Contacts of the helix formed by residues 102 - 128 (chain K) in PDB entry 1VEQ
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 VAL 102 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K VAL* 3.8 17.7 - - + -
43K VAL 3.1 12.0 + - - +
44K GLY* 3.9 13.0 - - - -
45K PRO* 4.8 1.3 - - + -
46K ASN* 3.6 37.2 - - - +
47K PHE 4.5 0.2 - - - +
50K VAL* 3.2 38.8 - - + -
101K THR* 1.3 76.5 - - - +
103K GLN* 1.3 73.4 + - + +
105K HIS* 3.2 2.1 + - - +
106K LEU* 3.1 32.6 + - + +
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Residues in contact with GLN 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F PRO* 4.4 20.5 - - - +
46K ASN* 4.7 3.8 + - - +
101K THR* 3.5 9.9 - - - +
102K VAL* 1.3 90.3 - - + +
104K ALA* 1.3 66.9 + - - +
106K LEU* 3.5 4.3 + - - +
107K ALA* 3.0 24.5 + - - +
155K HIS* 4.0 20.9 + - - +
156K LEU* 4.1 19.4 - - + +
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Residues in contact with ALA 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97K VAL* 4.8 6.7 - - + -
100K ASP* 3.5 28.9 - - + +
101K THR* 2.9 23.9 + - - +
102K VAL 3.1 0.2 + - - -
103K GLN* 1.3 77.2 - - - +
105K HIS* 1.3 66.4 + - - +
107K ALA* 3.3 4.9 + - - +
108K ALA* 3.0 21.0 + - - +
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Residues in contact with HIS 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K VAL* 4.0 20.3 - - + +
41K ASN* 3.2 19.5 + - + -
42K VAL* 3.7 22.9 - - + -
95K TYR* 2.6 39.5 + + - +
97K VAL* 3.0 29.8 - - + +
98K GLU 3.1 18.8 + - - -
100K ASP* 3.6 11.0 + - + -
101K THR 3.3 19.1 - - - -
102K VAL 3.2 6.0 + - - +
104K ALA* 1.3 78.0 - - - +
106K LEU* 1.3 55.3 + - + +
108K ALA* 2.9 3.3 + - - -
109K LEU* 2.6 37.1 + - - +
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Residues in contact with LEU 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K VAL* 6.4 0.7 - - + -
50K VAL* 3.9 11.4 - - + -
53K MET* 4.1 16.8 - - + -
54K ILE* 6.1 1.3 - - + -
102K VAL* 3.1 35.2 + - + +
103K GLN* 3.9 5.6 - - - +
105K HIS* 1.3 78.3 - - + +
107K ALA* 1.3 52.0 + - - +
109K LEU* 3.3 9.6 + - + -
110K ASP* 2.7 31.0 + - - +
152K VAL* 3.0 41.6 - - + +
155K HIS* 3.5 37.2 - - + -
156K LEU* 4.1 12.5 - - + +
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Residues in contact with ALA 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103K GLN 3.0 19.3 + - - +
104K ALA* 3.5 4.5 - - - +
106K LEU* 1.3 74.7 - - - +
108K ALA* 1.3 61.8 + - - +
110K ASP* 2.9 23.5 - - - +
111K LEU* 3.0 14.0 - - + +
156K LEU* 3.8 21.4 - - + +
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Residues in contact with ALA 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95K TYR* 3.6 23.3 - - + +
97K VAL* 4.1 12.8 - - + -
104K ALA 3.0 11.4 + - - +
105K HIS 2.9 7.5 + - - +
107K ALA* 1.3 76.1 - - - +
109K LEU* 1.3 60.5 + - - +
111K LEU* 3.3 15.7 + - - +
112K VAL* 3.0 24.4 + - - +
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Residues in contact with LEU 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K LEU* 5.6 0.4 - - + -
34K THR* 4.7 8.3 - - + -
35K LEU* 3.9 28.9 - - + -
38K VAL* 4.2 31.0 - - + -
54K ILE* 5.5 2.9 - - + -
95K TYR* 4.2 6.9 - - + -
105K HIS* 2.6 19.7 + - + +
106K LEU* 3.5 13.9 - - + +
108K ALA* 1.3 70.2 - - - +
110K ASP* 1.3 68.0 + - - +
112K VAL* 3.0 28.2 + - + +
113K TYR* 3.0 26.8 + - + -
148K PHE* 4.2 17.9 - - + -
152K VAL* 4.3 9.6 - - + -
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Residues in contact with ASP 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106K LEU 2.7 13.9 + - - +
107K ALA* 2.9 19.5 - - - +
109K LEU* 1.3 78.9 - - - +
111K LEU* 1.3 65.4 + - + +
113K TYR* 3.3 2.9 + - - +
114K ASN* 2.9 27.0 + - - +
149K GLN* 3.4 8.5 + - - +
152K VAL* 4.1 8.5 - - + +
153K ARG* 2.7 49.5 + - - +
156K LEU* 4.6 10.1 - - + +
