Contacts of the helix formed by residues 119 - 143 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D THR* 2.9 17.8 + - - +
118D SER* 1.3 85.3 - - - +
120D ALA* 1.3 62.6 + - - +
121D ALA 3.3 3.1 - - - -
122D SER* 3.0 24.4 + - - -
123D LEU* 3.3 11.7 + - + +
170D GLU* 3.2 46.9 - - + +
173D ALA* 5.4 4.3 - - + -
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Residues in contact with ALA 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D TYR* 3.4 21.8 - - + +
113D LEU* 3.4 37.3 - - + +
114D ALA* 3.8 12.6 - - + +
117D THR* 3.2 8.1 + - - +
118D SER 3.2 3.6 + - - -
119D VAL* 1.3 77.3 - - - +
121D ALA* 1.3 60.5 + - - +
123D LEU* 3.6 11.8 + - - +
124D PHE 3.2 17.5 + - - -
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Residues in contact with ALA 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D TYR* 3.6 24.1 - - + +
118D SER 4.9 2.3 + - - +
119D VAL 3.2 0.8 + - - -
120D ALA* 1.3 74.8 - - - +
122D SER* 1.3 66.5 + - - +
124D PHE* 3.7 3.9 + - - +
125D LYS* 3.4 22.3 + - - +
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Residues in contact with SER 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119D VAL* 3.0 19.8 + - - -
121D ALA* 1.3 76.5 - - - +
123D LEU* 1.3 66.8 + - - +
125D LYS* 3.0 19.4 + - - +
126D LYS* 3.1 22.3 + - - +
170D GLU* 2.7 26.0 + - - -
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 3.6 30.5 - - + -
117D THR* 4.5 7.4 - - + +
119D VAL* 3.3 14.2 + - + +
120D ALA* 3.8 11.2 - - - +
122D SER* 1.3 77.9 + - - +
124D PHE* 1.3 53.1 + - - +
126D LYS* 2.9 8.4 + - + +
127D LEU* 2.7 50.2 + - + +
165D GLU* 3.6 24.7 - - + +
166D LEU* 4.6 6.7 - - + -
170D GLU* 4.0 15.7 + - + +
171D GLY* 3.6 38.1 - - - +
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Residues in contact with PHE 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D PRO* 4.4 3.8 - - + -
106D VAL* 3.4 32.5 - - + -
107D VAL* 3.4 31.4 - - + -
110D TYR* 3.5 43.9 - + + +
120D ALA 3.2 3.6 + - - -
121D ALA 3.8 7.6 - - - +
122D SER 3.2 0.4 - - - -
123D LEU* 1.3 76.3 - - - +
125D LYS* 1.3 73.9 + - + +
127D LEU* 3.4 2.9 + - - +
128D LEU* 2.9 50.7 + - + +
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Residues in contact with LYS 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D ALA 3.4 10.6 + - - +
122D SER* 3.0 11.9 + - - +
124D PHE* 1.3 87.9 - - + +
126D LYS* 1.3 64.9 + - + +
128D LEU* 3.6 8.7 + - + +
129D ALA* 3.2 22.7 + - - +
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Residues in contact with LYS 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D SER* 3.1 19.3 + - - +
123D LEU* 2.9 11.0 + - + +
125D LYS* 1.3 80.2 - - + +
127D LEU* 1.3 60.6 + - + +
129D ALA* 3.3 6.3 + - - +
130D GLY 2.9 24.9 + - - -
161D TYR* 3.3 29.6 - - + +
165D GLU* 3.0 38.3 + - + +
170D GLU* 3.9 26.9 + - + +
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Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D VAL* 3.9 18.6 - - + -
109D PHE* 4.8 16.2 - - + -
110D TYR 6.1 0.2 - - - +
113D LEU* 4.7 6.1 - - + -
123D LEU* 2.7 37.1 + - + +
124D PHE* 4.6 1.1 - - - +
126D LYS* 1.3 68.5 - - + +
