Contacts of the helix formed by residues 45 - 71 (chain L) in PDB entry 1MFR
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 HIS 45 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E LYS* 4.0 2.9 - - - -
146E ASP* 3.0 34.3 + - + -
37L PHE 4.6 1.6 - - - -
38L ASP* 3.4 44.7 + - - -
43L ALA* 3.3 15.1 + - - -
44L LEU* 1.3 69.6 - - - +
46L ASN* 1.3 66.6 + - - +
48L ALA* 3.5 6.1 - - - +
49L GLU* 3.1 30.2 + - + +
167L ASP* 3.6 3.8 + - - +
67V LYS* 5.0 4.9 + - - -
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Residues in contact with ASN 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L HIS* 1.3 77.3 - - - +
47L VAL* 1.3 65.8 + - - +
49L GLU* 3.3 9.6 + - - +
50L PHE 3.0 17.7 + - - -
167L ASP* 3.0 46.2 + - - +
168L LYS* 4.4 11.3 - - - +
171L VAL* 3.2 27.2 - - + +
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Residues in contact with VAL 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L PHE* 3.9 20.4 - - + -
44L LEU* 3.5 18.8 - - + +
46L ASN* 1.3 77.9 - - - +
48L ALA* 1.3 61.9 + - - +
50L PHE* 3.2 9.1 + - - +
51L PHE* 3.2 44.3 + - + -
92L THR* 4.1 25.8 - - + +
96L MET* 4.6 4.5 - - + -
163L GLU 5.8 0.2 - - - +
166L PHE* 4.3 13.0 - - + -
167L ASP* 3.1 23.0 + - + +
171L VAL* 4.6 4.5 - - + -
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Residues in contact with ALA 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L TYR* 3.2 39.6 - - + +
37L PHE* 3.7 25.0 - - + +
38L ASP* 4.1 4.5 - - + +
44L LEU 3.0 14.3 + - - +
45L HIS* 3.5 14.6 - - - +
46L ASN 3.2 0.2 - - - -
47L VAL* 1.3 76.8 - - - +
49L GLU* 1.3 57.2 + - - +
51L PHE* 3.4 2.3 + - - -
52L LYS 3.0 21.1 + - - -
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Residues in contact with GLU 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L TYR* 3.6 23.0 + - - -
45L HIS* 3.1 18.4 + - + +
46L ASN* 3.3 11.2 + - - +
48L ALA* 1.3 74.8 - - - +
50L PHE* 1.3 61.5 + - - +
52L LYS* 3.6 24.4 + - - +
53L GLU* 2.9 39.8 + - + +
67V LYS* 5.8 2.1 - - - -
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Residues in contact with PHE 50 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 5.9 0.4 - + - -
46L ASN 3.0 13.4 + - - +
47L VAL* 3.2 11.2 + - - +
49L GLU* 1.3 75.6 - - - +
51L PHE* 1.3 93.2 + + - +
53L GLU* 3.5 8.4 + - + +
54L HIS* 3.2 54.7 + + - -
96L MET* 4.0 20.9 - - + -
143L ARG* 3.9 18.4 - - - -
144L ILE* 4.5 12.1 - - + -
147L PHE* 3.7 29.2 - + - -
171L VAL* 3.7 19.0 - - + +
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Residues in contact with PHE 51 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 3.6 49.8 - + + +
33L MET* 3.8 29.6 - - + -
34L TYR 4.0 4.5 - - - +
37L PHE* 3.7 22.9 - + - -
47L VAL* 3.2 37.2 + - + -
48L ALA 3.9 5.6 - - - +
50L PHE* 1.3 98.8 - + - +
52L LYS* 1.3 59.0 + - - +
54L HIS* 3.2 4.5 + - + +
55L SER* 2.9 24.1 + - - -
95L ALA* 4.1 12.6 - - + -
96L MET* 3.7 23.1 - - + -
99L ALA* 4.2 9.0 - - + -
