Contacts of the helix formed by residues 129 - 154 (chain D) in PDB entry 1FSK
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 LYS 129 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D THR* 6.4 0.7 - - + -
126D HIS* 3.8 21.2 - - + -
127D GLU* 3.3 37.1 + - - +
128D VAL* 1.3 72.1 - - - +
130D ALA* 1.3 54.8 + - - +
131D GLU* 2.4 33.8 + - + +
132D GLN* 2.8 24.5 + - + +
133D VAL 3.8 1.6 + - - -
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Residues in contact with ALA 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D VAL 2.8 9.7 + - - +
129D LYS* 1.3 68.8 - - - +
131D GLU* 1.3 66.5 + - - +
132D GLN 3.3 0.2 - - - -
133D VAL* 3.9 13.4 - - + +
134D LYS* 3.1 22.2 + - - +
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Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D LYS* 2.4 31.9 + - + +
130D ALA* 1.3 69.0 - - - +
132D GLN* 1.3 61.7 + - + +
134D LYS* 2.9 37.3 - - - +
135D ALA* 3.2 8.6 + - - +
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Residues in contact with GLN 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D PHE* 3.8 20.7 - - - -
90D PRO* 3.7 35.2 - - + +
95D LEU* 5.5 2.2 - - + -
98D ILE* 5.5 0.6 - - - +
120D TYR* 4.0 20.6 + - + -
128D VAL* 5.0 2.2 - - + -
129D LYS* 2.8 17.9 + - + +
131D GLU* 1.3 73.5 - - + +
133D VAL* 1.3 56.7 + - + +
134D LYS 2.5 16.7 + - - -
135D ALA* 2.8 23.1 + - - +
136D SER* 2.9 30.6 + - - +
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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
----------------------------------------------------------
5D TYR* 3.6 43.5 - - + +
120D TYR* 3.8 11.4 - - + +
128D VAL* 3.3 32.1 - - + -
130D ALA* 4.0 17.9 - - - +
131D GLU 3.5 0.4 - - - -
132D GLN* 1.3 74.0 - - - +
134D LYS* 1.3 59.7 + - - +
136D SER* 4.3 4.0 - - - -
137D LYS* 3.6 24.3 + - + +
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Residues in contact with LYS 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ALA 3.1 11.9 + - - +
131D GLU* 2.9 27.5 + - - +
132D GLN 2.5 4.6 + - - -
133D VAL* 1.3 72.2 - - - +
135D ALA* 1.3 62.9 + - - +
137D LYS* 3.1 20.4 + - - +
138D GLU* 3.0 44.2 + - - +
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Residues in contact with ALA 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D GLU 3.2 6.3 + - - +
132D GLN* 2.8 20.5 + - - +
134D LYS* 1.3 76.3 - - - +
136D SER* 1.3 56.3 + - - +
138D GLU* 2.8 13.0 + - - +
139D MET* 2.6 39.8 + - + +
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Residues in contact with SER 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D ILE* 5.8 1.6 - - - +
118D ASN* 5.0 12.3 - - - -
120D TYR* 2.9 27.2 + - - -
132D GLN* 2.9 21.9 + - - +
133D VAL* 4.3 3.8 - - - -
135D ALA* 1.3 76.9 - - - +
137D LYS* 1.3 60.5 + - - +
139D MET* 4.0 6.6 - - - +
140D GLY* 3.4 17.7 + - - -
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Residues in contact with LYS 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D THR* 3.6 40.9 - - + +
8D GLU 4.9 4.4 + - - -
133D VAL* 3.6 16.1 + - + +
134D LYS* 3.1 11.8 + - - +
135D ALA 2.9 0.6 - - - -
136D SER* 1.3 79.5 - - - +
138D GLU* 1.3 61.0 + - + +
140D GLY 4.0 0.5 - - - -
141D GLU* 2.9 50.9 + - - +
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Residues in contact with GLU 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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134D LYS* 3.0 46.9 + - + +
135D ALA* 2.8 14.2 + - - +
137D LYS* 1.3 72.5 - - + +
139D MET* 1.3 72.1 + - - +
141D GLU* 3.5 7.9 - - + -