128D LEU* 1.3 66.1 + - - +
130D GLY 3.4 0.2 + - - -
131D SER* 3.0 25.5 + - - -
162D MET* 3.6 59.5 - - + +
165D GLU* 5.1 5.8 - - + -
166D LEU* 3.8 31.2 - - + -
193D ILE* 4.7 0.4 - - + -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D PRO* 3.8 41.1 - - + -
106D VAL* 4.2 7.5 - - + +
124D PHE* 2.9 40.7 + - + +
125D LYS* 3.8 9.2 - - + +
127D LEU* 1.3 75.2 - - - +
129D ALA* 1.3 53.9 + - - +
131D SER* 2.7 23.7 + - - +
132D LEU* 2.8 44.5 + - + +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LYS 3.2 11.9 + - - +
126D LYS* 3.6 9.6 - - - +
128D LEU* 1.3 76.9 - - - +
130D GLY* 1.3 62.1 + - - +
132D LEU* 3.5 12.6 + - - +
133D VAL* 3.1 30.1 + - + +
161D TYR* 5.6 2.5 - - + -
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Residues in contact with GLY 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LYS 2.9 15.3 + - - -
127D LEU 3.8 2.2 - - - -
129D ALA* 1.3 74.7 - - - +
131D SER* 1.3 57.4 + - - +
133D VAL* 3.2 7.8 + - - +
134D MET* 2.9 22.9 + - - +
158D GLY* 3.5 26.5 - - - -
161D TYR* 4.0 16.7 - - - -
162D MET* 4.2 2.7 - - - -
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Residues in contact with SER 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D VAL* 3.7 28.9 - - - +
103D PRO* 5.4 0.7 - - - +
106D VAL* 4.4 2.0 - - - +
127D LEU 3.0 15.7 + - - -
128D LEU* 2.7 28.8 + - - +
130D GLY* 1.3 73.0 - - - +
132D LEU* 1.3 60.4 + - - +
134D MET* 3.3 10.3 + - - +
135D LEU* 2.9 36.5 + - - +
162D MET* 3.6 20.5 - - - -
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99D LEU* 4.1 26.2 - - + -
103D PRO* 5.2 4.3 - - + -
128D LEU* 2.8 50.3 + - + +
129D ALA* 3.7 9.9 - - - +
131D SER* 1.3 77.2 + - - +
133D VAL* 1.3 59.1 - - + +
135D LEU* 3.6 6.8 + - + +
136D GLY* 3.0 25.1 + - - -
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ALA* 3.1 15.7 + - + +
130D GLY* 3.4 10.3 - - - +
131D SER 3.2 0.2 - - - -
132D LEU* 1.3 75.8 - - + +
134D MET* 1.3 59.6 + - - +
136D GLY* 3.2 1.0 + - - -
137D ALA* 2.9 31.2 + - - +
154D ILE* 4.0 29.3 - - + +
157D ALA* 5.6 0.9 - - + -
158D GLY* 4.2 8.5 - - - +
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Residues in contact with MET 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D VAL* 6.3 0.9 - - - -
130D GLY 2.9 9.4 + - - +
131D SER* 3.3 13.4 + - - +
133D VAL* 1.3 78.8 - - - +
135D LEU* 1.3 59.6 + - - +
137D ALA* 3.8 2.1 + - - +
138D GLY 3.3 19.9 + - - -
155D GLY* 3.5 25.9 - - - +
158D GLY* 4.1 0.7 - - - -
159D TRP* 3.5 26.5 - - + +
162D MET* 3.4 33.7 - - - -
197D TRP* 4.1 5.6 - - + -
301D RET 3.2 63.8 - - + +
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Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D TYR* 3.5 13.0 - - + +
98D TRP* 3.8 59.7 - - + +
99D LEU* 4.0 17.5 - - + +
102D VAL* 4.3 14.8 - - + -
103D PRO* 5.5 1.3 - - + -
131D SER* 2.9 21.6 + - - +
132D LEU* 4.1 6.7 - - + +
134D MET* 1.3 78.6 - - - +
136D GLY* 1.3 60.3 + - - +
137D ALA 3.4 0.2 - - - -
139D PHE* 2.9 31.9 + - - +
301D RET 4.6 23.1 - - + -
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Residues in contact with GLY 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D LEU 3.0 18.6 + - - -
