Contacts of the helix formed by residues 113 - 139 (chain K) in PDB entry 1F33
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 113 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55K ARG* 3.4 9.0 - - - +
56K GLY* 5.0 5.0 - - - -
57K ALA 5.6 0.9 + - - -
112K HIS* 1.3 80.8 - - - +
114K VAL* 1.3 68.1 + - - +
115K GLN* 2.8 47.1 - - - +
116K ASP* 3.1 35.5 + - - +
117K HIS* 3.2 11.4 + - - -
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Residues in contact with VAL 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K MET* 4.4 12.8 - - + -
55K ARG 2.9 37.5 + - - +
56K GLY* 3.8 6.1 - - - +
57K ALA 3.4 28.3 - - - +
58K ASN* 4.4 1.3 - - + +
59K PHE* 4.2 10.8 - - - -
62K VAL* 4.2 23.6 - - + -
112K HIS 4.1 1.3 - - - -
113K ASN* 1.3 74.4 - - - +
115K GLN* 1.3 63.5 + - + +
117K HIS* 3.2 4.7 + - - +
118K LEU* 2.8 46.7 + - + +
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Residues in contact with GLN 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57J ALA* 5.8 0.6 - - - +
57K ALA* 5.3 4.2 + - + +
58K ASN* 5.9 2.6 - - - +
113K ASN* 2.8 23.5 - - - +
114K VAL* 1.3 78.0 - - + +
116K ASP* 1.3 61.5 + - - +
118K LEU* 3.3 13.2 + - - +
119K LYS* 3.0 42.7 + - - +
165K ASN 3.2 21.6 + - - -
166K ILE* 3.3 14.2 - - - +
167K GLU* 2.8 52.7 + - + +
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Residues in contact with ASP 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K ILE* 4.1 29.5 - - + +
112K HIS 4.8 0.5 + - - -
113K ASN* 3.1 32.5 + - - +
115K GLN* 1.3 79.7 - - - +
117K HIS* 1.3 62.8 + - - +
119K LYS* 3.3 13.7 + - - +
120K GLU* 3.0 26.9 + - + +
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Residues in contact with HIS 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49K GLN* 4.6 2.2 - - - -
50K ALA* 3.4 20.3 - - + +
53K ASN* 3.4 18.2 + - + -
54K MET* 3.6 27.4 - - + -
107K TYR* 2.6 36.0 + + - +
108K PRO 4.9 1.3 - - - -
111K ILE* 3.2 41.0 + - + +
112K HIS* 3.3 23.8 - - - -
113K ASN 3.2 8.3 + - - -
114K VAL 3.2 7.3 + - - +
116K ASP* 1.3 76.1 - - - +
118K LEU* 1.3 56.4 + - - +
120K GLU 3.2 0.5 + - - -
121K LEU* 2.7 41.3 + - - +
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Residues in contact with LEU 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K MET* 5.0 1.1 - - + -
58K ASN* 5.7 0.7 - - + +
62K VAL* 3.8 28.3 - - + -
65K MET* 5.1 3.6 - - + -
114K VAL* 2.8 33.2 + - + +
115K GLN* 3.5 16.4 - - - +
116K ASP 3.3 0.2 - - - -
117K HIS* 1.3 79.2 - - - +
119K LYS* 1.3 56.5 + - - +
121K LEU* 4.5 9.4 - - + -
122K ALA* 2.8 25.5 + - - +
162K ILE* 3.3 39.9 - - + +
165K ASN* 3.7 34.1 - - + +
166K ILE* 3.9 10.1 - - + +
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Residues in contact with LYS 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG* 4.3 9.9 + - - +
115K GLN* 3.0 35.3 + - - +
116K ASP* 3.7 13.0 + - - +
118K LEU* 1.3 73.0 - - - +
120K GLU* 1.3 68.0 + - + +
122K ALA* 3.3 7.9 + - - +
123K ASP* 3.1 30.2 + - - +
166K ILE* 4.0 33.2 - - + -
167K GLU 5.7 0.4 - - - -
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Residues in contact with GLU 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K TYR* 3.5 21.1 - - + +
108K PRO* 3.9 11.5 - - + +
111K ILE* 3.7 20.9 - - + +
116K ASP* 3.0 20.3 + - + +
117K HIS 3.7 2.5 - - - +
119K LYS* 1.3 76.7 - - - +
121K LEU* 1.3 61.4 + - - +
123K ASP* 3.5 11.5 + - - +
124K ARG* 2.8 59.7 + - - +
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Residues in contact with LEU 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46K ILE* 3.9 27.1 - - + +
47K THR* 4.2 9.2 - - - -
50K ALA* 3.6 32.1 - - + -
66K LEU* 3.7 32.5 - - + -
107K TYR* 4.0 2.9 - - + +
117K HIS* 2.7 31.1 + - + +
118K LEU* 3.7 11.4 - - + +
120K GLU* 1.3 70.8 - - - +
122K ALA* 1.3 56.6 + - - +
124K ARG* 3.1 3.8 + - - -
125K TYR* 2.7 51.6 + - + -
