Contacts of the helix formed by residues 129 - 150 (chain A) in PDB entry 5LOH
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A TYR* 5.9 1.9 - - - -
127A TYR* 4.1 11.9 + - + -
128A PHE* 1.3 77.6 - - - +
130A GLU* 1.3 66.6 + - - +
131A GLU* 3.4 22.0 + - - +
132A MET* 3.4 21.6 + - - +
133A ALA* 3.1 17.3 + - - +
772A LEU* 4.4 1.1 - - - -
849A PRO* 5.8 0.7 - - - +
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Residues in contact with GLU 130 (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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129A ASP* 1.3 77.3 + - - +
131A GLU* 1.3 58.7 + - - +
133A ALA* 3.3 1.9 + - - +
134A VAL* 2.9 37.6 + - + +
772A LEU* 3.9 18.4 - - + +
805A SER* 2.7 36.3 + - - -
807A ASN* 5.8 0.3 - - - +
808A ALA* 3.7 10.1 - - + +
834A LEU* 4.1 24.6 - - + +
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Residues in contact with GLU 131 (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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129A ASP* 3.4 15.3 + - - +
130A GLU* 1.3 78.7 - - - +
132A MET* 1.3 62.5 + - + +
134A VAL* 3.8 5.6 - - - +
135A LYS* 2.9 60.7 + - - +
849A PRO* 4.9 7.2 - - + +
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Residues in contact with MET 132 (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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121A LEU* 3.9 8.7 - - + -
125A TYR* 4.2 25.4 - - + -
128A PHE* 3.5 42.6 - - + -
129A ASP* 3.4 21.1 + - - +
130A GLU 3.3 0.4 - - - -
131A GLU* 1.3 78.3 - - + +
133A ALA* 1.3 60.4 + - - +
135A LYS* 3.3 1.9 + - - +
136A TYR* 3.0 64.9 + - + +
849A PRO* 3.7 37.0 - - + -
850A PHE* 4.4 5.6 - - + -
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Residues in contact with ALA 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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128A PHE* 4.1 5.5 - - + +
129A ASP 3.1 17.4 + - - +
130A GLU 3.8 1.1 - - - +
132A MET* 1.3 76.2 - - - +
134A VAL* 1.3 57.1 + - + +
136A TYR* 3.9 1.2 - - - +
137A ILE* 2.9 35.8 + - - +
768A LEU* 4.6 5.4 - - + -
771A PHE* 3.6 34.3 - - + -
772A LEU* 3.7 21.8 - - + -
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Residues in contact with VAL 134 (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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130A GLU* 2.9 26.7 + - + +
131A GLU* 3.9 6.3 - - - +
133A ALA* 1.3 76.1 - - + +
135A LYS* 1.3 55.5 + - + +
137A ILE* 4.5 3.8 - - - -
138A SER* 2.1 46.0 + - - +
768A LEU* 5.2 4.0 - - + -
772A LEU* 5.9 0.9 - - + -
834A LEU* 3.8 53.6 - - + +
835A PHE* 4.0 15.5 - - + -
838A VAL* 4.3 9.4 - - + -
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Residues in contact with LYS 135 (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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131A GLU* 2.9 47.7 + - - +
132A MET* 3.7 4.5 - - - +
134A VAL* 1.3 76.2 - - + +
136A TYR* 1.3 63.9 + - + +
138A SER* 3.1 6.3 + - - -
139A GLU* 3.0 29.4 + - - +
838A VAL* 6.2 0.4 - - - -
846A GLN* 3.6 34.3 + - - +
847A THR* 3.2 30.4 + - - +
848A MET* 4.3 7.6 - - + -
849A PRO* 4.1 20.8 - - + +
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Residues in contact with TYR 136 (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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118A VAL* 4.2 16.6 - - + -
121A LEU* 3.5 18.0 - - + +
128A PHE* 3.8 24.5 - + - -
132A MET* 3.0 57.1 + - + +
133A ALA 3.9 3.4 - - - +
135A LYS* 1.3 75.8 - - + +
137A ILE* 1.3 57.6 + - - +
139A GLU* 3.2 4.3 + - - +
