Contacts of the helix formed by residues 119 - 143 (chain E) in PDB entry 4KNF
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 119 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E THR* 3.7 13.9 - - + +
118E SER* 1.3 85.0 - - - +
120E ALA* 1.3 62.1 + - - +
121E ALA 3.4 2.7 - - - -
122E SER* 3.3 8.8 + - - -
123E LEU* 3.0 27.2 + - + +
170E GLU* 3.6 46.0 - - + +
173E ALA* 3.7 18.2 - - + -
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Residues in contact with ALA 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR* 3.6 22.7 - - + -
113E LEU* 3.9 13.2 - - + +
114E ALA* 3.8 34.3 - - + +
117E THR* 3.9 8.8 + - - +
118E SER 3.4 3.8 + - - -
119E VAL* 1.3 76.3 - - - +
121E ALA* 1.3 56.9 + - - +
123E LEU* 3.2 9.2 + - - +
124E PHE* 2.9 24.3 + - - -
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Residues in contact with ALA 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E TYR* 3.9 17.8 - - + +
118E SER 5.3 0.4 + - - -
119E VAL 3.4 0.8 - - - -
120E ALA* 1.3 74.6 - - - +
122E SER* 1.3 64.5 + - - +
124E PHE* 3.3 12.7 + - - +
125E LYS* 3.3 33.6 + - - +
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Residues in contact with SER 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119E VAL* 3.3 9.6 + - - -
121E ALA* 1.3 78.3 - - - +
123E LEU* 1.3 61.7 + - - +
125E LYS* 3.4 11.6 + - - +
126E LYS* 3.0 31.7 + - - +
170E GLU* 3.0 34.0 + - - -
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Residues in contact with LEU 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E LEU* 3.9 34.1 - - + -
117E THR* 4.5 5.4 - - + +
119E VAL* 3.0 35.1 + - + +
120E ALA* 3.2 8.5 + - - +
122E SER* 1.3 77.2 - - - +
124E PHE* 1.3 55.4 + - - +
126E LYS* 3.3 3.9 + - + +
127E LEU* 2.8 44.8 + - + +
165E GLU* 3.5 39.0 - - + +
166E LEU* 4.7 4.3 - - + +
170E GLU* 4.0 17.5 - - + +
171E GLY* 4.3 13.5 - - - +
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Residues in contact with PHE 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PRO* 4.3 2.0 - - + -
106E VAL* 3.6 23.7 - - + +
107E VAL* 3.4 41.3 - - + -
110E TYR* 3.8 34.5 - + + +
113E LEU* 5.4 0.9 - - - +
120E ALA 2.9 17.1 + - - +
121E ALA* 3.3 9.1 + - - +
123E LEU* 1.3 72.4 - - - +
125E LYS* 1.3 71.1 + - + +
127E LEU* 3.8 2.3 - - - -
128E LEU* 2.9 55.6 + - + +
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Residues in contact with LYS 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E ALA* 3.3 27.5 + - - +
122E SER* 3.9 9.9 - - - +
123E LEU 3.4 0.2 - - - -
124E PHE* 1.3 84.9 - - + +
126E LYS* 1.3 65.6 + - + +
128E LEU* 3.9 5.3 - - - +
129E ALA* 3.1 24.4 + - - +
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Residues in contact with LYS 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122E SER* 3.0 21.0 + - - +
123E LEU* 3.6 7.0 - - - +
125E LYS* 1.3 77.2 - - + +
127E LEU* 1.3 57.9 + - - +
129E ALA* 3.1 7.4 + - - +
130E GLY 2.9 24.8 + - - -
161E TYR* 3.3 28.1 - - - +
165E GLU* 3.4 35.1 + - + +
170E GLU* 2.4 50.5 + - + +
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Residues in contact with LEU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E VAL* 4.0 15.6 - - + +
109E PHE* 4.8 16.6 - - + -
110E TYR 6.1 0.2 - - - +
113E LEU* 4.2 20.0 - - + -
123E LEU* 2.8 28.7 + - + +
124E PHE* 3.9 3.4 - - - +