162K ILE* 4.1 12.1 - - + -
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Residues in contact with ALA 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG* 3.4 36.3 - - - +
118K LEU 2.8 18.3 + - - +
119K LYS* 3.3 4.5 + - - +
121K LEU* 1.3 75.8 - - - +
123K ASP* 1.3 56.9 + - - +
125K TYR* 4.5 1.1 - - - -
126K ALA* 2.8 32.6 + - - +
159K LEU* 3.5 9.0 - - - +
162K ILE* 3.9 15.4 - - + +
163K GLU* 4.3 7.6 - - + -
166K ILE* 4.3 2.5 - - + -
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Residues in contact with ASP 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG* 2.8 29.4 + - - +
119K LYS* 3.1 14.3 + - - +
120K GLU* 3.6 16.3 - - - +
121K LEU 3.2 0.2 - - - -
122K ALA* 1.3 77.2 - - - +
124K ARG* 1.3 69.4 + - - +
126K ALA* 3.3 4.1 + - - +
127K ILE* 3.1 29.7 + - + +
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Residues in contact with ARG 124 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K LEU* 3.8 18.6 - - + -
46K ILE* 4.2 13.7 - - + +
104K LEU* 3.8 19.1 - - + +
105K LYS* 3.0 50.1 + - - +
106K SER 3.7 6.5 + - - -
107K TYR* 2.8 36.7 - - - +
108K PRO* 3.6 14.5 - - - +
120K GLU* 2.8 43.2 + - - +
121K LEU* 3.1 6.2 + - - +
123K ASP* 1.3 77.2 - - - +
125K TYR* 1.3 68.0 + - - +
127K ILE* 3.2 9.6 + - - +
128K VAL* 3.1 25.3 + - - +
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Residues in contact with TYR 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43K LEU* 3.5 34.5 - - + -
47K THR* 2.7 32.3 + - + +
66K LEU* 5.4 0.7 - - + -
69K PHE* 3.6 16.4 - + - +
73K LEU* 3.5 12.2 - - + +
121K LEU* 2.7 41.9 + - + +
122K ALA 3.8 2.9 - - - +
124K ARG* 1.3 72.9 - - - +
126K ALA* 1.3 54.0 + - - +
128K VAL* 3.3 1.0 + - - +
129K ALA* 2.6 40.3 + - - +
155K LEU* 4.2 8.7 - - + +
158K PHE* 3.7 37.9 - + + -
159K LEU* 4.2 13.2 - - + -
162K ILE* 3.5 27.8 - - + -
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Residues in contact with ALA 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG* 3.4 33.0 - - + -
122K ALA 2.8 19.3 + - - +
123K ASP* 3.4 6.3 - - - +
125K TYR* 1.3 77.0 - - - +
127K ILE* 1.3 55.1 + - + +
129K ALA* 4.2 0.2 - - - -
130K ASN* 2.7 47.4 + - - +
159K LEU* 3.9 15.0 - - + +
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Residues in contact with ILE 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K GLN* 4.3 10.8 - - - +
103K PRO* 4.5 17.3 - - + +
104K LEU* 3.9 23.3 - - + -
105K LYS* 5.5 3.1 - - + +
123K ASP* 3.1 19.2 + - + +
124K ARG* 3.2 11.9 + - - +
126K ALA* 1.3 76.5 - - + +
128K VAL* 1.3 62.9 + - - +
130K ASN* 4.1 4.2 - - - +
131K ASP* 3.0 27.6 + - + +
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Residues in contact with VAL 128 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K GLN* 3.3 36.3 - - + +
40K PHE* 3.7 27.8 - - + -
43K LEU* 3.9 18.8 - - + -
104K LEU* 3.9 17.5 - - + -
124K ARG 3.1 14.3 + - - +
125K TYR 3.9 4.0 - - - +
127K ILE* 1.3 74.7 - - - +
129K ALA* 1.3 59.5 + - - +
131K ASP* 3.7 0.5 - - - +
132K VAL* 2.9 30.3 + - - +
155K LEU* 3.6 20.6 - - + -
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Residues in contact with ALA 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125K TYR 2.6 24.8 + - - +
126K ALA* 3.7 6.1 - - - +
128K VAL* 1.3 74.3 - - - +
130K ASN* 1.3 62.6 + - - +
132K VAL* 3.2 9.5 - - - +
133K ARG* 3.0 30.5 + - - +
155K LEU* 3.9 23.5 - - + +
156K ASP* 3.7 17.9 - - - +
159K LEU* 4.4 10.1 - - + -
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Residues in contact with ASN 130 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ARG 3.0 20.6 + - - -
19I ASN* 3.5 4.0 - - - -
20I ASP* 2.7 38.4 + - - +
126K ALA* 2.7 31.3 + - - +
127K ILE* 4.2 3.3 - - - +
129K ALA* 1.3 73.1 - - - +
131K ASP* 1.3 63.4 + - - +
133K ARG* 2.4 35.5 + - - +
134K LYS* 3.3 30.8 + - - +
