Contacts of the helix formed by residues 95 - 124 (chain K) in PDB entry 5JKL
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 95 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K TYR* 3.8 4.8 + - - -
41K PHE* 3.6 7.6 - - - -
46K VAL* 6.2 0.4 - - - -
93K TRP 2.9 7.6 + - - +
94K GLU* 1.3 77.7 + - - +
96K GLY* 1.3 65.1 + - - +
97K LEU 3.5 1.6 + - - -
98K ASN* 2.9 30.0 + - - +
99K ALA* 3.0 23.6 + - - +
161K PRO* 3.7 24.0 - - - +
167K GLU* 3.6 16.2 - - - -
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Residues in contact with GLY 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K PHE* 3.6 15.0 - - - -
48K LEU* 5.1 0.2 - - - -
51K PHE* 3.4 28.1 - - - -
95K SER* 1.3 71.2 - - - +
97K LEU* 1.3 60.9 + - - +
99K ALA* 3.4 3.6 + - - +
100K MET* 3.0 28.4 + - - +
155K LEU* 4.2 2.2 - - - -
167K GLU* 2.8 22.5 + - - -
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Residues in contact with LEU 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K SER* 4.0 3.6 - - - +
96K GLY* 1.3 75.5 - - - +
98K ASN* 1.3 62.8 + - - +
100K MET* 3.3 2.3 + - - +
101K GLU* 3.0 36.9 + - + +
152K VAL* 3.7 40.2 - - + +
155K LEU* 3.9 16.9 - - + +
156K ARG* 3.9 19.1 - - + +
160K ALA* 3.6 32.3 - - + +
161K PRO* 3.7 14.4 - - + -
167K GLU* 3.0 16.2 + - - +
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Residues in contact with ASN 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90K GLU* 5.6 3.8 - - - +
93K TRP* 2.9 32.8 + - - +
94K GLU* 3.5 25.9 + - + +
95K SER* 2.9 19.8 + - - +
97K LEU* 1.3 74.2 - - - +
99K ALA* 1.3 57.0 + - - +
101K GLU* 3.3 15.9 + - - +
102K GLU* 2.9 55.0 + - - +
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Residues in contact with ALA 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K MET* 3.4 16.6 - - - +
41K PHE* 3.6 28.5 - - + -
55K PHE* 4.0 11.9 - - + -
93K TRP* 3.8 13.8 + - + -
95K SER 3.0 18.6 + - - +
96K GLY 3.6 2.0 - - - +
97K LEU 3.3 0.2 - - - -
98K ASN* 1.3 74.1 - - - +
100K MET* 1.3 53.3 + - - +
102K GLU* 3.2 2.4 + - - -
103K ALA* 2.7 35.7 + - - +
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Residues in contact with MET 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51K PHE* 3.8 22.0 - - + -
54K TYR* 3.8 22.9 - - + -
55K PHE* 3.8 14.1 - - + -
96K GLY 3.0 22.0 + - - +
97K LEU 3.7 3.4 - - - +
99K ALA* 1.3 75.5 - - - +
101K GLU* 1.3 57.2 + - - +
103K ALA* 3.3 4.9 + - - +
104K LEU* 3.0 27.5 + - - +
148K LEU* 3.8 27.1 - - - +
151K HIS* 3.8 24.9 - - + -
152K VAL* 3.7 20.8 - - + +
155K LEU* 4.0 15.9 - - + -
170K PHE* 4.4 2.0 - - + -
175K LEU* 4.1 9.4 - - + -
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Residues in contact with GLU 101 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K LEU* 3.0 34.7 + - + +
98K ASN* 3.7 16.8 - - - +
100K MET* 1.3 73.2 - - - +
102K GLU* 1.3 61.5 + - + +
104K LEU* 3.3 8.0 + - + +
105K GLU* 3.0 39.9 + - - +
152K VAL* 3.9 22.2 - - + -
156K ARG* 2.7 37.4 + - - +
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Residues in contact with GLU 102 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37K MET* 3.8 16.4 - - + -
