Contacts of the helix formed by residues 136 - 157 (chain D) in PDB entry 1Z1G
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 136 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131D TYR* 2.9 29.3 + - + +
134D GLU* 4.3 31.9 + - + +
135D GLY* 1.3 76.0 - - - +
137D ALA* 1.3 70.2 + - - +
138D ALA 3.4 1.8 - - - -
139D SER* 3.1 14.7 + - - -
140D ALA 3.3 6.1 + - - -
7L A 4.0 0.6 + - - -
8L C 2.4 74.0 + - - +
9L T 3.5 11.9 - - - +
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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
----------------------------------------------------------
131D TYR 3.9 1.5 + - - -
132D ILE* 4.7 8.0 - - - +
135D GLY 3.1 10.4 + - - +
136D LYS* 1.3 77.2 - - - +
138D ALA* 1.3 70.5 + - - +
140D ALA* 2.7 21.7 + - - +
141D LYS* 3.5 1.6 + - - -
171D ALA* 4.9 13.9 - - + +
172D LYS 5.5 1.3 - - - +
173D SER* 3.8 22.2 - - - -
176D ARG* 5.4 5.4 - - - +
9L T 4.4 0.4 + - - -
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Residues in contact with ALA 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D LYS 3.4 0.6 - - - -
137D ALA* 1.3 80.8 - - + +
139D SER* 1.3 65.8 + - - +
141D LYS* 2.7 25.7 + - + +
142D LEU* 3.3 6.2 + - - +
171D ALA 6.2 0.2 - - - -
173D SER* 4.8 12.1 - - - -
176D ARG* 5.8 0.6 - - - +
9L T 3.9 24.1 + - + +
10L T 4.5 24.2 - - + +
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Residues in contact with SER 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D TYR* 4.4 5.6 - - - -
136D LYS* 3.1 16.5 + - - -
137D ALA 2.8 3.0 + - - -
138D ALA* 1.3 73.9 - - - +
140D ALA* 1.3 65.5 + - - +
142D LEU* 2.6 21.1 + - - +
143D ILE* 2.8 28.6 + - - +
8L C 3.6 27.2 + - - -
9L T 3.3 25.1 + - - +
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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
----------------------------------------------------------
128D LEU* 3.3 26.4 - - + +
131D TYR* 4.3 14.3 - - + +
132D ILE* 4.7 12.6 - - + -
136D LYS 3.3 4.9 + - - +
137D ALA 2.7 18.4 + - - +
139D SER* 1.3 74.7 - - - +
141D LYS* 1.3 65.2 + - - +
143D ILE* 3.1 9.1 + - - +
144D ARG* 2.7 26.0 + - - +
171D ALA* 4.9 8.3 - - + +
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Residues in contact with LYS 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D ALA 3.5 1.4 + - - +
138D ALA* 2.7 17.9 + - + +
140D ALA* 1.3 79.2 - - - +
142D LEU* 1.3 63.9 + - + +
144D ARG* 2.8 19.0 - - + +
145D SER* 2.6 58.1 + - - +
170D ALA* 4.7 12.1 - - + -
171D ALA* 4.5 24.6 - - + +
16I A 5.7 5.8 - - - -
17I A 4.1 32.6 + - - +
18I C 6.1 2.5 - - - -
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Residues in contact with LEU 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ASN* 6.1 0.4 - - + -
100D TYR* 6.3 2.7 - - + -
103D LYS* 3.9 32.8 - - + +
138D ALA 3.3 5.8 + - - +
139D SER* 2.6 16.2 + - - +
141D LYS* 1.3 92.6 - - + +
143D ILE* 1.3 58.4 + - + +
145D SER* 3.5 11.4 - - - +
146D THR* 2.2 37.3 + - - +
18I C 5.7 9.4 - - + +
19I A 5.2 6.7 - - - +
20I A 4.1 22.4 - - - +
21I A 5.9 0.4 - - - +
9L T 5.1 8.5 - - + +
10L T 4.5 12.6 - - + +
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Residues in contact with ILE 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D LYS* 4.8 12.6 - - + +
106D ALA* 4.3 15.3 - - + -
107D ILE* 4.5 20.9 - - + +
127D MSE 4.7 23.6 - - + -
128D LEU* 5.0 1.8 - - + -
131D TYR* 3.3 42.6 - - + -
139D SER* 2.8 24.9 - - - +
140D ALA* 3.3 6.1 - - - +
142D LEU* 1.3 76.0 - - + +