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Residues in contact with LYS 52 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L TYR* 3.7 39.2 + - + +
48L ALA 3.0 17.2 + - - +
49L GLU* 3.6 33.5 + - - +
50L PHE 3.3 0.2 - - - -
51L PHE* 1.3 77.2 - - - +
53L GLU* 1.3 63.6 + - + +
55L SER* 3.2 21.2 + - - +
56L HIS* 3.3 29.7 + - + +
63V GLU* 3.7 24.2 - - - +
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Residues in contact with GLU 53 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L GLU* 2.9 26.9 + - + +
50L PHE* 3.6 8.4 - - + +
51L PHE 3.2 0.2 - - - -
52L LYS* 1.3 78.6 - - + +
54L HIS* 1.3 63.3 + - + +
56L HIS* 3.3 10.0 + - - +
57L GLU* 3.1 36.1 + - - +
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Residues in contact with HIS 54 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 3.9 23.9 - + + -
50L PHE* 3.2 42.1 + + - +
51L PHE* 3.4 11.0 - - + +
53L GLU* 1.3 81.6 - - + +
55L SER* 1.3 63.1 + - - +
57L GLU* 3.6 17.9 + - - +
58L GLU* 3.2 32.4 + - - +
103L GLU* 3.6 18.2 + - - -
140L ASP* 3.7 26.2 - - + -
143L ARG* 3.1 27.3 + - - -
144L ILE* 4.9 4.0 - - + -
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Residues in contact with SER 55 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27L SER* 2.9 46.5 + - - +
30L TYR* 3.7 14.5 - - - +
31L SER* 3.8 15.3 + - - -
51L PHE 2.9 9.6 + - - -
52L LYS* 3.2 16.5 + - - +
53L GLU 3.3 0.2 - - - -
54L HIS* 1.3 73.8 - - - +
56L HIS* 1.3 76.1 + - - +
58L GLU 3.4 1.0 + - - -
59L ARG* 3.1 12.2 + - - +
63V GLU* 4.4 5.2 + - - -
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Residues in contact with HIS 56 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52L LYS* 3.3 34.8 + - + +
53L GLU* 3.3 11.9 + - - +
54L HIS 3.2 0.4 - - - -
55L SER* 1.3 91.0 + - - +
57L GLU* 1.3 56.1 + - - +
59L ARG* 3.5 8.2 + - + +
60L GLU* 3.1 25.6 + - - +
59V ARG* 6.1 2.9 - - + +
63V GLU* 3.1 29.6 + - - -
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Residues in contact with GLU 57 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L GLU* 3.1 21.5 + - - +
54L HIS* 3.6 25.5 + - - +
55L SER 3.2 0.2 - - - -
56L HIS* 1.3 75.4 - - - +
58L GLU* 1.3 64.7 + - + +
60L GLU* 3.2 7.2 + - + +
61L HIS* 3.0 46.3 + - + +
140L ASP* 4.1 18.2 - - - +
143L ARG* 5.8 1.7 + - - -
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Residues in contact with GLU 58 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L GLU* 2.7 30.8 - - - +
26L ALA* 4.2 9.2 - - + -
27L SER* 3.8 12.6 - - - -
30L TYR* 4.0 16.4 - - + -
54L HIS* 3.2 21.3 + - - +
55L SER 3.4 0.2 + - - -
57L GLU* 1.3 81.7 - - - +
59L ARG* 1.3 57.5 + - - +
61L HIS* 3.1 11.1 + - - +
62L ALA* 3.0 25.6 + - - +
103L GLU* 3.4 15.4 - - - +
106L VAL* 4.9 1.0 - - - +
176L MG 2.0 32.3 - - - -
177L MG 2.6 24.8 - - - -
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Residues in contact with ARG 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L LEU* 4.9 11.9 - - + -
27L SER* 3.6 13.9 + - - +
55L SER 3.1 17.5 + - - +
56L HIS* 3.6 10.3 - - + +
58L GLU* 1.3 74.5 - - - +