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Residues in contact with LEU 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107K ALA* 3.0 20.6 - - + +
108K ALA* 3.3 11.4 + - - +
109K LEU 3.1 0.2 - - - -
110K ASP* 1.3 85.6 - - + +
112K VAL* 1.3 67.1 + - + +
114K ASN* 2.9 29.6 + - + +
115K GLY* 3.2 5.2 + - - -
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Residues in contact with VAL 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30K ASP* 5.0 11.0 - - - +
31K LEU* 4.6 16.6 - - + -
34K THR* 5.2 8.3 - - + -
92K TRP* 5.7 6.5 - - + -
95K TYR* 4.3 14.1 - - + -
108K ALA 3.0 20.4 - - - +
109K LEU* 3.0 24.9 + - + +
111K LEU* 1.3 74.6 - - - +
113K TYR* 1.3 64.2 + - + +
115K GLY* 3.3 3.2 + - - -
116K VAL* 3.1 29.7 + - + +
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Residues in contact with TYR 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31K LEU* 3.4 30.7 - - + +
35K LEU* 3.6 16.3 - - + +
57K GLN* 3.1 31.3 + - - +
109K LEU* 3.0 28.2 + - + +
110K ASP 3.6 4.0 - - - +
112K VAL* 1.3 74.7 - - + +
114K ASN* 1.3 57.0 + - - +
116K VAL* 4.1 5.8 - - + -
117K ILE* 2.7 41.6 + - + +
145K LEU* 3.5 43.7 - - + -
148K PHE* 3.4 31.0 - + - -
149K GLN* 3.4 27.8 - - + +
152K VAL* 5.5 1.3 - - + -
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Residues in contact with ASN 114 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110K ASP* 2.9 23.6 + - - +
111K LEU* 2.9 19.3 + - - +
113K TYR* 1.3 77.4 - - - +
115K GLY* 1.3 58.0 + - - +
117K ILE* 3.9 0.2 - - - -
118K GLU* 2.9 35.9 + - - +
149K GLN* 2.9 13.0 + - - -
153K ARG* 3.1 14.4 + - - +
7L PRO* 3.7 28.3 - - + +
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Residues in contact with GLY 115 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92K TRP* 4.2 14.5 - - - -
111K LEU 3.2 7.7 + - - -
112K VAL 3.3 5.1 + - - -
113K TYR 3.2 0.2 - - - -
114K ASN* 1.3 78.9 - - - +
116K VAL* 1.3 59.0 + - - +
118K GLU* 4.1 7.4 - - - -
119K ASP* 3.1 32.6 + - - +
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Residues in contact with VAL 116 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLN* 5.5 0.2 - - - +
27K THR* 3.9 31.2 - - + +
28K TYR* 4.7 7.9 - - + -
31K LEU* 4.6 31.6 - - + -
92K TRP* 4.7 7.4 - - + -
112K VAL* 3.1 21.3 - - + +
113K TYR* 3.0 11.5 + - + +
115K GLY* 1.3 78.6 - - - +
117K ILE* 1.3 60.2 + - + +
118K GLU 3.3 0.2 - - - -
119K ASP* 4.1 1.8 - - - +
120K THR* 2.7 40.3 + - - +
145K LEU* 4.7 16.2 - - + -
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Residues in contact with ILE 117 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113K TYR* 2.7 23.3 + - + +
114K ASN 4.0 2.0 - - - +
116K VAL* 1.3 70.2 - - + +
118K GLU* 1.3 60.2 + - - +
120K THR* 3.3 5.9 + - - -
121K ARG* 2.9 38.9 + - + +
142K ALA* 5.6 3.4 - - + -
145K LEU* 4.5 10.8 - - + -
146K GLU* 3.5 54.7 - - + +
149K GLN* 3.4 41.7 - - + +
6L ILE* 4.1 13.2 - - + -
7L PRO* 4.3 10.5 - - + +
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Residues in contact with GLU 118 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114K ASN* 2.9 20.8 + - - +
115K GLY* 4.4 5.5 - - - +
117K ILE* 1.3 74.6 - - - +
119K ASP* 1.3 71.6 + - - +
120K THR 3.0 1.2 + - - -
121K ARG* 3.1 5.3 + - + +
122K LYS* 3.1 22.7 + - - +
7L PRO* 3.8 31.8 + - + +
8L GLY* 5.0 3.3 + - - +
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Residues in contact with ASP 119 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K LYS* 3.4 32.9 + - + -
24K GLN* 4.7 7.0 - - - +
27K THR* 5.2 9.2 + - + +
91K THR* 5.1 4.3 + - - -
92K TRP* 5.0 10.5 - - - -
115K GLY* 3.1 24.8 + - - +
116K VAL* 4.1 3.8 - - - +
118K GLU* 1.3 83.7 - - - +
120K THR* 1.3 57.0 + - - +
122K LYS* 3.8 6.2 + - - +
123K SER* 3.1 31.1 + - - -
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Residues in contact with THR 120 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLN* 2.6 24.7 + - - +