89K ASP* 4.9 10.2 - - - +
90K GLU* 4.6 12.4 - - - +
93K TRP* 3.7 20.1 - - + -
98K ASN* 2.9 40.9 + - - +
99K ALA 3.7 3.1 - - - +
101K GLU* 1.3 73.0 - - + +
103K ALA* 1.3 61.7 + - - +
105K GLU* 3.3 23.0 + - - +
106K LEU* 2.9 28.4 + - - +
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Residues in contact with ALA 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K TYR* 3.9 30.7 - - + +
37K MET* 3.8 8.7 - - + +
55K PHE* 4.3 5.6 - - + -
99K ALA 2.7 16.3 + - - +
100K MET 3.7 4.9 - - - +
101K GLU 3.2 0.4 - - - -
102K GLU* 1.3 75.3 - - - +
104K LEU* 1.3 60.6 + - - +
106K LEU* 3.2 6.6 + - - +
107K GLU* 2.9 33.4 + - - +
148K LEU* 3.7 15.5 - - + -
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Residues in contact with LEU 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K MET 3.0 13.5 + - - +
101K GLU* 3.3 11.9 + - + +
103K ALA* 1.3 75.4 - - - +
105K GLU* 1.3 65.2 + - + +
107K GLU* 3.3 2.1 + - - +
108K LYS* 3.0 41.4 + - + +
145K ILE* 3.7 41.1 - - + +
148K LEU* 3.8 14.5 - - + +
149K GLY* 4.2 18.6 - - - +
152K VAL* 4.5 15.0 - - + -
156K ARG* 6.3 0.4 - - - +
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Residues in contact with GLU 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101K GLU* 3.0 25.3 + - - +
102K GLU* 3.3 31.9 - - - +
103K ALA 3.3 0.2 - - - -
104K LEU* 1.3 78.5 - - + +
106K LEU* 1.3 61.6 + - - +
108K LYS* 3.4 7.9 + - + +
109K ASN* 3.0 36.2 + - - +
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Residues in contact with LEU 106 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K LEU* 5.4 1.3 - - + -
29K TYR* 4.1 30.3 - - + -
30K ALA* 4.0 20.4 - - + -
33K VAL* 3.8 33.9 - - + -
34K TYR* 4.1 23.3 - - + +
102K GLU 2.9 17.4 + - - +
103K ALA* 3.4 9.0 - - - +
105K GLU* 1.3 71.6 - - - +
107K GLU* 1.3 61.4 + - + +
109K ASN* 3.1 10.9 + - + +
110K VAL* 2.9 44.7 + - + +
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Residues in contact with GLU 107 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K ALA* 6.2 0.7 - - - -
34K TYR* 2.6 38.5 + - + +
58K GLN* 5.3 2.4 - - - +
62K GLU* 3.4 14.9 - - - +
103K ALA 2.9 19.6 + - - +
104K LEU 3.3 2.2 + - - +
106K LEU* 1.3 81.6 - - + +
108K LYS* 1.3 56.7 + - - +
110K VAL* 3.4 4.8 + - - +
111K ASN* 2.9 26.0 + - - +
141K GLN* 2.8 43.5 + - - +
144K ALA* 3.9 16.7 - - + +
145K ILE* 3.8 20.1 - - + +
148K LEU* 3.6 13.5 - - + -
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Residues in contact with LYS 108 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104K LEU* 3.0 36.6 + - + +
105K GLU* 3.8 8.5 - - + +
107K GLU* 1.3 73.2 - - - +
109K ASN* 1.3 63.7 + - - +
111K ASN* 3.3 2.9 + - - +
112K GLN* 2.9 29.1 + - - +
145K ILE* 4.0 29.8 - - + -
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Residues in contact with ASN 109 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K LEU* 4.6 5.2 - - + +
105K GLU* 3.0 28.6 + - - +
106K LEU* 3.1 10.5 + - + +
108K LYS* 1.3 76.9 - - - +
110K VAL* 1.3 65.0 + - + +