60L GLU* 1.3 64.0 + - - +
62L ALA* 3.2 8.6 + - - +
63L GLU* 3.1 36.4 + - + +
56V HIS* 6.0 2.5 - - + +
59V ARG* 5.7 9.2 - - + -
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Residues in contact with GLU 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56L HIS 3.1 15.7 + - - +
57L GLU* 3.6 10.8 - - - +
59L ARG* 1.3 75.3 - - - +
61L HIS* 1.3 59.9 + - + +
63L GLU* 3.5 12.6 + - - +
64L LYS* 3.1 32.4 + - - +
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Residues in contact with HIS 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L GLU* 3.4 15.3 - - - +
57L GLU* 3.0 29.5 + - + +
58L GLU* 3.1 18.2 + - - +
59L ARG 3.2 0.2 - - - -
60L GLU* 1.3 78.1 - - + +
62L ALA* 1.3 64.4 + - - +
64L LYS* 4.4 18.0 + - - +
65L PHE* 3.3 12.7 + - - -
132L GLU 4.6 7.0 + - - -
133L TYR* 3.0 40.2 + + + -
136L GLU* 5.1 15.0 - - + +
137L GLN* 5.1 0.9 - - - -
140L ASP* 5.6 0.4 - - - -
176L MG 2.7 23.8 - - - -
177L MG 4.3 10.5 - - - -
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Residues in contact with ALA 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LEU* 3.7 16.6 - - + +
23L GLU* 3.8 9.8 - - + +
24L LEU* 3.7 34.8 - - + -
58L GLU 3.0 12.5 + - - +
59L ARG 3.2 9.4 + - - +
61L HIS* 1.3 74.4 - - - +
63L GLU* 1.3 64.1 + - + +
65L PHE* 3.3 8.9 + - - +
66L MET* 3.1 26.2 + - + +
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Residues in contact with GLU 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L LEU* 6.4 0.4 - - + -
59L ARG* 3.1 24.6 + - + +
60L GLU* 3.8 12.6 - - - +
61L HIS 3.3 0.2 - - - -
62L ALA* 1.3 75.1 - - + +
64L LYS* 1.3 64.0 + - - +
66L MET* 3.2 24.9 + - + +
67L LYS* 3.1 24.7 + - - +
31V SER* 4.9 4.5 + - - -
34V TYR* 5.1 11.4 - - + -
52V LYS* 3.6 20.9 + - - +
55V SER* 4.5 4.3 + - - -
56V HIS* 3.0 36.2 + - - -
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Residues in contact with LYS 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60L GLU* 3.1 20.2 + - - +
61L HIS* 3.6 18.0 + - - +
62L ALA 3.3 0.2 - - - -
63L GLU* 1.3 76.5 - - - +
65L PHE* 1.3 57.3 + - - +
67L LYS* 3.5 7.6 + - - +
68L TYR* 2.9 27.2 + - - +
128L PHE* 3.7 10.5 - - + -
132L GLU* 2.9 52.7 + - + +
133L TYR* 3.2 21.3 - - + +
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Residues in contact with PHE 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16L VAL* 3.9 29.9 - - + +
19L MET* 3.4 33.2 - - + -
20L LEU* 4.2 18.2 - - + -
23L GLU* 4.1 15.0 - - + -
61L HIS 3.3 16.7 + - - -
62L ALA 3.3 8.4 + - - +
63L GLU 3.2 0.6 - - - -
64L LYS* 1.3 77.4 - - - +
66L MET* 1.3 64.3 + - - +
68L TYR* 3.5 3.6 - + + +
69L GLN* 3.0 24.4 + - - +
110L LEU* 4.0 11.2 - - + -
113L LEU* 4.5 7.2 - - + -
125L LEU* 5.3 0.2 - - + -
128L PHE* 3.5 25.4 - + - -
129L LEU* 4.0 12.1 - - + -
133L TYR* 3.4 30.3 - + - -
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Residues in contact with MET 66 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L LEU* 3.8 29.6 - - + +
24L LEU* 5.1 7.6 - - + -
