Contacts of the helix formed by residues 92 - 119 (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 THR 92 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L PHE* 3.6 19.3 - - - -
44L LEU* 3.8 8.5 - - - +
47L VAL* 4.1 17.5 - - + +
91L ASN* 1.3 72.8 - - - +
93L LEU* 1.3 58.5 + - - +
95L ALA* 3.6 1.2 + - - +
96L MET* 3.0 39.7 + - + +
151L LEU* 4.1 7.9 - - + -
156L LEU* 4.0 7.6 - - - -
163L GLU* 2.8 30.5 + - + +
166L PHE* 3.8 34.1 - - + -
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Residues in contact with LEU 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91L ASN* 2.9 10.7 + - - +
92L THR* 1.3 75.3 - - - +
94L GLU* 1.3 61.4 + - - +
96L MET* 3.3 1.2 + - - +
97L GLN* 2.9 52.9 + - - +
148L ILE* 3.9 29.6 - - + +
151L LEU* 3.9 23.6 - - + -
152L LYS* 4.3 16.2 - - + -
156L LEU* 3.4 18.4 - - + +
157L PRO* 3.7 35.2 - - + -
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Residues in contact with GLU 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86L ARG* 3.0 39.6 + - - +
89L TRP 3.4 12.1 - - - +
90L GLY* 3.7 8.5 - - - -
91L ASN* 3.1 27.0 + - - +
93L LEU* 1.3 80.4 - - - +
95L ALA* 1.3 57.3 + - - +
97L GLN* 3.5 14.4 + - - +
98L ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L MET* 3.8 9.8 - - - +
37L PHE* 3.7 27.4 - - + -
51L PHE* 4.1 11.2 - - + -
89L TRP* 3.7 16.5 + - + -
91L ASN 3.0 17.8 + - - +
92L THR 3.9 2.5 - - - +
94L GLU* 1.3 75.6 - - - +
96L MET* 1.3 59.7 + - - +
98L ALA* 3.4 7.7 + - - +
99L ALA* 2.9 27.5 + - - +
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Residues in contact with MET 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47L VAL* 4.6 3.6 - - + -
50L PHE* 4.0 17.0 - - + -
51L PHE* 3.7 31.0 - - + -
92L THR* 3.0 27.6 + - + +
93L LEU 3.7 3.8 - - - +
95L ALA* 1.3 73.8 - - - +
97L GLN* 1.3 60.5 + - - +
99L ALA* 3.5 2.0 - - - +
100L LEU* 2.8 24.3 + - - +
144L ILE* 3.4 19.6 - - + +
147L PHE* 3.9 32.3 - - + -
148L ILE* 3.7 17.7 - - + +
151L LEU* 3.8 17.3 - - + -
166L PHE* 4.3 16.4 - - + -
171L VAL* 5.3 1.6 - - + -
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Residues in contact with GLN 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93L LEU* 2.9 43.4 + - + +
94L GLU* 3.8 15.3 - - - +
96L MET* 1.3 74.0 - - - +
98L ALA* 1.3 65.4 + - - +
100L LEU* 3.3 3.9 + - + +
101L GLN* 3.1 25.3 + - - +
148L ILE* 4.0 20.5 - - + +
152L LYS* 4.1 21.3 + - - -
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Residues in contact with ALA 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L MET* 4.0 4.2 - - + +
85L GLU* 5.4 3.6 - - - +
86L ARG* 5.6 2.9 - - - +
89L TRP* 3.8 32.3 - - + -
94L GLU 3.0 16.2 + - - +
95L ALA 3.5 8.5 - - - +
96L MET 3.3 0.2 - - - -
97L GLN* 1.3 74.4 - - - +
99L ALA* 1.3 57.6 + - - +
101L GLN* 3.4 6.6 + - - +
102L LEU* 3.0 27.8 + - - +
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Residues in contact with ALA 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L TYR* 3.9 27.6 - - + +
33L MET* 4.2 5.5 - - + +
51L PHE* 4.2 8.5 - - + -
95L ALA 2.9 17.7 + - - +
96L MET* 3.5 10.1 - - - +
98L ALA* 1.3 74.5 - - - +
100L LEU* 1.3 59.2 + - - +
102L LEU* 3.2 5.6 + - - +
103L GLU* 2.9 35.0 + - - +
144L ILE* 4.1 12.3 - - + -
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Residues in contact with LEU 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L MET 2.8 20.4 + - - +
97L GLN* 3.3 6.3 + - + +
99L ALA* 1.3 71.3 - - - +
101L GLN* 1.3 59.4 + - + +
103L GLU* 3.4 3.5 + - - +
104L LYS* 3.0 42.3 + - + +
141L ILE* 3.9 41.1 - - + +
144L ILE* 3.9 12.5 - - + +
145L GLY* 4.5 2.9 - - - +
148L ILE* 3.7 23.6 - - + -
3T GLN* 3.8 38.1 - - + +
4T VAL* 4.9 0.4 - - + -
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Residues in contact with GLN 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L GLN 3.1 12.6 + - - +