133D VAL* 3.2 1.8 + - - -
135D LEU* 1.3 73.6 - - - +
137D ALA* 1.3 64.7 + - - +
139D PHE* 3.4 5.0 + - - +
140D ALA* 3.0 25.5 + - - +
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D VAL 2.9 16.1 + - - +
136D GLY* 1.3 74.2 - - - +
138D GLY* 1.3 63.8 + - - +
140D ALA* 3.0 17.6 + - - +
141D GLY 3.0 10.4 + - - -
151D ALA* 3.3 29.4 - - - +
154D ILE* 3.7 17.0 - - + -
155D GLY* 3.3 20.2 - - - +
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Residues in contact with GLY 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D TYR* 3.1 17.0 - - - -
134D MET 3.3 8.8 + - - -
135D LEU 3.9 2.0 - - - -
137D ALA* 1.3 76.9 - - - +
139D PHE* 1.3 62.6 + - - +
141D GLY* 3.2 3.3 + - - -
142D GLU* 3.1 26.2 + - - +
151D ALA 4.3 1.1 + - - -
204D TYR* 3.9 8.5 - - - -
301D RET 3.6 22.7 - - - +
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Residues in contact with PHE 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ILE* 3.7 46.4 - - + -
91D THR* 3.7 20.9 - - + -
92D VAL* 4.4 13.7 - - + -
95D TYR* 3.4 40.6 - + + -
135D LEU 2.9 23.0 + - - +
136D GLY* 3.9 4.7 - - - +
137D ALA 3.2 0.2 + - - -
138D GLY* 1.3 71.6 - - - +
140D ALA* 1.3 56.7 + - - +
141D GLY 3.2 0.2 + - - -
142D GLU 3.2 0.5 + - - -
143D ALA* 2.8 56.9 + - + +
145D LEU* 4.8 11.4 - - + -
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Residues in contact with ALA 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D GLY 3.0 14.0 + - - +
137D ALA* 3.4 10.5 - - - +
139D PHE* 1.3 75.7 - - - +
141D GLY* 1.3 61.3 + - - +
143D ALA* 4.6 0.4 - - - -
144D GLY 3.2 1.7 + - - -
145D LEU* 2.8 45.6 + - + -
146D ALA* 3.1 26.0 + - + -
151D ALA* 5.0 1.1 - - + -
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Residues in contact with GLY 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ALA 3.0 9.7 + - - -
138D GLY 3.5 4.3 - - - -
139D PHE 3.1 0.2 - - - -
140D ALA* 1.3 76.4 - - - +
142D GLU* 1.3 60.3 + - - +
144D GLY* 3.2 14.0 + - - -
146D ALA 3.9 6.7 - - - +
148D VAL* 3.7 18.6 - - - +
151D ALA* 3.7 12.4 - - - +
204D TYR* 3.6 21.1 - - - -
208D TYR* 5.1 0.5 - - - -
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Residues in contact with GLU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D THR* 3.7 26.4 + - + +
95D TYR* 2.5 30.3 + - + +
138D GLY 3.1 16.2 + - - +
139D PHE 4.2 0.9 - - - +
141D GLY* 1.3 74.1 - - - +
143D ALA* 1.3 59.2 + - - +
144D GLY 3.2 1.6 + - - -
204D TYR* 3.8 6.4 - - + -
208D TYR* 2.6 53.8 + - + +
220D LEU* 3.7 8.3 - - - +
224D TYR* 2.3 34.2 + - - -
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Residues in contact with ALA 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 5.7 4.7 - - + -
91D THR* 4.5 3.5 - - - +
139D PHE* 2.8 48.3 + - + +
142D GLU* 1.3 72.7 - - - +
144D GLY* 1.3 62.3 + - - +
145D LEU* 3.2 25.8 + - + +
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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
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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