142D THR* 2.8 32.0 + - + +
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Residues in contact with MET 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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37D ALA* 4.3 21.3 - - + -
38D ILE* 5.5 2.7 - - - -
58D PHE* 4.3 29.4 - - + -
62D LEU* 4.9 12.1 - - + -
63D PRO* 6.3 3.8 - - + -
135D ALA* 2.6 26.7 + - + +
136D SER* 4.0 7.0 - - - +
138D GLU* 1.3 76.7 - - - +
140D GLY* 1.3 63.3 + - - +
141D GLU 3.0 0.2 + - - -
142D THR* 3.3 11.2 + - - -
143D LEU* 3.3 28.6 - - + +
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Residues in contact with GLY 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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22D PHE* 4.6 6.8 - - - -
116D ILE* 6.1 4.4 - - - +
136D SER 3.4 13.3 + - - -
137D LYS 4.0 1.1 - - - -
139D MET* 1.3 80.7 - - - +
141D GLU* 1.3 63.8 + - - +
143D LEU* 3.9 12.5 - - - +
144D LEU* 3.2 21.0 + - - +
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Residues in contact with GLU 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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7D THR* 6.0 0.3 - - - +
9D THR* 4.1 11.1 + - - +
137D LYS* 2.9 45.5 + - - +
138D GLU* 2.9 15.6 + - + +
140D GLY* 1.3 74.3 - - - +
142D THR* 1.3 67.3 + - + +
144D LEU* 3.2 7.1 + - - +
145D ARG* 2.9 61.3 + - + -
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Residues in contact with THR 142 (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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34D ALA* 5.1 0.9 - - - +
36D GLN* 5.0 8.5 + - - -
37D ALA* 4.8 7.3 - - - +
138D GLU* 2.8 22.9 + - + +
139D MET* 3.3 6.9 + - - +
141D GLU* 1.3 74.7 - - + +
143D LEU* 1.3 70.4 + - - +
145D ARG* 2.7 14.7 + - - +
146D ALA* 2.6 35.8 + - - +
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D PHE* 3.9 15.5 - - + -
30D PHE* 4.4 21.3 - - + -
34D ALA* 3.7 26.0 - - + -
37D ALA* 4.1 14.4 - - + -
38D ILE* 4.1 25.6 - - + -
139D MET* 3.3 25.1 - - + +
140D GLY* 3.9 10.1 - - - +
141D GLU 3.2 0.4 - - - -
142D THR* 1.3 87.2 + - - +
144D LEU* 1.3 63.9 + - - +
146D ALA* 3.2 5.3 + - - +
147D VAL* 3.0 26.9 + - - +
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Residues in contact with LEU 144 (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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9D THR* 3.7 17.5 - - + +
10D THR 4.4 1.8 - - - +
11D SER* 4.7 0.7 - - - +
18D LEU* 4.0 26.0 - - + -
22D PHE* 3.7 20.1 - - + -
114D LEU* 3.6 39.3 - - + -
140D GLY 3.2 10.8 + - - +
141D GLU* 3.2 11.2 + - - +
143D LEU* 1.3 77.9 - - - +
145D ARG* 1.3 82.2 + - - +
147D VAL* 3.4 0.7 + - - +
148D GLU* 2.9 37.4 + - + +
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Residues in contact with ARG 145 (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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9D THR* 3.2 16.3 + - - -
10D THR 2.7 26.9 + - - -
141D GLU* 2.9 43.3 + - + +
142D THR* 2.7 17.7 + - - +
144D LEU* 1.3 83.2 - - - +
146D ALA* 1.3 62.9 + - - +
148D GLU* 2.6 50.5 + - - +
149D SER* 3.0 14.0 + - - -
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Residues in contact with ALA 146 (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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33D VAL* 3.8 36.9 - - + +
34D ALA* 4.1 12.6 - - + -
36D GLN* 5.9 0.9 - - - +
142D THR* 2.6 18.0 + - - +
143D LEU* 3.2 4.9 + - - +
145D ARG* 1.3 72.1 - - - +
147D VAL* 1.3 58.5 + - - +
149D SER* 2.6 22.2 + - - -