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Residues in contact with ASP 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35K ARG* 2.8 40.6 + - - -
36K GLN* 3.6 2.1 - - - +
39K GLN* 3.0 26.3 + - - +
103K PRO* 5.8 0.2 - - - +
127K ILE* 3.0 21.6 + - + +
128K VAL 3.7 2.5 - - - +
130K ASN* 1.3 73.9 - - - +
132K VAL* 1.3 67.3 + - - +
134K LYS* 3.0 11.6 + - - +
135K ALA* 3.0 16.5 + - - +
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Residues in contact with VAL 132 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K GLN* 3.6 27.8 - - - +
40K PHE* 4.3 19.7 - - + -
128K VAL 2.9 19.0 + - - +
129K ALA* 3.2 16.6 - - - +
131K ASP* 1.3 74.9 - - - +
133K ARG* 1.3 66.8 + - - +
135K ALA* 3.2 10.7 + - - +
136K ILE* 3.3 13.4 + - - +
148K LEU* 3.9 35.9 - - + +
151K ALA* 4.7 2.0 - - + -
152K SER* 4.0 20.2 - - - +
155K LEU* 4.8 3.6 - - + -
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Residues in contact with ARG 133 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ASN* 3.0 21.1 + - - +
20I ASP* 3.0 15.1 + - - -
21I VAL* 3.3 22.6 - - - +
83I ARG* 4.1 5.4 - - - +
141I ASP* 4.3 6.7 - - - +
142I ASP* 4.4 7.0 - - + +
143I ASP* 4.0 8.7 - - - +
129K ALA* 3.0 21.4 + - - +
130K ASN* 2.4 34.6 + - - +
131K ASP 3.2 0.2 - - - -
132K VAL* 1.3 77.9 - - - +
134K LYS* 1.3 65.2 + - + +
136K ILE* 3.4 23.5 - - + +
137K GLY 4.4 0.5 + - - -
152K SER* 3.6 14.8 - - - +
156K ASP* 2.5 43.6 + - - -
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Residues in contact with LYS 134 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ASP* 2.4 44.9 + - - -
130K ASN* 3.3 19.2 + - - +
131K ASP* 3.0 10.1 + - - +
133K ARG* 1.3 76.7 - - + +
135K ALA* 1.3 66.3 + - - +
136K ILE 3.0 3.7 + - - -
137K GLY* 3.1 12.6 + - - -
138K GLU* 3.3 14.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 135 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LEU* 3.9 19.6 - - + +
35K ARG* 4.3 4.0 - - - +
36K GLN* 3.6 23.3 - - - +
131K ASP 3.0 8.7 + - - +
132K VAL* 3.2 10.5 + - - +
134K LYS* 1.3 77.7 - - - +
136K ILE* 1.3 57.0 + - - +
138K GLU* 3.1 13.7 + - - +
139K ALA* 2.8 31.0 + - - +
148K LEU* 3.8 13.2 - - + +
----------------------------------------------------------
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Residues in contact with ILE 136 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I ASP* 3.8 27.8 - - + +
143I ASP* 3.5 25.8 - - - +
132K VAL 3.5 8.3 - - - +
133K ARG* 3.4 19.5 - - + +
134K LYS 3.0 0.2 - - - -
135K ALA* 1.3 77.4 - - - +
137K GLY* 1.3 62.3 + - - +
139K ALA* 3.2 20.7 + - - +
145K ALA* 4.0 14.3 - - + +
148K LEU* 3.9 22.4 - - + +
149K THR* 3.5 29.8 - - - +
152K SER* 3.7 12.1 - - - +
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Residues in contact with GLY 137 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I ASP* 4.4 9.6 + - - -
133K ARG 4.4 0.4 + - - -
134K LYS 3.1 7.4 + - - -
136K ILE* 1.3 81.9 - - - +
138K GLU* 1.3 59.7 + - - +
139K ALA 3.1 6.1 + - - +
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Residues in contact with GLU 138 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LEU* 3.6 30.3 - - + +
35K ARG* 3.8 12.7 + - - -
134K LYS* 3.3 12.8 + - - +
135K ALA* 3.1 13.3 + - - +
137K GLY* 1.3 77.0 - - - +
139K ALA* 1.3 60.4 + - - +
140K LYS* 3.5 12.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 139 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LEU* 4.1 11.4 - - + -
135K ALA 2.8 10.8 + - - +
136K ILE 3.4 16.6 - - - +
137K GLY 3.1 6.1 - - - +
138K GLU* 1.3 76.2 - - - +
140K LYS* 1.3 64.3 + - - +
141K ASP 4.4 1.1 - - - +
144K THR* 4.3 7.0 - - + -
145K ALA* 4.0 30.9 - - - +
148K LEU* 4.1 10.5 - - + -
----------------------------------------------------------
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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