Contacts of the helix formed by residues 146 - 168 (chain A) in PDB entry 1PR9
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 HIS 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 6.0 0.2 - - + -
88A LEU 5.9 0.4 - - - -
89A LEU* 3.6 41.7 - - + +
138A CYS* 4.7 1.6 - - - -
143A VAL* 3.0 31.0 + - + +
144A THR 2.8 24.0 + - - -
145A ASN* 1.3 81.2 - - + +
147A SER* 1.3 59.6 + - - +
148A VAL 3.3 2.5 - - - -
149A TYR* 3.8 21.5 - + + -
150A CYS* 2.8 42.7 + - - +
190A THR* 4.6 5.9 + - + +
191A TRP* 4.3 12.0 + + - -
247A 2HP 3.7 23.4 + - - -
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Residues in contact with SER 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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90A GLN 4.3 2.0 + - - -
92A PHE* 4.1 27.8 - - - -
95A VAL* 3.5 25.1 - - - +
143A VAL 4.5 0.4 + - - -
145A ASN* 3.6 3.2 + - - +
146A HIS* 1.3 76.3 - - - +
148A VAL* 1.3 70.4 + - - +
150A CYS* 4.0 2.8 - - - +
151A SER* 2.9 30.0 + - - -
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU 4.7 11.0 + - - +
90A GLN* 5.3 2.9 + - - +
95A VAL* 3.6 35.9 - - + -
99A ALA* 4.3 7.4 - - + +
100A PHE* 4.3 22.4 - - + +
103A SER* 3.4 35.0 - - - +
104A PHE* 4.3 10.0 - - + -
146A HIS 3.3 0.2 - - - -
147A SER* 1.3 83.5 + - - +
149A TYR* 1.3 64.8 + - - +
151A SER* 3.1 7.9 + - - -
152A THR* 2.9 21.1 + - - +
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Residues in contact with TYR 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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85A ALA* 5.0 0.4 - - + -
86A VAL 3.6 24.5 - - - +
87A ALA* 3.8 21.8 - - + -
88A LEU 4.9 4.7 + - - +
89A LEU* 4.4 16.6 - - + -
103A SER* 5.7 1.3 - - - -
107A ASN* 4.0 5.8 - - - +
136A SER* 3.9 3.7 - - - -
138A CYS* 3.5 19.5 - - - -
146A HIS* 3.4 18.5 + + + +
148A VAL* 1.3 80.4 - - - +
150A CYS* 1.3 60.8 + - - +
152A THR* 2.8 24.1 + - - -
153A LYS* 3.2 27.3 + - + +
186A MET* 4.4 4.1 - - - -
245A NAP 2.7 44.5 + - - -
246A K 3.7 7.7 - - - -
247A 2HP 3.4 21.1 + - - -
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Residues in contact with CYS 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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138A CYS* 2.1 61.8 - - - +
139A SER* 4.4 0.7 - - - +
141A ARG 4.2 2.2 - - - +
142A ALA* 4.7 4.0 - - - -
143A VAL* 4.1 15.3 - - - -
146A HIS* 2.8 37.6 + - - +
147A SER* 4.1 2.7 - - - +
149A TYR* 1.3 73.8 - - - +
151A SER* 1.3 58.0 + - - +
153A LYS* 3.2 1.6 + - - +
154A GLY* 2.8 26.7 + - - -
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Residues in contact with SER 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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100A PHE* 6.1 0.4 - - - -
104A PHE* 4.0 16.3 - - - -
147A SER* 2.9 24.4 + - - -
148A VAL* 3.1 6.7 + - - -
150A CYS* 1.3 75.8 - - - +
152A THR* 1.3 60.5 + - - +
154A GLY* 4.3 1.6 - - - +
155A ALA* 2.8 29.8 + - - +
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Residues in contact with THR 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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103A SER* 3.8 24.2 - - - +
104A PHE* 3.6 37.5 - - + -
107A ASN* 3.0 34.9 + - - +
108A LEU* 4.2 4.3 - - - +
148A VAL 2.9 18.8 + - - +
149A TYR* 2.8 16.9 + - - -
151A SER* 1.3 78.0 - - - +
153A LYS* 1.3 61.0 + - - +
155A ALA* 3.4 3.1 + - - +
156A LEU* 2.9 26.7 + - - +
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Residues in contact with LYS 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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84A ALA 5.3 0.6 + - - -
85A ALA* 3.9 9.8 - - - +