62L ALA* 3.1 21.5 + - + +
63L GLU* 3.2 23.7 + - + +
65L PHE* 1.3 75.6 - - - +
67L LYS* 1.3 62.4 + - - +
69L GLN* 3.4 4.7 - - - +
70L ASN* 3.3 27.4 + - - -
76L VAL* 3.9 20.1 - - + +
78L LEU* 4.7 8.5 - - + -
28V TYR* 5.6 0.2 - - + -
31V SER* 3.4 39.7 - - - +
34V TYR* 4.5 17.0 - - + -
35V ALA* 4.4 12.1 - - + -
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Residues in contact with LYS 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63L GLU 3.1 10.0 + - - +
64L LYS* 3.6 11.0 - - - +
66L MET* 1.3 79.5 - - - +
68L TYR* 1.3 57.6 + - - +
70L ASN* 3.5 3.6 + - - +
71L LYS* 3.0 43.2 + - + +
142M LYS* 6.0 0.6 - - - +
34V TYR* 3.4 28.5 - - - +
38V ASP* 3.2 31.9 + - - +
45V HIS* 5.1 5.1 + - - -
49V GLU* 5.8 1.3 - - - -
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Residues in contact with TYR 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L TYR* 3.9 19.1 - + - -
16L VAL* 4.6 8.3 - - + -
64L LYS 2.9 18.5 + - - +
65L PHE* 3.5 6.5 - - - +
66L MET 3.2 0.2 - - - -
67L LYS* 1.3 74.0 - - - +
69L GLN* 1.3 67.8 + - - +
71L LYS* 3.1 17.2 + - + +
72L ARG* 2.8 52.1 + - + +
124L HIS* 2.8 41.2 + + - -
125L LEU* 3.2 36.3 - - + +
128L PHE* 3.6 42.8 - + + -
135M GLU* 5.3 0.4 - - - -
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Residues in contact with GLN 69 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8L TYR* 3.0 36.1 + - - -
13L GLU* 3.2 27.8 + - - +
16L VAL* 3.5 13.9 - - + +
17L ASN* 3.4 19.0 + - - -
20L LEU* 5.8 0.6 - - + +
65L PHE 3.0 14.6 + - - +
66L MET* 3.4 6.7 - - - +
68L TYR* 1.3 82.9 - - - +
70L ASN* 1.3 61.3 + - - +
72L ARG* 3.2 5.0 + - - +
73L GLY 3.1 3.6 + - - -
74L GLY* 2.9 43.2 + - - +
75L ARG 4.0 6.1 - - - -
76L VAL* 3.7 24.0 - - + +
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Residues in contact with ASN 70 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L VAL* 4.5 0.7 - - - +
66L MET 3.3 13.3 + - - -
67L LYS 3.9 4.0 - - - +
68L TYR 3.3 0.2 - - - -
69L GLN* 1.3 76.1 - - - +
71L LYS* 1.3 65.4 + - - +
73L GLY* 3.2 10.0 + - - -
74L GLY 3.9 12.4 - - - +
75L ARG* 4.0 2.4 + - - +
76L VAL* 4.6 9.0 + - - +
142M LYS* 3.3 17.6 - - - +
34V TYR* 6.3 0.2 - - - -
35V ALA* 3.1 29.5 + - - +
38V ASP* 3.1 38.8 + - - +
39V ARG* 3.4 27.7 - - - +
40V ASP* 5.0 3.5 + - - +
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Residues in contact with LYS 71 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L VAL* 3.4 17.3 - - - +
67L LYS* 3.0 29.4 + - + +
68L TYR* 3.1 22.8 + - + +
70L ASN* 1.3 76.0 - - - +
72L ARG* 1.3 61.2 + - + +
124L HIS* 5.4 0.2 - - + -
128L PHE* 6.2 2.6 - - - -
135M GLU* 2.8 36.0 + - - +
138M VAL* 4.2 25.7 - - + +
139M LYS* 4.5 12.5 - - - +
142M LYS* 4.1 28.2 - - + +
----------------------------------------------------------
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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
------------------------------------------------------------
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