144D ARG* 1.3 71.7 + - - +
146D THR* 3.4 3.6 - - - -
147D LEU* 2.7 22.4 + - + +
8L C 5.8 0.9 - - - +
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Residues in contact with ARG 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128D LEU* 3.8 19.2 - - + +
140D ALA 2.7 13.6 + - - +
141D LYS* 2.8 16.0 - - - +
143D ILE* 1.3 81.3 - - - +
145D SER* 1.3 72.4 + - - +
147D LEU* 2.6 15.2 + - - +
148D SER* 2.8 11.9 + - - -
165D VAL* 4.3 12.7 + - + +
166D ALA* 4.0 9.9 + - - +
168D THR* 1.9 60.0 + - - +
169D ARG* 3.6 5.7 - - - +
170D ALA* 3.4 40.8 - - - +
17I A 3.7 20.0 + - - -
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Residues in contact with SER 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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141D LYS* 2.6 46.6 + - - +
142D LEU* 3.5 15.4 - - - +
144D ARG* 1.3 75.8 - - - +
146D THR* 1.3 66.5 + - - +
148D SER* 3.1 18.1 + - - -
149D ASP* 3.1 7.3 + - - +
17I A 5.0 3.3 - - - +
18I C 3.7 22.2 + - - -
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Residues in contact with THR 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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83D TYR* 4.0 22.7 - - + +
100D TYR* 4.3 26.7 - - + +
103D LYS* 4.0 25.8 - - + +
104D ILE* 5.5 3.1 - - + +
107D ILE* 5.5 4.0 - - + -
142D LEU* 2.2 30.0 + - - +
143D ILE 3.4 2.5 - - - -
144D ARG 2.7 3.0 + - - -
145D SER* 1.3 74.8 + - - +
147D LEU* 1.3 71.7 + - - +
149D ASP* 2.5 19.5 + - + +
150D ALA* 3.0 9.3 + - - +
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Residues in contact with LEU 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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76D LEU* 5.2 5.4 - - + -
80D LEU* 5.2 4.5 - - + -
107D ILE* 4.0 38.0 - - + +
111D LEU* 5.4 6.7 - - + -
119D ILE* 6.4 0.2 - - + -
124D ILE* 4.1 31.4 - - + -
127D MSE 5.1 9.2 - - + -
128D LEU* 5.9 0.2 - - + -
143D ILE* 2.7 16.3 + - + +
144D ARG* 2.6 15.4 + - - +
146D THR* 1.3 73.0 - - - +
148D SER* 1.3 66.1 + - - +
150D ALA* 3.0 12.2 + - + +
151D PHE* 3.0 36.5 + - + +
165D VAL* 4.3 15.7 - - + -
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Residues in contact with SER 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ARG* 2.8 10.6 + - - -
145D SER* 3.1 15.3 + - - -
146D THR 2.7 0.2 + - - -
147D LEU* 1.3 76.7 - - - +
149D ASP* 1.3 68.8 + - - -
151D PHE* 2.8 14.9 + - - +
152D ARG* 2.9 14.0 + - - +
163D ASN* 3.3 10.9 + - - +
165D VAL* 3.8 26.6 - - - +
166D ALA* 5.8 1.3 - - - -
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Residues in contact with ASP 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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169C ARG* 4.3 13.9 + - - +
83D TYR* 2.7 24.2 + - - +
87D LEU* 4.6 3.6 - - - +
90D ARG* 4.3 22.7 + - - -
100D TYR* 5.5 4.3 - - + -
145D SER 3.1 6.4 + - - +
146D THR* 2.5 17.3 + - - +
148D SER* 1.3 77.5 + - - +
150D ALA* 1.3 65.1 + - - +
152D ARG* 2.7 25.2 + - - +
153D GLU* 3.0 19.5 + - - +
18I C 5.2 10.5 - - - +
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Residues in contact with ALA 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TRP* 3.2 19.8 + - + +
80D LEU* 5.0 8.7 - - + -
83D TYR* 3.1 41.0 - - + -
107D ILE* 6.4 0.4 - - + -
146D THR 3.0 7.4 + - - +
147D LEU* 3.3 15.9 - - + +
149D ASP* 1.3 77.6 - - - +
151D PHE* 1.3 68.1 + - + +
153D GLU* 3.5 0.9 + - - -
154D ALA 2.8 17.2 + - - -