107A ASN* 4.7 6.5 + - + +
134A VAL 2.8 24.7 + - - -
135A SER* 3.8 18.8 - - - +
136A SER* 3.8 13.0 - - - -
139A SER* 3.5 31.8 - - - +
149A TYR* 3.2 31.5 + - + +
150A CYS* 3.9 4.9 - - - +
151A SER 3.1 0.4 - - - -
152A THR* 1.3 84.1 + - - +
154A GLY* 1.3 61.9 - - - +
156A LEU* 3.2 13.7 + - + +
157A ASP* 3.0 24.9 + - - +
245A NAP 3.0 33.6 + - - -
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Residues in contact with GLY 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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139A SER* 3.7 19.4 - - - -
150A CYS 2.8 16.7 + - - -
151A SER* 3.8 2.0 - - - -
153A LYS* 1.3 75.0 - - - +
155A ALA* 1.3 63.2 + - - +
157A ASP* 3.5 5.9 + - - +
158A MET* 3.4 20.3 + - - +
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Residues in contact with ALA 155 (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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104A PHE* 4.3 8.3 - - + -
108A LEU* 3.7 26.1 - - + +
151A SER 2.8 17.9 + - - +
152A THR 3.6 5.4 - - - +
154A GLY* 1.3 77.0 - - - +
156A LEU* 1.3 58.1 + - - +
158A MET* 3.3 5.9 + - - +
159A LEU* 2.8 30.0 + - - +
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Residues in contact with LEU 156 (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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82A ASN 5.5 0.9 - - - +
107A ASN 4.5 7.6 - - - +
108A LEU* 3.8 16.5 - - + +
111A VAL* 3.9 34.1 - - + -
133A ASN* 4.0 22.2 - - + +
134A VAL 3.5 32.3 - - - +
135A SER* 3.9 12.3 - - - +
152A THR 2.9 17.1 + - - +
153A LYS* 3.2 16.5 + - + +
155A ALA* 1.3 75.5 - - - +
157A ASP* 1.3 68.3 + - - +
159A LEU* 3.2 5.2 + - + +
160A THR* 2.9 27.6 + - - +
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Residues in contact with ASP 157 (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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135A SER* 2.9 26.0 + - - -
139A SER* 2.5 27.7 + - - +
140A GLN* 3.0 20.3 - - - +
153A LYS 3.0 11.0 + - - -
154A GLY* 3.8 8.5 - - - +
155A ALA 3.3 0.2 - - - -
156A LEU* 1.3 76.4 - - - +
158A MET* 1.3 62.1 + - - +
160A THR* 3.2 20.9 - - - -
161A LYS* 3.3 20.1 + - - +
176A ALA* 4.3 1.7 - - - +
178A ASN* 3.4 7.2 + - - -
234A THR* 3.5 22.1 - - + +
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Residues in contact with MET 158 (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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154A GLY 3.4 8.8 + - - +
155A ALA* 3.3 9.5 + - - +
156A LEU 3.2 0.4 - - - -
157A ASP* 1.3 82.2 - - - +
159A LEU* 1.3 60.7 + - - +
161A LYS* 3.1 33.5 + - + +
162A VAL* 3.1 42.9 + - + +
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Residues in contact with LEU 159 (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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108A LEU* 3.8 24.7 - - + -
111A VAL* 3.8 26.9 - - + -
112A ILE* 3.9 31.6 - - + -
133A ASN* 5.3 0.2 - - - +
155A ALA 2.8 17.2 + - - +
156A LEU* 3.6 7.6 - - + +
158A MET* 1.3 76.3 - - - +
160A THR* 1.3 53.8 + - - +
162A VAL* 3.1 10.0 + - + +
163A MET* 2.8 57.8 + - + +
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Residues in contact with THR 160 (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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133A ASN* 3.0 29.0 + - - +
156A LEU 2.9 17.5 + - - -
157A ASP* 3.2 13.2 - - - +
159A LEU* 1.3 76.4 - - - +
161A LYS* 1.3 55.8 + - - +
163A MET* 3.6 2.5 - - - +
164A ALA* 2.9 27.7 + - - +
174A VAL* 3.6 28.1 - - + +
175A ASN* 3.7 20.9 - - - -
176A ALA* 3.9 8.8 - - + +
232A GLY* 4.3 5.6 - - - -
233A SER 4.0 8.7 - - - +