112K GLN* 3.3 9.0 + - - +
113K SER* 3.1 21.0 + - - -
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Residues in contact with VAL 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLN* 3.8 7.8 + - - +
26K LEU* 4.0 28.7 - - + +
27K GLU* 3.6 26.2 - - - +
30K ALA* 4.6 12.6 - - + -
62K GLU* 6.4 0.2 - - - -
106K LEU* 2.9 33.8 + - + +
107K GLU* 3.8 7.6 - - - +
109K ASN* 1.3 75.7 - - + +
111K ASN* 1.4 58.1 + - - +
113K SER* 3.2 5.2 + - - -
114K LEU* 2.9 28.2 + - + +
141K GLN* 3.8 19.5 - - - +
201K FE 4.5 3.4 - - - -
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Residues in contact with ASN 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K GLU 2.9 18.6 + - - +
108K LYS* 3.6 5.6 - - - +
109K ASN 3.3 0.2 - - - -
110K VAL* 1.4 75.8 - - - +
112K GLN* 1.3 56.9 + - - +
114K LEU* 3.2 3.1 + - - +
115K LEU* 2.8 50.6 + - - +
138K LEU* 4.2 17.5 - - - +
141K GLN* 3.4 30.0 - - + +
142K VAL* 5.0 9.7 - - - +
145K ILE* 3.9 19.4 - - + +
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Residues in contact with GLN 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108K LYS 2.9 17.6 + - - +
109K ASN* 3.5 9.9 - - - +
110K VAL 3.3 0.2 - - - -
111K ASN* 1.3 75.7 - - - +
113K SER* 1.3 55.3 + - - +
115K LEU* 3.3 18.0 + - - +
116K GLU* 2.9 65.1 + - - +
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Residues in contact with SER 113 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLN* 2.7 22.4 + - - -
26K LEU* 3.5 24.9 - - - +
109K ASN 3.1 9.1 + - - -
110K VAL 3.4 8.5 - - - -
112K GLN* 1.3 75.3 - - - +
114K LEU* 1.3 57.6 + - - +
116K GLU* 3.3 12.2 + - - +
117K LEU* 2.9 28.4 + - - +
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Residues in contact with LEU 114 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K GLN* 3.6 27.4 - - + +
27K GLU* 4.5 0.2 - - - +
69K LEU* 5.7 1.3 - - + -
110K VAL* 2.9 23.8 + - + +
111K ASN* 3.2 5.4 + - - +
113K SER* 1.3 74.5 - - - +
115K LEU* 1.3 60.4 + - - +
117K LEU* 3.3 15.3 + - + +
118K HIS* 2.9 27.0 + - - +
133K ILE* 4.1 10.0 - - + +
137K TYR* 3.9 41.5 - - + +
138K LEU* 3.9 14.1 - - + -
141K GLN* 3.4 37.2 - - + +
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Residues in contact with LEU 115 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K ASN* 2.8 43.2 + - - +
112K GLN* 3.7 20.4 - - - +
114K LEU* 1.3 74.0 - - - +
116K GLU* 1.3 59.4 + - - +
118K HIS* 3.3 6.2 + - + +
119K LYS* 3.0 27.7 + - - +
138K LEU* 4.0 27.1 - - + -
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Residues in contact with GLU 116 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112K GLN* 2.9 52.2 + - - +
113K SER* 3.7 9.8 - - - +
115K LEU* 1.3 74.6 - - - +
117K LEU* 1.3 62.5 + - - +
119K LYS* 3.4 13.5 + - + +
120K LEU* 3.0 22.9 + - - +
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Residues in contact with LEU 117 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K SER* 4.6 1.6 - - - +
19K ALA* 3.4 40.6 - - + +
20K ILE* 4.0 26.0 - - + +
23K GLN* 4.3 25.6 - - + +
69K LEU* 5.1 2.2 - - + -
113K SER 2.9 17.5 + - - +
