 10.5 - - - +
112K TYR* 3.4 40.4 - - + -
118K ILE* 3.7 31.4 - - + -
120K CYS* 4.0 19.7 - - - -
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Residues in contact with GLU 71 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234I LEU* 5.1 1.8 - - - +
67K THR* 3.0 22.1 + - + +
68K ASP* 3.9 5.4 - - - +
70K MET* 1.3 75.9 - - - +
72K ARG* 1.3 61.5 + - - +
74K VAL* 3.5 6.6 - - - +
75K GLN* 2.9 59.5 + - + +
112K TYR* 2.9 34.8 + - - +
116K TYR* 4.8 5.2 + - - -
327K GLN* 4.9 5.4 - - - +
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Residues in contact with ARG 72 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292I THR* 4.4 4.4 + - - -
295I HIS 4.5 0.2 - - - -
296I SER* 3.3 25.7 + - - +
68K ASP 3.2 16.5 + - - +
69K VAL 3.6 4.7 - - - +
71K GLU* 1.3 78.4 - - - +
73K MET* 1.3 68.2 + - - +
75K GLN* 3.2 15.3 + - - +
76K VAL* 3.3 19.1 + - + +
78K PHE* 5.8 0.7 - - + -
322K GLY 3.2 27.3 + - - -
323K GLY* 4.8 0.2 - - - -
327K GLN* 3.7 63.5 + - + +
328K CYS* 4.3 6.3 - - - +
330K SER* 4.4 6.5 - - - +
331K GLU* 2.8 33.2 + - + +
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Residues in contact with MET 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69K VAL* 2.9 25.4 + - + +
70K MET 3.6 5.8 - - - +
72K ARG* 1.3 76.3 - - - +
74K VAL* 1.3 61.1 + - - +
76K VAL 3.4 0.5 + - - -
77K GLY 3.1 4.0 + - - -
78K PHE* 3.1 77.0 + - + +
80K ALA 3.5 22.0 - - - +
81K ILE* 3.7 30.3 - - + -
118K ILE* 3.6 16.2 - - + -
330K SER* 4.3 19.3 - - - +
331K GLU* 5.1 0.4 - - - -
334K ALA* 3.9 14.4 - - + -
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Residues in contact with VAL 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I LEU* 4.1 5.7 - - - +
234I LEU* 3.7 23.9 - - + +
16J TYR* 3.3 36.5 - - + +
70K MET 3.1 18.1 + - - +
71K GLU* 3.5 13.9 - - - +
73K MET* 1.3 73.5 - - - +
75K GLN* 1.3 64.1 + - - +
76K VAL 3.1 6.4 + - - -
77K GLY* 3.4 2.3 + - - -
112K TYR* 4.2 4.3 - - + -
116K TYR* 3.9 41.3 - - + -
118K ILE* 4.1 22.4 - - + -
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Residues in contact with GLN 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I GLY* 3.3 21.1 - - - -
233I LEU* 2.8 28.8 + - - +
234I LEU* 2.9 46.7 + - + +
235I ASN* 3.8 14.6 + - - +
298I VAL* 5.3 1.6 - - - +
71K GLU* 2.9 49.1 + - + +
72K ARG* 3.2 12.8 + - - +
74K VAL* 1.3 76.2 - - - +
76K VAL* 1.3 62.8 + - + +
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Residues in contact with VAL 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232I GLY* 6.0 0.7 - - - -
233I LEU* 3.8 6.1 - - - -
296I SER* 3.5 24.7 - - - +
297I ASP 3.6 9.9 - - - +
298I VAL* 4.7 4.9 - - + -
363I ARG* 3.0 31.9 + - - +
72K ARG* 3.3 19.7 + - - +
74K VAL 3.1 0.8 - - - -
75K GLN* 1.3 82.7 - - + +
77K GLY* 1.3 60.5 + - - +
78K PHE* 3.4 31.4 - - + -
331K GLU* 3.8 7.9 - - - +
335K TYR* 3.5 28.0 - - + +
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Residues in contact with GLY 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I LEU* 3.6 8.7 - - - +
363I ARG* 3.7 3.8 - - - -
13J LEU* 3.3 11.1 - - - +
14J THR 2.9 47.6 + - - -
16J TYR* 3.7 8.3 - - - -
73K MET 3.1 3.4 + - - -
74K VAL 3.4 3.8 + - - -
76K VAL* 1.3 80.2 - - - +
78K PHE* 1.3 62.1 + - - +
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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