234A THR* 5.8 0.4 - - + -
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Residues in contact with LYS 161 (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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157A ASP* 3.3 18.1 + - - +
158A MET* 3.1 35.4 + - + +
160A THR* 1.3 75.4 - - - +
162A VAL* 1.3 64.7 + - - +
164A ALA* 3.4 7.8 + - - +
165A LEU* 3.0 22.5 + - - +
232A GLY* 3.6 26.0 - - - +
234A THR* 5.5 9.4 + - - +
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Residues in contact with VAL 162 (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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158A MET* 3.1 33.4 + - + +
159A LEU* 3.1 10.5 + - + +
161A LYS* 1.3 73.7 - - - +
163A MET* 1.3 66.6 + - + +
165A LEU* 3.1 14.5 + - + +
166A GLU* 2.9 46.5 + - + +
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Residues in contact with MET 163 (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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111A VAL* 4.9 1.8 - - - +
112A ILE* 5.8 2.2 - - - -
115A SER* 3.6 34.1 - - - +
131A ILE* 4.1 15.3 - - + -
133A ASN* 4.2 13.0 - - - +
159A LEU* 2.8 49.8 + - + +
160A THR 3.6 5.2 - - - +
162A VAL* 1.3 76.4 - - - +
164A ALA* 1.3 57.0 + - - +
165A LEU 3.2 0.2 + - - -
166A GLU* 5.0 2.2 - - - -
167A LEU* 2.8 47.1 + - + +
174A VAL* 3.8 24.9 - - + -
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Residues in contact with ALA 164 (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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160A THR 2.9 19.3 + - - +
161A LYS 3.5 6.1 - - - +
163A MET* 1.3 76.9 - - - +
165A LEU* 1.3 62.7 + - - +
168A GLY* 3.0 23.3 + - - +
172A ILE 4.8 1.5 - - - +
174A VAL* 4.0 9.8 - - - +
231A THR* 3.5 33.5 + - + +
232A GLY* 3.5 19.7 - - - +
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Residues in contact with LEU 165 (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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161A LYS 3.0 13.5 + - - +
162A VAL* 3.1 19.7 + - + +
164A ALA* 1.3 79.7 - - - +
166A GLU* 1.3 68.0 + - + +
167A LEU 3.5 0.2 + - - -
168A GLY* 4.2 0.5 - - - -
169A PRO* 3.5 15.2 - - - +
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Residues in contact with GLU 166 (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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162A VAL* 2.9 35.8 + - + +
163A MET* 4.2 2.7 - - - +
165A LEU* 1.3 83.9 - - + +
167A LEU* 1.3 68.1 + - + +
169A PRO* 3.5 11.0 - - - +
170A HIS* 4.1 11.1 - - - -
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Residues in contact with LEU 167 (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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115A SER* 6.1 0.2 - - - -
119A ALA* 4.4 25.8 - - + -
123A ILE* 4.8 4.7 - - + -
131A ILE* 4.5 2.7 - - + -
163A MET* 2.8 38.3 + - + +
166A GLU* 1.3 86.4 - - + +
168A GLY* 1.3 61.0 + - - +
169A PRO* 3.3 1.6 - - - -
170A HIS* 2.9 37.4 + - + +
172A ILE* 3.4 40.5 + - + +
174A VAL* 4.1 16.2 - - + -
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Residues in contact with GLY 168 (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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164A ALA 3.0 19.3 + - - -
165A LEU 4.2 0.4 - - - -
167A LEU* 1.3 76.8 - - - +
169A PRO* 1.3 68.2 - - - +
171A LYS* 3.0 15.8 + - - +
172A ILE 3.9 8.4 + - - -
231A THR* 6.1 3.1 - - - -
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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
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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