140A VAL* 2.9 34.7 + - + +
162A MET* 6.2 0.4 - - - -
164A ILE* 5.0 2.7 - - + +
168A GLY 4.3 5.8 + - - -
170A ILE* 3.4 30.7 - - + +
771A PHE* 3.9 13.2 - + + -
848A MET* 3.5 23.3 - - + -
849A PRO* 4.5 5.6 - - + -
850A PHE* 4.0 16.1 + - - +
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Residues in contact with ILE 137 (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 ALA 2.9 22.4 + - - +
134A VAL* 4.1 2.2 - - - +
136A TYR* 1.3 75.4 - - - +
138A SER* 1.3 57.1 + - - +
140A VAL* 3.4 4.9 + - + +
141A ALA* 2.9 27.8 + - + +
162A MET* 5.2 0.7 - - + -
764A LEU* 3.6 38.6 - - + +
767A CYS* 4.1 3.6 - - + -
768A LEU* 3.6 49.4 - - + +
771A PHE* 3.8 19.1 - - + -
815A LEU* 5.6 0.2 - - + -
835A PHE* 3.6 27.8 - - + -
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Residues in contact with SER 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 VAL 2.1 30.4 + - - -
135A LYS* 3.4 6.9 - - - -
137A ILE* 1.3 77.8 - - - +
139A GLU* 1.3 62.4 + - - +
141A ALA* 3.0 4.2 + - - +
142A LEU* 2.9 21.1 + - - +
835A PHE* 3.5 15.6 - - - -
838A VAL* 3.8 11.8 - - - +
840A TRP* 3.7 25.3 - - - -
843A LEU* 3.6 20.6 - - - -
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Residues in contact with GLU 139 (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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92A PHE* 3.3 36.6 - - + -
135A LYS 3.0 14.5 + - - +
136A TYR 3.7 5.4 - - - +
138A SER* 1.3 74.4 - - - +
140A VAL* 1.3 63.0 + - - +
142A LEU* 3.3 4.7 + - - +
143A ALA* 3.0 22.7 + - - +
169A HIS* 3.3 23.6 + - - -
170A ILE* 2.9 39.6 + - + +
843A LEU* 3.7 17.0 - - + +
846A GLN* 3.5 16.7 + - - +
848A MET* 3.5 10.7 - - - +
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Residues in contact with VAL 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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136A TYR* 2.9 19.9 + - + +
137A ILE* 3.9 6.1 - - + +
139A GLU* 1.3 75.5 - - - +
141A ALA* 1.3 56.0 + - - +
143A ALA* 3.4 6.7 + - - +
144A LEU* 2.9 26.7 + - - +
157A LEU* 3.9 18.6 - - + -
162A MET* 3.7 35.9 - - + -
170A ILE* 3.6 24.5 - - + -
172A LEU* 4.0 7.9 - - + -
764A LEU* 3.6 22.2 - - + -
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Residues in contact with ALA 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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137A ILE 2.9 18.4 + - - +
138A SER* 3.0 8.0 + - - +
140A VAL* 1.3 75.6 - - - +
142A LEU* 1.3 60.7 + - - +
144A LEU* 3.2 4.8 + - - +
145A ASP* 2.9 29.5 + - - +
761A TRP* 3.7 28.9 - - + -
764A LEU* 4.3 2.7 - - + +
826A MET* 4.0 12.3 - - + +
829A LEU* 4.1 14.4 - - + -
835A PHE* 5.8 0.2 - - + -
840A TRP* 4.6 2.7 - - + -
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Residues in contact with LEU 142 (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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92A PHE* 3.7 22.7 - - + -
138A SER 2.9 7.7 + - - +
139A GLU 3.6 7.4 - - - +
141A ALA* 1.3 77.0 - - - +
143A ALA* 1.3 61.6 + - - +
145A ASP* 3.3 5.0 + - + +
146A TYR* 2.9 25.5 + - - +
826A MET* 3.6 19.5 - - + +
830A LYS* 5.3 5.4 - - - +
840A TRP* 3.9 29.2 - - + +
843A LEU* 3.6 38.8 - - + -
844A GLN* 6.0 0.2 - - - +
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Residues in contact with ALA 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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90A SER* 5.6 0.4 - - - -
92A PHE* 3.4 38.5 - - + +
93A ILE* 4.3 5.9 - - + +
139A GLU 3.0 9.3 + - - +
140A VAL* 3.6 8.3 - - - +
142A LEU* 1.3 76.5 - - - +
