Contacts of the helix formed by residues 117 - 138 (chain A) in PDB entry 3M6L
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 GLY 117 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER* 4.1 0.2 + - - -
116A LEU* 1.3 73.1 - - - +
118A GLN* 1.3 66.3 + - - +
119A GLY 3.2 2.6 + - - -
120A VAL* 3.3 15.0 + - - +
121A ALA* 3.4 7.8 + - - +
154A ASP* 2.8 36.7 + - - +
157A GLU* 4.3 1.3 - - - -
159A ILE* 3.5 25.7 - - - +
160A SER 4.8 1.0 + - - -
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Residues in contact with GLN 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ALA 5.4 3.6 - - - +
113A THR* 5.5 2.0 - - + -
115A PRO* 3.3 36.7 + - + +
116A LEU 3.1 9.9 + - - -
117A GLY* 1.3 77.9 - - - +
119A GLY* 1.3 51.1 + - - +
121A ALA* 3.0 4.7 + - - +
122A ASN* 2.7 48.3 + - - +
159A ILE* 3.9 9.0 - - - +
392A HIS* 2.9 34.5 + - - -
396A ALA* 3.7 9.2 - - - +
399A ASN* 5.0 1.2 + - - -
423A PRO* 3.9 12.3 - - - +
424A ALA* 3.4 28.3 - - - +
427A ILE* 4.6 11.3 - - + +
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Residues in contact with GLY 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 3.6 15.9 - - - +
64A SER* 3.2 23.1 + - - +
113A THR* 4.1 6.2 - - - +
115A PRO 4.7 1.0 + - - -
117A GLY 3.2 0.8 - - - -
118A GLN* 1.3 77.2 - - - +
120A VAL* 1.3 59.4 + - - +
122A ASN* 3.2 13.2 + - - +
123A ALA* 2.8 31.2 + - - +
148A CYS* 4.2 0.4 - - - -
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Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.1 13.8 + - - +
117A GLY 3.3 7.4 + - - +
118A GLN 3.3 0.6 - - - -
119A GLY* 1.3 75.1 - - - +
121A ALA* 1.4 59.0 + - - +
123A ALA* 3.2 3.6 + - - +
124A VAL* 3.0 28.2 + - + +
148A CYS* 4.0 10.1 - - - -
150A CYS* 3.9 24.0 - - + -
154A ASP* 3.9 12.3 - - + -
155A LEU* 4.5 7.2 - - + -
160A SER* 4.4 17.5 - - - +
163A ALA* 5.0 0.2 - - + -
164A CYS* 3.9 28.0 - - - -
175A PHE* 4.3 3.3 - - + -
177A LEU* 4.3 15.0 - - + -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A GLY 3.4 2.9 + - - +
118A GLN 3.0 8.1 + - - +
120A VAL* 1.4 77.2 - - - +
122A ASN* 1.3 61.6 + - - +
124A VAL* 3.3 0.9 + - - +
125A GLY* 2.9 23.7 + - - -
159A ILE* 3.9 20.6 - - + +
163A ALA* 3.5 25.6 - - + -
393A ALA* 4.5 5.2 - - - +
396A ALA* 3.6 21.1 - - + -
397A ILE* 3.6 11.0 - - - +
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Residues in contact with ASN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 4.9 0.4 - - + -
111A ILE* 3.4 47.7 - - + +
112A ALA 4.3 3.0 + - - -
113A THR* 4.2 4.6 - - - +
118A GLN* 2.7 34.1 + - - +
119A GLY* 3.2 16.7 + - - +
121A ALA* 1.3 74.7 - - - +
123A ALA* 1.3 56.6 + - - +
125A GLY 3.1 1.7 + - - -
126A PHE* 2.8 30.5 + - + -
396A ALA* 2.9 31.1 - - - +
399A ASN* 4.2 5.4 + - - +
400A ALA* 3.1 9.3 - - + +
427A ILE* 5.7 2.1 - - - +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL* 4.4 6.0 - - + +
119A GLY 2.8 20.3 + - - +
120A VAL 3.2 3.6 + - - +
122A ASN* 1.3 70.5 - - - +
124A VAL* 1.4 64.0 + - - +
126A PHE* 3.2 6.1 + - - -
127A ALA* 3.0 22.3 + - - +
146A ILE* 3.6 20.0 - - + +
148A CYS* 3.6 19.5 - - + -
175A PHE* 3.5 24.9 - - + -
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A VAL 3.0 15.5 + - - +
121A ALA 3.7 6.3 - - - +
123A ALA* 1.4 75.1 - - - +
125A GLY* 1.4 58.8 + - - +
127A ALA* 3.1 7.9 + - - +
128A MSE 2.9 41.5 + - - +
163A ALA* 3.5 36.3 - - + +