98L ALA* 3.7 8.7 - - - +
100L LEU* 1.3 75.7 - - + +
102L LEU* 1.3 60.7 + - - +
104L LYS* 3.2 10.1 + - - +
105L THR* 2.9 34.5 + - - +
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Residues in contact with LEU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L LEU* 5.4 1.8 - - + -
25L TYR* 4.1 26.9 - - + -
26L ALA* 3.9 25.1 - - + +
29L THR* 3.7 28.9 - - + -
30L TYR* 3.9 33.2 - - + +
33L MET* 5.2 0.2 - - + -
98L ALA 3.0 17.0 + - - +
99L ALA* 3.2 5.1 + - - +
101L GLN* 1.3 75.7 - - - +
103L GLU* 1.3 58.6 + - - +
105L THR* 3.4 10.2 + - + -
106L VAL* 3.1 35.9 + - + +
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Residues in contact with GLU 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L ALA* 6.5 0.4 - - - -
30L TYR* 2.8 28.9 + - - +
54L HIS* 3.6 14.6 + - - -
58L GLU* 3.4 12.6 - - - +
99L ALA 2.9 14.1 + - - +
100L LEU* 3.8 5.2 - - - +
102L LEU* 1.3 75.3 - - - +
104L LYS* 1.3 60.5 + - - +
106L VAL* 3.3 6.0 + - - +
107L ASN* 2.8 26.2 + - - +
137L GLN* 3.0 28.7 + - - +
140L ASP* 4.4 7.2 - - + -
141L ILE* 3.9 14.6 - - + -
144L ILE* 3.9 14.4 - - + -
177L MG 2.9 27.9 - - - -
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Residues in contact with LYS 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L LEU* 3.0 29.9 + - + +
101L GLN* 3.7 9.2 - - - +
103L GLU* 1.3 74.4 - - - +
105L THR* 1.3 57.8 + - - +
107L ASN* 4.1 0.9 - - - -
108L GLN* 2.9 26.0 + - - +
141L ILE* 4.2 12.1 - - + -
2T SER 5.0 0.8 + - - -
3T GLN* 2.9 30.6 + - - +
4T VAL 4.4 5.4 - - - +
5T ARG 3.5 17.0 + - - -
6T GLN* 3.1 44.2 + - + +
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Residues in contact with THR 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22L LEU* 4.6 19.3 - - + -
25L TYR* 6.5 0.7 - - + -
101L GLN* 2.9 20.6 + - - +
102L LEU* 3.5 12.3 - - + +
104L LYS* 1.3 77.3 - - - +
106L VAL* 1.3 63.1 + - - +
108L GLN* 3.4 6.8 + - - +
109L ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L MET* 5.1 2.2 - - - -
22L LEU* 3.9 29.6 - - + +
23L GLU* 4.0 9.9 - - - +
26L ALA* 4.2 24.5 - - + -
58L GLU* 4.9 0.4 - - - +
102L LEU* 3.1 20.3 + - + +
103L GLU* 3.7 10.1 - - - +
105L THR* 1.3 71.5 - - - +
107L ASN* 1.3 67.1 + - - +
109L ALA* 3.2 3.5 + - - +
110L LEU* 3.0 30.5 + - + +
137L GLN* 3.9 11.4 - - - +
176L MG 3.8 22.7 - - - -
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Residues in contact with ASN 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L GLU 2.8 21.2 + - - +
104L LYS 3.6 0.2 - - - +
106L VAL* 1.3 73.3 - - - +
108L GLN* 1.3 58.4 + - - +
110L LEU* 3.1 10.0 + - - +
111L LEU* 2.9 42.9 + - - +
134L LEU* 4.8 8.3 - - - +
137L GLN* 3.6 22.9 - - - +
138L VAL* 5.0 9.8 - - - +
141L ILE* 3.9 16.6 - - + +
6T GLN* 3.1 38.8 + - - +
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Residues in contact with GLN 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L LYS 2.9 18.1 + - - +
105L THR* 3.6 7.0 - - - +
107L ASN* 1.3 78.7 - - - +
109L ALA* 1.3 57.1 + - - +
111L LEU* 3.4 16.6 + - - +
112L ASP* 2.9 63.9 + - - +
6T GLN* 3.5 21.2 + - - +
7T ASN* 5.8 2.0 - - - +
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Residues in contact with ALA 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L MET* 3.1 20.7 - - + +
22L LEU* 3.7 22.9 - - + -
105L THR 3.1 13.8 + - - +
106L VAL 3.4 9.0 - - - +
108L GLN* 1.3 78.2 - - - +
110L LEU* 1.3 58.3 + - - +
112L ASP* 3.4 10.0 + - - +
113L LEU* 2.9 22.3 + - - +
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Residues in contact with LEU 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L MET* 3.7 24.7 - - + -
23L GLU* 4.9 1.1 - - - +
65L PHE* 4.0 21.5 - - + -
106L VAL* 3.0 26.0 + - + +
107L ASN* 3.1 6.7 + - - +
109L ALA* 1.3 75.4 - - - +
111L LEU* 1.3 60.8 + - - +
113L LEU* 3.4 3.3 + - - +
