Contacts of the helix formed by residues 131 - 152 (chain A) in PDB entry 3LM0
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 SER 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A MET 4.1 1.0 - - - -
130A VAL* 1.3 78.3 - - - +
132A GLU* 1.3 64.1 + - - +
133A ASN* 3.5 11.6 + - - +
134A ASP* 3.1 33.3 + - - +
135A VAL* 3.3 21.7 + - - +
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Residues in contact with GLU 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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131A SER* 1.3 73.4 - - - +
133A ASN* 1.3 68.0 + - - +
134A ASP 3.2 0.2 + - - -
135A VAL* 3.3 7.7 + - + +
136A ILE* 3.1 37.9 + - + +
229A LEU* 5.6 8.4 - - + +
263A SER* 3.4 17.4 + - - -
266A ALA* 5.0 1.2 - - - +
292A TRP* 3.4 23.6 + - + +
330A EDO 2.7 33.5 + - - -
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Residues in contact with ASN 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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131A SER* 3.3 11.6 + - - +
132A GLU* 1.3 80.0 - - - +
134A ASP* 1.3 59.7 + - - +
136A ILE* 3.7 3.5 + - - +
137A ARG* 3.1 26.5 + - - +
295A GLN* 3.2 37.8 + - - +
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Residues in contact with ASP 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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129A MET 4.4 4.3 - - - +
130A VAL* 4.0 13.5 - - + +
131A SER* 3.1 31.3 + - - +
132A GLU 3.1 0.6 - - - -
133A ASN* 1.3 77.2 - - - +
135A VAL* 1.3 58.0 + - - +
137A ARG* 3.1 15.2 + - - +
138A LEU* 2.7 41.0 + - - +
172A LEU* 3.7 32.9 - - + +
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Residues in contact with VAL 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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130A VAL* 3.9 18.6 - - + +
131A SER 3.3 13.0 + - - +
132A GLU* 3.3 7.9 + - - +
134A ASP* 1.3 76.9 - - - +
136A ILE* 1.3 62.1 + - - +
138A LEU* 3.2 6.7 + - - +
139A ILE* 2.9 31.4 + - + +
225A ALA 5.1 0.9 - - - +
228A LEU* 4.0 32.5 - - + +
229A LEU* 4.0 26.0 - - + -
292A TRP* 3.7 26.5 - - + -
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Residues in contact with ILE 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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132A GLU* 3.1 42.3 + - + +
133A ASN* 3.9 4.9 - - - +
135A VAL* 1.3 75.2 - - - +
137A ARG* 1.3 64.7 + - - +
140A LYS* 3.0 26.1 + - + +
292A TRP* 3.5 44.2 - - + +
293A LEU* 3.7 37.9 - - + +
295A GLN* 3.9 31.0 - - + +
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Residues in contact with ARG 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 ASN 3.1 18.8 + - - +
134A ASP* 3.1 12.0 + - - +
136A ILE* 1.3 79.4 - - - +
138A LEU* 1.3 67.9 + - - +
140A LYS* 3.4 9.6 + - + +
141A GLN* 3.0 53.2 + - + +
172A LEU* 3.3 37.7 + - - +
173A GLY 3.0 28.3 + - - -
174A ASP* 3.5 6.5 + - - -
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Residues in contact with LEU 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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118A ILE* 4.6 8.5 - - + -
121A LEU* 3.8 28.5 - - + -
130A VAL* 5.4 2.5 - - + -
134A ASP* 2.7 26.9 + - + +
135A VAL* 3.8 4.3 - - - +
137A ARG* 1.3 75.7 - - - +
139A ILE* 1.3 66.1 + - - +
141A GLN* 3.3 3.1 + - - +
142A ILE* 2.9 33.0 + - + +
166A LEU* 3.8 15.3 - - + -
172A LEU* 3.9 19.1 - - + -
173A GLY 4.2 8.7 - - - +
175A ILE* 3.6 26.4 - - + +
228A LEU* 4.6 21.1 - - + -