28K TYR* 4.8 2.1 + - - +
116K VAL* 2.7 27.3 + - - +
117K ILE* 3.4 7.6 - - - +
118K GLU 3.0 0.4 + - - -
119K ASP* 1.3 74.1 - - - +
121K ARG* 1.3 68.9 + - - +
123K SER* 2.8 16.8 + - - -
124K ILE* 2.8 29.2 + - + +
138K LEU* 3.6 28.0 - - + +
141K HIS* 5.8 0.2 - - + -
142K ALA* 4.5 14.6 - - + +
145K LEU* 5.7 3.8 - - + +
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Residues in contact with ARG 121 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117K ILE* 2.9 29.1 + - + +
118K GLU* 3.5 5.8 - - + +
120K THR* 1.3 72.8 - - + +
122K LYS* 1.3 63.1 + - - +
124K ILE* 2.9 25.7 + - + +
125K GLU* 3.0 14.6 + - - +
142K ALA* 5.8 0.7 - - + -
146K GLU* 2.9 38.2 + - - -
6L ILE* 3.4 20.5 - - - +
7L PRO 4.2 11.0 - - - +
8L GLY* 5.1 11.1 + - - -
9L LEU* 4.2 19.7 - - - +
71L ARG* 3.7 5.7 - - - +
130L LEU 5.3 0.2 + - - -
131L ASP* 2.6 34.2 + - - +
132L LEU* 4.8 2.6 - - - +
133L VAL* 4.0 9.6 - - - +
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Residues in contact with LYS 122 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118K GLU 3.1 11.8 + - - +
119K ASP* 3.9 6.7 - - - +
121K ARG* 1.3 79.5 - - - +
123K SER* 1.3 63.8 + - - +
124K ILE 3.0 0.2 + - - -
125K GLU* 3.3 6.6 + - - +
126K LYS* 2.9 39.9 + - - +
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Residues in contact with SER 123 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 3.3 32.1 + - - +
23K LYS* 5.8 3.3 - - - +
24K GLN* 4.3 10.9 + - - -
119K ASP 3.1 14.3 + - - -
120K THR* 2.8 17.1 + - - -
122K LYS* 1.3 75.6 - - - +
124K ILE* 1.3 57.5 + - - +
126K LYS* 4.0 7.8 - - - +
127K LEU* 3.0 33.8 + - - +
138K LEU* 5.1 9.2 - - - -
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Residues in contact with ILE 124 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120K THR* 2.8 32.3 + - + +
121K ARG* 2.9 16.3 + - - +
123K SER* 1.3 73.8 - - - +
125K GLU* 1.3 60.1 + - - +
126K LYS 3.1 1.3 - - - -
127K LEU* 2.7 31.2 + - - +
128K GLU 3.2 8.8 + - - -
135K GLN* 3.5 27.2 + - + +
138K LEU* 4.1 15.3 - - + +
139K ILE* 3.9 37.2 - - + +
142K ALA* 4.4 8.3 - - + -
132L LEU* 4.5 13.7 - - + -
133L VAL* 4.9 7.2 - - + -
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Residues in contact with GLU 125 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121K ARG 3.0 7.3 + - - +
122K LYS* 3.8 9.4 - - - +
124K ILE* 1.3 80.9 - - - +
126K LYS* 1.3 61.8 + - - +
127K LEU 3.3 0.3 + - - -
128K GLU* 3.4 27.0 + - - +
129K ASP* 4.6 6.1 - - - +
135K GLN* 5.1 0.4 - - - +
132L LEU* 4.6 18.3 - - + +
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Residues in contact with LYS 126 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K LEU* 4.5 25.2 - - + +
122K LYS* 2.9 26.8 + - - +
123K SER* 4.0 7.2 - - - +
125K GLU* 1.3 77.9 - - - +
127K LEU* 1.3 61.0 + - - +
129K ASP* 4.1 10.1 + - - +
130K LEU* 3.6 18.7 - - + +
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Residues in contact with LEU 127 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K VAL* 3.9 29.4 - - + -
20K LEU* 4.1 12.3 - - + -
21K LEU* 5.0 7.0 - - + -
123K SER* 3.0 22.2 + - - +
124K ILE* 2.7 14.0 + - - +
126K LYS* 1.3 76.2 - - - +
128K GLU* 1.3 54.3 + - - -
129K ASP 2.8 13.0 + - - -
130K LEU* 2.8 32.3 + - + +
131K ASP 3.2 25.9 + - - +
134K SER* 3.2 28.9 - - - +
135K GLN* 4.2 9.4 - - + -
138K LEU* 4.6 11.4 - - + -
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Residues in contact with GLU 128 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J GLU* 4.1 14.0 - - - +
124K ILE 3.2 6.1 + - - -
125K GLU* 3.4 23.4 + - - +
127K LEU* 1.3 74.2 - - - +
129K ASP* 1.3 64.9 + - - +
130K LEU 5.2 0.4 - - - -
132K LEU* 4.5 22.9 - - + +
135K GLN* 3.3 30.1 + - - +
128L GLU* 4.0 19.0 - - - +
132L LEU* 4.7 15.0 - - + +
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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