Contacts of the helix formed by residues 132 - 154 (chain A) in PDB entry 1P4X
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 ASP 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASP* 3.4 18.2 - - + +
115A ILE* 3.5 13.6 - - - +
130A PRO 3.6 0.6 - - - -
131A LYS* 1.3 83.3 + - - +
133A SER* 1.3 65.0 + - - +
134A LYS* 3.3 13.3 + - - +
135A GLU* 3.1 33.4 + - - +
136A PHE* 2.9 21.5 + - - +
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Residues in contact with SER 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A THR* 3.5 29.7 + - - +
45A HIS* 4.2 5.9 + - - -
108A VAL* 3.5 20.2 - - - +
111A PHE* 3.8 14.1 - - - -
112A ASP* 2.9 21.9 + - - -
115A ILE* 3.5 13.1 - - - +
132A ASP* 1.3 70.2 - - - +
134A LYS* 1.3 61.5 + - - +
136A PHE* 3.1 4.3 + - - +
137A LEU* 2.8 30.7 + - - +
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Residues in contact with LYS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A THR* 3.9 9.1 - - - +
45A HIS* 2.9 41.1 + - + +
132A ASP* 3.3 9.7 + - - +
133A SER* 1.3 82.1 + - - +
135A GLU* 1.3 64.6 + - + +
137A LEU* 3.4 4.9 + - - +
138A ASN* 3.1 25.5 + - - +
249A PHE* 3.4 36.1 - - + +
250A GLU* 3.3 38.1 + - - +
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Residues in contact with GLU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A MET 4.7 2.3 - - - +
129A ILE 3.7 6.2 - - - +
130A PRO* 3.6 9.7 - - + +
131A LYS* 3.0 39.9 + - - +
132A ASP* 3.1 21.3 + - - +
134A LYS* 1.3 78.0 - - + +
136A PHE* 1.3 66.9 + - - +
138A ASN* 3.3 7.5 + - + +
139A LEU* 2.9 34.5 + - + +
246A HIS* 6.1 2.7 - - - +
250A GLU* 6.2 0.2 - - - +
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Residues in contact with PHE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TYR* 4.2 4.7 - + - -
19A MET* 3.5 35.7 - - + +
22A PHE* 3.6 44.2 - + - -
34A ILE* 3.9 17.0 - - + -
38A ILE* 3.8 24.9 - - + -
111A PHE* 3.8 14.4 - + + -
115A ILE* 3.7 25.1 - - + -
130A PRO* 3.5 19.2 - - + +
132A ASP 2.9 13.0 + - - +
133A SER* 3.3 8.3 - - - +
135A GLU* 1.3 77.6 - - - +
137A LEU* 1.3 64.8 + - - +
139A LEU 3.8 0.3 - - - -
140A MET* 2.9 28.8 + - + +
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Residues in contact with LEU 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.2 49.6 - - + +
41A THR* 4.4 7.0 - - + -
42A TYR* 4.3 8.5 - - + +
60A LEU* 4.1 14.6 - - + -
133A SER 2.8 12.3 + - - +
134A LYS* 3.4 9.2 - - - +
136A PHE* 1.3 80.7 - - - +
138A ASN* 1.3 66.5 + - - +
140A MET* 3.2 4.8 + - - +
141A MET* 3.0 25.2 + - + +
248A VAL* 3.6 39.9 - - + -
249A PHE* 4.1 16.2 - - + -
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Residues in contact with ASN 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A LYS* 3.1 22.1 + - - +
135A GLU* 3.8 10.0 - - + +
137A LEU* 1.3 84.1 - - - +
139A LEU* 1.3 64.1 + - + +
141A MET* 3.1 7.0 + - - +
142A TYR* 3.0 20.8 + - - +
244A HIS 4.7 3.1 - - - +
245A LEU 3.3 25.0 + - - +
246A HIS* 4.0 4.8 - - - +
247A LEU* 3.6 4.3 + - - +
248A VAL* 3.0 33.6 + - - +
249A PHE* 3.1 36.4 + - - +
250A GLU* 4.8 0.4 + - - -