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Residues in contact with ILE 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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135A VAL* 2.9 25.3 + - + +
136A ILE 4.0 2.9 - - - +
138A LEU* 1.3 76.2 - - - +
140A LYS* 1.3 63.0 + - - +
142A ILE* 3.3 9.6 + - + +
143A LEU* 2.9 31.4 + - + +
221A ILE* 4.5 11.0 - - + +
224A ILE* 4.1 8.5 - - + -
225A ALA* 4.0 28.7 - - + +
228A LEU* 4.1 12.3 - - + -
269A PHE* 3.7 30.5 - - + -
292A TRP* 4.1 23.6 - - + -
293A LEU* 4.4 4.0 - - + -
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Residues in contact with LYS 140 (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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136A ILE* 3.0 21.1 + - + +
137A ARG* 3.5 10.5 - - + +
138A LEU 3.3 0.2 - - - -
139A ILE* 1.3 76.9 - - - +
141A GLN* 1.3 62.9 + - + +
143A LEU* 3.3 5.8 + - - +
144A GLU* 3.1 43.9 + - - +
288A LEU* 3.7 13.6 - - + +
293A LEU* 4.4 33.9 + - + +
295A GLN 5.9 1.0 + - - -
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Residues in contact with GLN 141 (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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92A ARG* 3.7 40.5 + - - +
137A ARG* 3.0 44.4 + - + +
138A LEU* 3.8 2.5 - - - +
139A ILE 3.3 0.2 - - - -
140A LYS* 1.3 73.5 - - + +
142A ILE* 1.3 66.9 + - - +
144A GLU* 3.2 19.8 + - - +
145A GLY 3.2 9.7 + - - -
174A ASP* 3.2 28.6 + - - +
175A ILE* 3.0 42.2 + - + +
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Residues in contact with ILE 142 (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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118A ILE* 4.9 3.6 - - + -
138A LEU* 2.9 26.5 + - + +
139A ILE* 3.7 14.4 - - + +
141A GLN* 1.3 75.6 - - - +
143A LEU* 1.3 62.5 + - - +
145A GLY* 3.2 2.8 + - - -
146A VAL* 3.0 28.0 + - + +
159A LEU* 5.3 1.6 - - + -
164A ILE* 3.5 42.0 - - + -
175A ILE* 3.9 22.9 - - + -
177A ILE* 4.3 5.0 - - + +
221A ILE* 4.2 26.2 - - + -
224A ILE* 4.1 22.9 - - + -
228A LEU* 5.4 0.7 - - + -
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Residues in contact with LEU 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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139A ILE* 2.9 28.3 + - + +
140A LYS 3.6 4.3 - - - +
141A GLN 3.2 0.2 - - - -
142A ILE* 1.3 77.5 - - - +
144A GLU* 1.3 57.3 + - - +
146A VAL* 4.5 3.1 - - - +
147A TYR* 2.8 30.7 + - - +
218A MET* 3.8 10.8 - - + -
221A ILE* 3.5 29.6 - - + -
269A PHE* 4.1 3.6 - - + -
284A ALA* 4.0 10.6 - - + +
287A CYS* 3.8 36.1 - - + -
288A LEU* 3.7 15.3 - - + +
293A LEU* 3.6 30.3 - - + -
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Residues in contact with GLU 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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90A CYS* 4.7 1.2 - - - -
92A ARG* 2.8 42.5 + - + -
140A LYS* 3.1 43.7 + - - +
141A GLN* 3.2 8.6 + - - +
143A LEU* 1.3 76.7 - - - +
145A GLY* 1.3 62.9 + - - +
147A TYR* 3.8 8.9 + - - +
148A TYR* 3.3 20.8 + - - +
288A LEU* 4.1 16.8 - - + -
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Residues in contact with GLY 145 (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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90A CYS* 4.0 8.1 - - - -
92A ARG* 3.6 25.3 - - - +
93A VAL* 4.9 1.0 - - - +
141A GLN 3.2 7.7 + - - -
142A ILE 3.2 2.0 + - - -
144A GLU* 1.3 79.3 - - - +
146A VAL* 1.3 60.0 + - - +