114L HIS* 2.9 26.5 + - - +
129L LEU* 4.2 13.8 - - + +
133L TYR* 3.9 31.9 - - + -
134L LEU* 3.9 15.5 - - + +
137L GLN* 3.7 31.2 - - + +
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Residues in contact with LEU 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107L ASN* 2.9 43.7 + - - +
108L GLN* 3.7 19.7 - - - +
110L LEU* 1.3 75.8 - - - +
112L ASP* 1.3 61.3 + - - +
114L HIS* 3.2 6.4 + - - +
115L LYS* 3.0 27.2 + - - +
134L LEU* 4.6 15.9 - - + -
6T GLN* 4.5 3.8 - - + +
7T ASN* 3.8 32.3 - - + +
123T PRO* 3.7 34.4 - - + +
124T HIS* 5.3 4.5 - - + +
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Residues in contact with ASP 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108L GLN* 2.9 49.4 + - - +
109L ALA* 3.4 9.2 - - - +
111L LEU* 1.3 76.8 - - - +
113L LEU* 1.3 61.1 + - - +
115L LYS* 3.3 8.6 + - - +
116L LEU* 3.0 25.8 + - - +
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Residues in contact with LEU 113 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L CYS* 4.3 8.7 - - - +
15L ALA* 3.5 31.9 - - + +
16L VAL* 4.3 17.0 - - + -
19L MET* 3.7 36.1 - - + -
65L PHE* 4.5 2.5 - - + -
109L ALA 2.9 16.7 + - - +
110L LEU* 3.7 4.9 - - + +
112L ASP* 1.3 75.4 - - - +
114L HIS* 1.3 58.3 + - - +
116L LEU* 3.4 9.4 + - + +
117L ALA* 3.0 25.6 + - - +
125L LEU* 4.4 10.1 - - + -
129L LEU* 3.9 26.2 - - + -
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Residues in contact with HIS 114 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110L LEU 2.9 15.8 + - - +
111L LEU* 3.3 12.6 - - - +
112L ASP 3.1 0.2 - - - -
113L LEU* 1.3 75.3 - - - +
115L LYS* 1.3 62.2 + - - +
117L ALA* 3.3 4.4 + - - +
118L THR* 2.9 42.2 + - - -
126L CYS* 3.6 31.1 + - - +
129L LEU* 3.8 17.4 - - + +
130L GLU* 2.9 25.1 + - - -
134L LEU* 4.2 6.7 - - + -
121T VAL* 6.1 0.8 - - - +
123T PRO* 3.5 35.3 - - + +
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Residues in contact with LYS 115 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111L LEU 3.0 12.7 + - - +
112L ASP* 3.5 11.4 - - - +
114L HIS* 1.3 74.8 + - - +
116L LEU* 1.3 60.9 + - - +
118L THR* 3.2 9.6 + - + +
119L ASP* 2.9 29.1 + - - +
121T VAL* 4.3 25.1 - - + -
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Residues in contact with LEU 116 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L ASP* 3.6 40.4 - - + +
12L CYS* 4.0 11.2 - - - -
15L ALA* 3.7 20.0 - - + -
18L ARG* 5.4 2.0 - - - +
112L ASP 3.0 13.8 + - - +
113L LEU* 3.6 11.4 - - + +
115L LYS* 1.3 76.4 - - - +
117L ALA* 1.3 56.5 + - - +
119L ASP* 3.3 5.4 + - + +
120L LYS* 2.9 50.7 + - + +
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Residues in contact with ALA 117 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12L CYS* 4.3 10.5 - - - -
113L LEU 3.0 14.3 + - - +
114L HIS* 3.5 10.1 - - - +
116L LEU* 1.3 73.5 - - - +
118L THR* 1.3 64.5 + - - +
120L LYS 3.5 0.7 + - - -
121L VAL 3.1 3.8 + - - -
122L ASP* 2.9 35.1 + - + +
125L LEU* 3.9 27.4 - - + -
126L CYS* 3.6 18.4 - - - +
129L LEU* 5.1 0.2 - - + -
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Residues in contact with THR 118 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114L HIS* 2.9 31.1 + - - -
115L LYS* 3.2 11.0 + - + +
117L ALA* 1.3 78.3 - - - +
119L ASP* 1.3 62.5 + - - +
121L VAL* 3.1 18.8 + - - +
126L CYS* 3.5 14.9 - - - -
121T VAL* 6.4 2.0 - - + -
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Residues in contact with ASP 119 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115L LYS 2.9 16.2 + - - +
116L LEU* 3.6 9.4 - - + +
118L THR* 1.3 78.8 - - - +
120L LYS* 1.3 72.8 + - + +
121L VAL* 3.2 9.4 + - - +
----------------------------------------------------------
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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