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.7 27.5 - - + +
19A MET* 4.3 1.1 - - + -
128A MET* 3.5 25.6 - - - +
130A PRO* 3.3 36.1 - - + -
135A GLU* 2.9 25.3 + - + +
136A PHE 4.0 2.2 - - - +
138A ASN* 1.3 73.4 - - + +
140A MET* 1.3 62.9 + - - +
142A TYR* 3.2 13.9 + - - +
143A THR* 3.3 17.3 + - - +
245A LEU* 3.3 44.4 - - + +
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Residues in contact with MET 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A MET* 3.6 39.6 - - + +
23A LYS* 4.1 23.8 - - - +
34A ILE* 4.5 5.6 - - + -
38A ILE* 3.7 22.0 - - + -
62A TYR* 4.4 4.3 - - - +
136A PHE* 2.9 29.2 + - + +
137A LEU 3.6 4.0 - - - +
139A LEU* 1.3 76.5 - - - +
141A MET* 1.3 71.0 + - + +
143A THR* 2.7 32.7 + - - -
144A MET* 3.4 14.3 + - - +
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Residues in contact with MET 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 4.3 10.1 - - + -
60A LEU* 4.1 8.3 - - - -
61A CYS* 3.4 46.3 - - - +
62A TYR* 3.7 34.8 - - + +
137A LEU* 3.0 22.4 + - + +
138A ASN 3.1 7.4 + - - +
140A MET* 1.3 88.1 - - + +
142A TYR* 1.3 60.3 + - - +
144A MET* 3.3 6.5 + - - +
145A TYR* 2.9 29.1 + - - +
247A LEU* 4.1 8.3 - - + -
248A VAL* 3.8 27.8 - - + -
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Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 2.7 31.0 + - - +
11A ASP* 3.9 8.5 - - + -
12A PHE* 3.5 29.2 - - + -
15A ILE* 3.9 20.0 - - + -
138A ASN 3.0 9.6 + - - +
139A LEU* 3.2 11.9 + - - +
141A MET* 1.3 78.4 - - - +
143A THR* 1.3 58.8 + - + +
145A TYR* 3.3 14.3 + + - -
146A PHE* 2.8 52.3 + + + +
239A LEU* 3.8 6.8 - - + +
244A HIS* 3.5 50.9 - + + +
245A LEU* 4.3 5.2 - - + -
247A LEU* 3.9 7.4 - - - +
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Residues in contact with THR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 3.6 16.7 - - + -
15A ILE* 3.6 24.0 - - + +
16A GLU* 3.4 34.2 + - - +
19A MET* 4.7 3.6 - - + -
139A LEU 3.5 13.0 - - - +
140A MET* 2.7 32.0 + - - -
142A TYR* 1.3 78.3 - - + +
144A MET* 1.3 58.8 + - - +
147A LYS* 3.0 38.6 + - - +
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Residues in contact with MET 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A CYS* 3.6 33.2 - - + +
62A TYR* 3.4 42.6 - - + -
63A LYS 5.5 0.2 - - - +
140A MET* 3.6 15.3 - - - +
141A MET* 3.3 27.1 + - - +
142A TYR 3.2 0.6 - - - -
143A THR* 1.3 81.1 + - - +
145A TYR* 1.3 61.7 + - - +
147A LYS* 3.3 10.4 + - + +
148A ASN* 3.0 37.1 + - - +
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Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A CYS* 4.3 9.1 - - - -
141A MET 2.9 17.1 + - - +
142A TYR* 3.6 17.0 - + - +
144A MET* 1.3 74.6 - - - +
146A PHE* 1.3 68.1 + - - +
148A ASN* 3.3 12.0 + - + +
149A ILE* 3.1 52.8 + - + +
238A LEU 4.1 8.7 + - - -
239A LEU* 4.1 11.8 - - + -
242A LYS* 3.5 46.3 - - + +
244A HIS* 5.2 1.8 - - + -
247A LEU* 3.7 23.8 - - + -
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Residues in contact with PHE 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.3 13.2 - - + -
12A PHE* 3.3 66.0 - + + -