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Residues in contact with PHE 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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76D LEU* 5.3 6.1 - - + -
79D TRP* 5.6 3.4 - + - -
116D LEU* 4.6 26.7 - - + -
119D ILE* 4.1 36.6 - - + -
124D ILE* 5.4 1.3 - - + -
147D LEU* 3.0 26.5 + - + +
148D SER 2.8 11.4 + - - +
150D ALA* 1.3 82.5 - - + +
152D ARG* 1.3 58.2 + - - +
154D ALA* 2.5 34.8 + - + +
155D ILE* 2.8 8.3 + - - +
160D ILE* 4.5 14.4 - - + -
162D THR 4.3 5.6 - - - -
163D ASN* 3.5 14.6 - - + +
164D HIS* 3.9 26.2 - + + -
165D VAL* 3.9 17.7 - - + -
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Residues in contact with ARG 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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144C ARG* 4.6 3.4 - - - +
166C ALA 2.8 26.8 + - - -
167C ALA* 3.4 22.0 + - - +
168C THR 3.6 11.7 + - - -
169C ARG* 3.7 45.5 - - + +
148D SER* 2.9 13.2 + - - +
149D ASP* 2.7 22.6 + - - +
151D PHE* 1.3 69.8 - - - +
153D GLU* 1.3 55.2 + - - +
155D ILE* 2.7 37.8 + - + +
156D ALA* 2.8 10.2 + - + +
163D ASN* 4.1 5.9 - - - +
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Residues in contact with GLU 153 (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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169C ARG* 4.4 22.8 - - + +
79D TRP* 3.5 12.7 - - + -
83D TYR* 5.4 8.1 - - + -
86D ILE* 4.8 24.7 - - + +
90D ARG* 3.1 26.1 + - - +
149D ASP* 3.0 19.6 + - - +
150D ALA 4.6 1.1 - - - +
152D ARG* 1.3 76.9 - - + +
154D ALA* 1.3 66.8 + - - +
156D ALA* 2.9 26.0 + - + +
157D GLU* 3.0 11.6 + - - +
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Residues in contact with ALA 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D TRP* 2.8 33.1 - - + +
116D LEU* 4.4 5.6 - - + -
150D ALA 2.8 14.5 + - - +
151D PHE* 2.5 22.9 + - + +
153D GLU* 1.3 72.2 - - - +
155D ILE* 1.3 58.7 + - - -
157D GLU* 3.0 14.2 + - - +
158D GLY 3.1 7.6 + - - -
159D HIS* 3.4 8.2 + - + -
160D ILE* 2.9 23.1 - - + -
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Residues in contact with ILE 155 (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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121C THR* 3.6 12.9 - - + +
167C ALA* 4.7 20.4 - - + -
151D PHE 3.4 15.7 - - - +
152D ARG* 2.7 20.6 + - + +
154D ALA* 1.3 74.3 - - - +
156D ALA* 1.3 57.9 + - - +
158D GLY* 2.7 18.9 + - - +
160D ILE* 3.1 47.6 - - + +
161D THR 4.5 9.2 - - - +
162D THR* 4.6 3.1 - - - +
163D ASN* 4.3 26.7 - - + +
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Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C THR* 3.7 21.3 - - + +
122C LYS* 4.0 12.3 - - - +
125C ALA* 4.5 12.3 - - + +
167C ALA 4.9 10.1 + - - +
168C THR* 5.6 5.8 - - - +
169C ARG* 6.0 2.2 - - + +
152D ARG* 2.8 7.2 + - + +
153D GLU* 2.9 37.9 + - + +
155D ILE* 1.3 77.9 - - - +
157D GLU* 1.3 64.3 + - + +
158D GLY 3.2 0.4 + - - -
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Residues in contact with GLU 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C LYS* 4.3 37.8 - - + +
79D TRP* 4.1 3.6 - - + -
82D ARG* 2.6 37.4 + - - -
86D ILE* 4.8 2.8 - - - +
153D GLU 3.0 8.9 + - - +
154D ALA 3.0 5.7 + - - +
155D ILE 3.0 0.6 - - - -
156D ALA* 1.3 83.3 - - + +
158D GLY* 1.3 57.6 + - - +
159D HIS* 3.0 36.5 - - + +
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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