144A LEU* 1.3 57.1 + - - +
146A TYR* 3.4 7.8 + - - +
147A LEU* 2.9 33.7 + - - +
170A ILE* 6.2 0.2 - - + -
172A LEU* 3.7 20.9 - - + -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A VAL* 2.9 21.4 + - + +
141A ALA 3.2 5.1 + - - +
143A ALA* 1.3 76.9 - - - +
145A ASP* 1.3 57.4 + - - +
147A LEU* 3.1 6.9 + - + +
148A HIS* 2.9 38.4 + - + +
154A HIS* 4.2 15.3 - - + -
157A LEU* 3.7 30.7 - - + -
172A LEU* 4.2 9.9 - - + -
760A ASP* 3.8 39.7 - - + +
761A TRP* 4.0 29.8 - - + -
764A LEU* 4.0 8.1 - - + -
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Residues in contact with ASP 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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141A ALA 2.9 16.5 + - - +
142A LEU* 3.9 6.8 - - + +
144A LEU* 1.3 73.2 - - - +
146A TYR* 1.3 67.1 + - - +
148A HIS* 3.3 5.5 + - - +
149A ARG* 2.9 54.1 + - - +
761A TRP* 4.6 1.2 - - + -
826A MET* 3.5 35.7 - - + +
830A LYS* 5.6 1.4 - - - -
902A CL 3.6 5.7 - - - +
753B ARG* 3.2 23.7 + - - -
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Residues in contact with TYR 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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87A LEU 5.0 0.2 + - - -
88A SER* 3.5 38.9 - - - -
89A LYS 3.6 12.3 + - - -
90A SER* 3.7 34.8 - - - +
93A ILE* 4.1 13.9 - - + -
142A LEU 2.9 17.4 + - - +
143A ALA* 3.6 5.4 - - - +
145A ASP* 1.3 76.0 - - - +
147A LEU* 1.3 67.4 + - + +
149A ARG* 3.6 8.0 + - + +
150A HIS* 3.0 63.1 + + - -
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Residues in contact with LEU 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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88A SER* 5.6 2.0 - - - +
93A ILE* 4.0 21.1 - - + -
143A ALA 2.9 19.5 + - - +
144A LEU* 3.1 8.0 + - + +
146A TYR* 1.3 81.1 - - + +
148A HIS* 1.3 65.0 + - + +
150A HIS* 3.3 8.4 + - + +
152A ILE* 2.9 66.4 + - + +
154A HIS* 3.8 36.6 - - + +
172A LEU* 4.6 5.6 - - + -
175A PHE* 3.9 25.8 - - + -
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Residues in contact with HIS 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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144A LEU* 2.9 24.7 + - + +
145A ASP 3.3 1.5 + - - +
147A LEU* 1.3 75.5 - - + +
149A ARG* 1.3 60.7 + - - +
151A GLY 3.0 7.6 + - - -
152A ILE 3.1 20.2 - - - -
153A ILE* 4.4 0.4 - - - -
757A PRO* 3.9 24.6 + - + +
760A ASP* 2.7 38.9 + - + +
761A TRP* 3.4 26.9 + + - -
902A CL 3.3 19.2 - - + +
753B ARG* 3.5 18.9 - - - +
754B ALA* 2.8 35.1 + - + +
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Residues in contact with ARG 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 ASP* 2.9 44.5 + - - +
146A TYR* 3.9 8.7 - - - +
148A HIS* 1.3 75.8 - - - +
150A HIS* 1.3 65.1 + - + +
151A GLY 3.3 1.4 + - - -
826A MET* 5.9 0.4 - - - +
827A LYS* 6.0 4.4 - - - +
751B LEU 4.7 3.6 - - - +
752B GLY 4.1 8.3 - - - +
753B ARG* 3.6 47.0 + - + +
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Residues in contact with HIS 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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87A LEU 5.8 1.8 + - - -
88A SER* 4.8 9.0 - - - +
146A TYR* 3.0 60.3 + + + +
147A LEU* 3.3 9.7 + - + +
148A HIS 3.1 1.0 - - - -
149A ARG* 1.3 82.6 - - + +
151A GLY* 1.3 60.4 + - - +
152A ILE* 3.3 20.1 + - + +
752B GLY 3.9 3.3 - - - +
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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
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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