114K LEU* 3.5 13.5 - - + +
115K LEU 3.2 0.2 - - - -
116K GLU* 1.3 76.7 - - - +
118K HIS* 1.4 55.5 + - - +
120K LEU* 3.3 9.2 + - + +
121K ALA* 3.0 28.4 + - - +
129K LEU* 5.0 6.1 - - + -
133K ILE* 3.6 24.9 - - + -
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Residues in contact with HIS 118 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K LEU 2.9 16.0 + - - +
115K LEU* 3.6 10.3 - - + +
116K GLU 3.3 0.2 - - - -
117K LEU* 1.4 72.5 - - - +
119K LYS* 1.3 59.9 + - - +
121K ALA* 3.3 3.7 + - - +
122K THR* 2.9 49.5 + - - -
130K CYS* 3.6 32.2 - - - +
133K ILE* 3.9 20.3 - - + +
134K GLU* 2.7 37.6 + - + +
138K LEU* 4.4 9.0 - - + -
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Residues in contact with LYS 119 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115K LEU 3.0 14.0 + - - +
116K GLU* 3.5 15.0 - - + +
118K HIS* 1.3 78.6 + - - +
120K LEU* 1.3 55.9 + - - +
122K THR* 3.2 7.5 + - + -
123K ASP* 2.9 51.9 + - - +
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Residues in contact with LEU 120 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K ASP* 3.6 38.8 - - + +
16K SER* 4.0 11.2 - - - +
19K ALA* 3.8 18.2 - - + -
22K ARG* 5.8 1.6 - - - +
116K GLU 3.0 13.7 + - - +
117K LEU* 3.5 10.5 - - + +
119K LYS* 1.3 74.2 - - - +
121K ALA* 1.3 59.6 + - - +
123K ASP* 3.2 9.4 + - + +
124K LYS* 2.8 58.0 + - + +
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Residues in contact with ALA 121 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16K SER* 4.8 1.8 - - - -
117K LEU 3.0 16.5 + - - +
118K HIS* 3.7 4.0 - - - +
120K LEU* 1.3 77.3 - - - +
122K THR* 1.3 61.1 + - - +
124K LYS* 3.5 3.3 + - - -
125K ASN 3.2 3.5 + - - -
126K ASP* 2.9 37.4 + - + +
129K LEU* 3.8 33.0 - - + -
130K CYS* 3.7 20.6 - - - +
133K ILE* 4.7 0.4 - - + -
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Residues in contact with THR 122 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118K HIS* 2.9 41.3 + - - -
119K LYS* 3.4 8.9 - - - -
120K LEU 3.2 0.2 - - - -
121K ALA* 1.3 76.9 - - - +
123K ASP* 1.3 64.5 + - - +
125K ASN* 3.0 26.4 + - - +
130K CYS* 3.5 8.2 - - - -
----------------------------------------------------------
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Residues in contact with ASP 123 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119K LYS* 2.9 50.7 + - - +
120K LEU* 3.5 11.0 - - + +
122K THR* 1.3 81.9 - - - +
124K LYS* 1.3 68.6 + - + +
125K ASN* 3.4 10.3 + - - -
----------------------------------------------------------
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Residues in contact with LYS 124 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K ASN* 4.3 8.5 - - - +
13K HIS* 3.8 49.4 + - + +
15K ASP* 3.7 22.9 + - - -
16K SER* 4.3 8.3 - - - +
120K LEU* 2.8 36.6 + - + +
121K ALA* 3.5 3.1 + - - +
122K THR 3.2 0.2 - - - -
123K ASP* 1.3 84.3 - - - +
125K ASN* 1.3 70.2 + - - +
126K ASP* 3.3 7.0 + - + +
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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