150D TYR* 3.3 11.6 + - - +
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Residues in contact with VAL 147 (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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18D LEU* 4.3 12.8 - - + -
21D ALA* 4.5 2.2 - - + -
22D PHE* 3.9 20.6 - - + +
29D LEU* 4.5 15.5 - - + -
30D PHE* 3.9 25.8 - - + -
33D VAL* 4.2 13.2 - - + -
143D LEU 3.0 17.4 + - - +
144D LEU 3.8 2.9 - - - +
145D ARG 3.0 0.8 - - - -
146D ALA* 1.3 76.8 - - - +
148D GLU* 1.3 56.5 + - - +
149D SER 3.2 0.2 - - - -
150D TYR* 3.7 4.4 - - - +
151D LEU* 2.7 62.7 + - + +
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Residues in contact with GLU 148 (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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11D SER* 2.6 41.2 + - - +
12D VAL* 3.8 7.8 + - - +
13D ILE* 3.8 16.2 - - + +
144D LEU* 2.9 21.1 + - + +
145D ARG* 2.6 52.9 + - - +
147D VAL* 1.3 76.2 - - - +
149D SER* 1.3 64.2 - - - +
151D LEU* 3.4 1.7 + - - +
152D LEU* 2.9 35.4 + - + +
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Residues in contact with SER 149 (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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145D ARG 3.0 6.4 + - - -
146D ALA* 2.6 23.3 + - - -
148D GLU* 1.3 78.1 - - - +
150D TYR* 1.3 71.6 + - - +
152D LEU* 2.7 23.2 + - - +
153D ALA* 2.9 15.1 + - - +
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Residues in contact with TYR 150 (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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29D LEU* 4.6 10.5 - - + -
32D LYS* 3.9 27.7 - - + +
33D VAL* 3.4 26.0 - - + -
146D ALA 3.3 14.7 + - - +
147D VAL* 3.7 4.7 - - + +
149D SER* 1.3 82.0 + - - +
151D LEU* 1.3 75.1 + - + +
152D LEU 3.0 0.3 + - - -
153D ALA* 4.6 2.0 - - - -
154D HIS* 3.0 74.0 + + + +
157D ALA* 4.6 4.5 - - + +
158D TYR* 4.4 19.1 - + - -
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Residues in contact with LEU 151 (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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13D ILE* 3.7 32.5 - - + -
17D ARG* 2.5 50.2 + - + +
18D LEU* 4.0 10.3 - - + -
21D ALA* 3.6 17.7 - - + -
29D LEU* 5.9 0.7 - - + -
147D VAL* 2.7 43.8 + - + +
148D GLU 3.5 4.3 - - - +
150D TYR* 1.3 79.3 - - + +
152D LEU* 1.3 62.2 + - - +
154D HIS 3.5 8.5 - - - -
157D ALA* 4.8 2.9 - - + -
158D TYR* 3.8 30.3 - - + -
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Residues in contact with LEU 152 (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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12D VAL* 4.4 25.1 - - + -
13D ILE* 4.5 7.0 - - + -
17D ARG* 4.8 1.1 - - - +
148D GLU* 2.9 27.4 + - + +
149D SER* 2.7 18.0 + - - +
151D LEU* 1.3 69.5 - - - +
153D ALA* 1.3 64.7 + - - +
154D HIS 3.1 3.2 + - - -
155D SER* 3.5 13.7 + - - -
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D SER 2.9 11.4 + - - +
150D TYR* 3.8 3.8 - - - +
152D LEU* 1.3 75.7 - - - +
154D HIS* 1.3 83.0 + - + +
155D SER* 3.6 2.9 + - - -
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Residues in contact with HIS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D ARG* 4.0 0.2 + - - -
150D TYR* 3.0 64.9 + + + +
151D LEU 3.5 6.6 - - - +
152D LEU 3.1 0.2 - - - -
153D ALA* 1.3 98.2 - - + +
155D SER* 1.3 50.9 + - - +
156D ASP* 2.8 12.0 + - - +
157D ALA* 2.8 36.7 + - + +
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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