126E LYS* 1.3 69.9 - - + +
128E LEU* 1.3 60.9 + - - +
130E GLY 3.5 0.2 + - - -
131E SER* 3.0 23.9 + - - -
162E MET* 3.4 61.2 - - + +
165E GLU* 4.6 8.3 - - + -
166E LEU* 4.1 27.4 - - + -
193E ILE* 4.9 1.1 - - + -
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Residues in contact with LEU 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PRO* 3.8 37.9 - - + +
106E VAL* 4.1 11.8 - - + +
124E PHE* 2.9 41.0 + - + +
125E LYS* 3.9 6.1 - - - +
127E LEU* 1.3 72.8 - - - +
129E ALA* 1.3 65.5 + - - +
131E SER* 2.9 23.9 + - - +
132E LEU* 3.0 31.3 + - + +
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Residues in contact with ALA 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E LYS 3.1 17.2 + - - +
126E LYS* 3.1 7.2 + - - +
128E LEU* 1.3 73.3 - - - +
130E GLY* 1.3 68.6 + - - +
131E SER 3.2 0.5 + - - -
132E LEU* 3.2 8.4 + - - +
133E VAL* 3.2 24.9 + - + +
161E TYR* 5.5 2.7 - - + -
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Residues in contact with GLY 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E LYS 2.9 14.0 + - - -
127E LEU 3.7 4.0 - - - -
129E ALA* 1.3 76.4 - - - +
131E SER* 1.3 54.9 + - - +
133E VAL* 3.3 2.4 + - - +
134E MET* 3.0 24.1 + - - +
158E GLY* 3.5 30.5 - - - -
161E TYR* 4.1 13.3 - - - -
162E MET* 4.0 6.1 - - - -
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Residues in contact with SER 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E VAL* 3.7 28.4 - - - +
103E PRO 5.1 0.5 - - - -
106E VAL* 4.4 2.9 - - - +
127E LEU 3.0 16.4 + - - -
128E LEU* 2.9 25.5 + - - +
130E GLY* 1.3 74.9 - - - +
132E LEU* 1.3 62.4 + - - +
134E MET* 3.2 14.2 - - - +
135E LEU* 3.0 31.6 + - - +
162E MET* 3.7 15.5 - - - -
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Residues in contact with LEU 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 3.7 30.7 - - + -
103E PRO* 4.9 12.8 - - + -
128E LEU* 3.0 32.8 + - + +
129E ALA* 3.2 6.3 + - - +
131E SER* 1.3 82.1 - - - +
133E VAL* 1.3 60.5 + - + +
135E LEU* 3.9 6.9 - - + +
136E GLY* 2.8 29.1 + - - -
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Residues in contact with VAL 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ALA 3.2 13.5 + - - +
130E GLY* 3.7 7.2 - - - +
132E LEU* 1.3 73.8 - - + +
134E MET* 1.3 67.9 + - - +
135E LEU 3.2 0.2 + - - -
136E GLY* 5.2 0.7 - - - -
137E ALA* 2.9 28.5 + - - +
154E ILE* 4.1 31.2 - - + +
157E ALA* 5.7 0.7 - - + -
158E GLY* 4.2 10.5 - - - +
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Residues in contact with MET 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E VAL* 4.4 7.2 - - + -
130E GLY 3.0 14.3 + - - +
131E SER* 3.2 25.1 - - - +
133E VAL* 1.3 78.9 - - - +
135E LEU* 1.3 64.8 + - + +
138E GLY 3.3 15.1 + - - -
155E GLY* 3.5 31.0 - - - +
158E GLY* 4.2 0.4 - - - -
159E TRP* 3.8 15.3 - - - +
162E MET* 3.4 28.9 - - + -
197E TRP* 4.0 6.7 - - + -
301E RET 3.3 62.9 - - + +
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Residues in contact with LEU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E TYR* 3.5 14.8 - - + +
98E TRP* 3.6 64.4 - - + +
99E LEU* 3.7 20.0 - - + +
102E VAL* 4.1 10.1 - - + -
131E SER 3.0 19.9 + - - +
132E LEU* 3.9 8.5 - - + +
133E VAL 3.2 0.2 - - - -
134E MET* 1.3 87.4 - - + +
136E GLY* 1.3 62.1 + - - +
137E ALA 3.2 1.3 - - - -