142A TYR* 2.8 37.8 + - + +
143A THR 3.8 0.4 - - - +
145A TYR* 1.3 78.1 - - - +
147A LYS* 1.3 64.0 + - - +
149A ILE* 3.2 9.7 + - - +
150A ILE* 3.1 45.4 + - + +
158A PHE* 5.2 3.6 - - + -
161A PHE* 3.8 28.5 - + - -
235A VAL* 4.4 5.2 - - + -
239A LEU* 3.7 28.3 - - + -
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE* 4.0 11.9 - - + -
16A GLU* 3.0 39.6 + - - -
143A THR* 3.0 25.1 + - - +
144A MET* 3.6 10.0 - - + +
145A TYR 3.2 0.2 - - - -
146A PHE* 1.3 77.6 - - - +
148A ASN* 1.3 65.4 + - - +
150A ILE* 3.3 8.3 + - - +
151A LYS* 3.1 40.4 + - - +
158A PHE* 3.7 40.6 - - + +
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Residues in contact with ASN 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A CYS* 4.9 17.0 + - - +
63A LYS* 6.1 0.7 - - - -
144A MET* 3.0 25.9 + - - +
145A TYR* 3.3 10.4 + - + +
147A LYS* 1.3 75.2 - - - +
149A ILE* 1.3 65.2 + - + +
151A LYS* 3.4 23.1 + - - +
152A LYS* 3.0 24.6 + - - +
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Residues in contact with ILE 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A TYR* 3.1 44.2 + - + +
146A PHE 3.4 9.9 - - - +
148A ASN* 1.3 78.3 - - + +
150A ILE* 1.3 71.4 + - + +
152A LYS* 3.2 3.8 + - + -
153A HIS* 3.0 46.3 + - + +
154A LEU* 5.3 0.2 - - - +
235A VAL* 5.3 3.6 - - + -
238A LEU* 4.1 26.2 - - + +
239A LEU* 3.4 33.0 - - + -
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Residues in contact with ILE 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PHE* 3.1 49.2 + - + +
147A LYS* 3.5 9.4 - - - +
148A ASN 3.3 0.2 - - - -
149A ILE* 1.3 79.5 - - + +
151A LYS* 1.3 58.3 + - + +
154A LEU* 3.0 49.3 + - + +
156A LEU 3.4 21.9 - - - +
157A SER* 3.9 18.4 - - - +
158A PHE* 4.0 9.2 - - + +
161A PHE* 4.0 19.7 - - + -
235A VAL* 4.6 10.5 - - + -
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LYS* 3.1 31.5 - - - +
148A ASN* 3.5 27.3 + - - +
150A ILE* 1.3 79.3 - - + +
152A LYS* 1.3 59.2 + - - +
154A LEU 3.7 11.6 - - - +
156A LEU 5.0 3.4 - - - -
158A PHE* 6.1 2.0 - - - -
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Residues in contact with LYS 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ASN 3.0 17.4 + - - +
149A ILE* 3.2 6.7 + - + +
151A LYS* 1.3 82.4 - - - +
153A HIS* 1.3 89.2 + - + +
154A LEU 4.6 0.7 - - - +
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Residues in contact with HIS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A ILE* 3.0 31.0 + - + +
152A LYS* 1.3 113.6 + - + +
154A LEU* 1.3 73.4 + - + +
238A LEU* 3.7 46.6 - - + +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 3.0 36.4 + - + +
151A LYS* 3.7 14.0 - - - +
152A LYS 4.6 0.9 - - - +
153A HIS* 1.3 94.5 - - + +
155A THR* 1.3 66.8 + - - +
156A LEU* 3.9 18.2 - - + +
161A PHE* 3.8 34.1 - - + -
231A LEU* 4.1 27.4 - - + -
234A GLN* 5.5 5.8 - - + +
235A VAL* 4.2 12.6 - - + -
238A LEU* 5.8 1.3 - - + -
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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
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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