148A TYR* 3.2 4.7 + - - +
149A LEU* 3.0 30.5 + - - +
177A ILE* 4.2 11.0 - - - -
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Residues in contact with VAL 146 (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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142A ILE* 3.0 21.2 + - + +
143A LEU* 4.1 2.7 - - - +
145A GLY* 1.3 74.1 - - - +
147A TYR* 1.3 63.9 + - - +
149A LEU* 4.4 9.2 - - + -
150A HIS* 3.0 56.7 + - + +
159A LEU* 3.6 28.7 - - + -
177A ILE* 4.1 12.6 - - + -
217A ASP* 4.3 6.1 - - + +
218A MET* 4.3 14.1 - - - -
221A ILE* 4.1 12.1 - - + -
284A ALA* 4.5 1.8 - - + -
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Residues in contact with TYR 147 (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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143A LEU 2.8 23.4 + - - +
144A GLU* 3.8 9.2 - - - +
146A VAL* 1.3 74.2 - - - +
148A TYR* 1.3 61.5 + - + +
150A HIS* 3.4 3.6 + - + +
151A GLN* 2.9 67.4 + - + +
284A ALA* 3.7 13.0 - - + +
285A GLU* 4.0 49.7 + - + -
288A LEU* 4.4 12.8 - - + -
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Residues in contact with TYR 148 (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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86A LEU 3.0 22.7 + - - -
87A ALA* 3.6 24.8 - - + -
89A SER* 3.3 24.5 + - - -
90A CYS* 3.8 30.1 - - + -
93A VAL* 5.3 0.4 - - + -
144A GLU 3.3 12.3 + - - +
145A GLY 3.2 9.5 + - - +
147A TYR* 1.3 87.0 - - + +
149A LEU* 1.3 67.1 + - + +
151A GLN* 3.5 4.7 + - + +
152A ASN* 2.8 54.3 + - + -
154A ILE* 6.0 0.9 - - + -
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Residues in contact with LEU 149 (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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87A ALA* 4.3 17.9 - - + -
93A VAL* 4.4 5.8 - - + -
145A GLY 3.0 18.9 + - - +
146A VAL* 3.7 15.7 - - + +
147A TYR 3.2 0.2 - - - -
148A TYR* 1.3 78.9 - - + +
150A HIS* 1.3 60.0 + - + +
152A ASN* 2.9 19.9 + - - +
154A ILE* 2.9 54.4 + - + +
156A HIS* 4.6 16.6 - - + +
177A ILE* 4.6 11.4 - - + -
180A PHE* 3.8 39.5 - - + -
217A ASP* 5.6 0.7 - - - +
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Residues in contact with HIS 150 (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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146A VAL* 3.0 40.4 + - + +
147A TYR* 3.9 4.9 - - + +
149A LEU* 1.3 72.6 - - + +
151A GLN* 1.3 62.0 + - - +
152A ASN 3.0 1.1 - - - -
153A ASN* 3.0 22.1 + - - +
154A ILE 3.2 20.0 - - - +
155A VAL* 4.4 0.4 - - - -
186A ILE* 4.6 5.2 - - - +
214A THR* 3.4 52.6 + - + +
217A ASP* 2.8 27.3 + - + +
218A MET* 4.2 11.2 - - + +
284A ALA* 4.6 7.2 + - + +
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Residues in contact with GLN 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 TYR* 2.9 63.6 + - + +
148A TYR* 3.5 9.0 - - + +
149A LEU 3.3 0.2 - - - -
150A HIS* 1.3 76.4 - - - +
152A ASN* 1.3 65.4 + - - +
153A ASN* 3.4 5.5 + - - +
285A GLU* 5.2 2.3 - - - +
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Residues in contact with ASN 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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86A LEU* 4.0 24.7 - - + +
148A TYR* 2.8 50.7 + - + +
149A LEU 2.9 9.2 + - - +
151A GLN* 1.3 85.3 - - - +
153A ASN* 1.3 73.2 + - - +
154A ILE* 3.3 20.2 - - + +
185A LYS* 4.5 6.8 + - - -
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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