138E GLY 3.4 0.5 + - - -
139E PHE* 3.0 32.2 + - - +
301E RET 4.6 11.2 - - + -
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Residues in contact with GLY 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E LEU 2.8 19.9 + - - -
133E VAL* 3.9 1.1 - - - -
135E LEU* 1.3 72.4 - - - +
137E ALA* 1.3 60.9 + - - +
139E PHE* 3.8 7.7 - - - +
140E ALA* 3.1 24.8 + - - +
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Residues in contact with ALA 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E VAL 2.9 13.1 + - - +
136E GLY* 1.3 73.1 - - - +
138E GLY* 1.3 66.4 + - - +
140E ALA* 3.1 8.7 + - - +
141E GLY 3.1 18.7 + - - -
151E ALA* 3.4 17.7 - - - +
154E ILE* 3.8 14.6 - - + -
155E GLY* 3.2 36.3 - - - +
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Residues in contact with GLY 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E TYR* 3.3 16.4 - - - -
134E MET 3.3 8.3 + - - -
135E LEU 3.4 2.2 + - - -
137E ALA* 1.3 79.5 - - - +
139E PHE* 1.3 57.2 + - - +
141E GLY 3.4 0.9 + - - -
142E GLU* 3.0 31.7 + - - +
151E ALA 5.0 1.8 - - - -
204E TYR* 3.6 8.2 - - - -
301E RET 3.7 25.0 - - - +
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Residues in contact with PHE 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D ILE* 3.5 42.6 - - + -
91E THR* 4.0 14.1 - - + -
92E VAL* 4.4 17.9 - - + -
95E TYR* 3.5 39.9 - + + -
96E ILE* 6.1 1.8 - - + -
135E LEU 3.0 18.2 + - - +
136E GLY* 3.8 7.9 - - - +
138E GLY* 1.3 75.4 - - - +
140E ALA* 1.3 52.7 + - + +
142E GLU 2.8 5.0 + - - -
143E ALA* 2.6 56.1 + - + +
145E LEU* 4.2 14.1 - - + -
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Residues in contact with ALA 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E GLY 3.1 15.1 + - - +
137E ALA* 3.4 11.0 - - - +
139E PHE* 1.3 75.2 - - + +
141E GLY* 1.3 61.7 + - - +
144E GLY 3.3 1.4 + - - -
145E LEU* 2.8 51.4 + - + -
146E ALA* 3.1 22.8 + - + -
151E ALA* 4.9 1.3 - - + -
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Residues in contact with GLY 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E ALA 3.1 7.9 + - - -
138E GLY 3.6 1.3 - - - -
140E ALA* 1.3 77.5 - - - +
142E GLU* 1.3 62.6 + - - +
144E GLY* 3.1 14.6 + - - -
146E ALA 3.6 15.4 - - - +
148E VAL* 4.1 12.7 - - - +
151E ALA* 3.7 7.6 - - - +
204E TYR* 3.5 23.1 - - - -
208E TYR* 5.2 0.7 - - - -
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Residues in contact with GLU 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E THR* 4.9 1.2 - - - +
91E THR* 3.6 29.9 + - + +
95E TYR* 2.7 25.8 + - + +
138E GLY 3.0 19.7 + - - +
139E PHE 2.8 6.5 + - - +
141E GLY* 1.3 72.4 - - - +
143E ALA* 1.3 61.5 + - - +
144E GLY 3.3 0.9 + - - -
204E TYR* 3.7 5.2 - - + -
208E TYR* 2.5 55.9 + - + +
220E LEU* 4.1 8.0 - - - +
224E TYR* 2.5 31.9 + - - -
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Residues in contact with ALA 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ILE* 5.5 5.8 - - + +
91E THR* 4.3 4.6 - - - +
139E PHE* 2.6 47.2 + - + +
142E GLU* 1.3 72.2 - - - +
144E GLY* 1.3 59.3 + - - +
145E LEU* 3.4 24.2 - - + +
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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) + - + + + + + -
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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