164A CYS* 4.4 4.3 - - - +
166A LEU* 4.8 0.4 - - + -
167A ALA* 4.0 8.3 - - + +
172A LEU* 3.9 16.8 - - + -
175A PHE* 3.7 25.4 - - + -
397A ILE* 4.2 9.6 - - + -
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ALA 2.9 13.7 + - - -
122A ASN 3.1 4.5 + - - -
124A VAL* 1.4 76.8 - - - +
126A PHE* 1.3 54.9 + - - +
128A MSE 3.7 2.3 - - - +
129A ALA* 2.8 31.7 + - - +
397A ILE* 3.8 35.0 - - - +
400A ALA* 3.7 6.5 - - - -
401A PHE* 3.9 2.9 - - - -
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Residues in contact with PHE 126 (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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58A ARG* 6.2 0.2 - - - -
60A ARG* 4.3 21.5 - - + -
62A VAL* 3.9 29.6 - - + -
110A GLU* 4.0 22.4 - - + -
111A ILE* 4.1 16.6 - - + -
122A ASN 2.8 26.7 + - - -
123A ALA* 3.2 5.6 + - - +
125A GLY* 1.3 72.5 - - - +
127A ALA* 1.3 57.2 + - - +
129A ALA* 3.8 3.4 - - - +
130A ALA* 2.9 30.0 + - - +
146A ILE* 3.9 15.8 - - + +
400A ALA* 3.4 32.3 - - + -
403A ARG* 3.7 24.0 - - + -
404A TYR* 3.8 22.2 - + - -
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Residues in contact with ALA 127 (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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123A ALA 3.0 13.1 + - - +
124A VAL* 3.5 8.1 - - - +
126A PHE* 1.3 75.0 - - - +
128A MSE 1.3 59.8 + - - +
130A ALA 3.4 0.3 + - - -
131A LYS* 2.9 26.7 + - - +
146A ILE* 3.6 17.7 - - + +
172A LEU* 3.9 16.4 - - + -
174A ASN* 3.1 28.0 + - - +
175A PHE* 4.0 14.1 - - + -
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Residues in contact with MSE 128 (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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124A VAL* 2.9 23.6 + - - +
125A GLY 3.8 3.8 - - - +
127A ALA* 1.3 78.7 - - - +
129A ALA* 1.3 56.1 + - - +
131A LYS* 3.2 2.2 + - - +
132A LYS 3.0 22.9 + - - -
166A LEU* 4.7 12.3 - - + -
170A HIS* 4.0 20.9 - - + +
172A LEU* 3.6 23.8 - - + -
379A PHE* 3.4 38.9 - - + -
385A ILE* 4.2 22.7 - - + -
387A PHE* 5.3 0.7 - - + -
397A ILE* 4.1 33.4 - - + -
401A PHE* 3.8 14.1 - - + -
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Residues in contact with ALA 129 (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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125A GLY 2.8 21.2 + - - +
126A PHE* 4.3 0.9 - - - -
128A MSE 1.3 71.8 - - - +
130A ALA* 1.3 51.7 + - - +
132A LYS* 3.2 1.4 + - - -
133A ALA* 2.7 35.3 + - - +
401A PHE* 3.6 34.2 - - + -
404A TYR* 3.7 33.0 - - + -
407A PHE* 3.4 8.9 - - + -
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Residues in contact with ALA 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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126A PHE 2.9 18.3 + - - +
129A ALA* 1.3 72.5 - - - +
131A LYS* 1.4 61.1 + - - +
133A ALA 3.2 0.7 + - - -
134A GLN* 2.8 30.7 + - - +
142A ILE* 3.5 7.4 - - + +
144A HIS* 3.5 33.4 - - + +
146A ILE* 4.1 0.7 - - + -
174A ASN* 3.5 20.6 - - - +
404A TYR* 3.6 11.4 - - - -
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Residues in contact with LYS 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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127A ALA 2.9 19.0 + - - +
128A MSE 3.2 7.8 + - - +
130A ALA* 1.4 77.9 - - - +
132A LYS* 1.4 55.7 + - - +
134A GLN* 3.5 31.3 + - - +
135A ASN* 3.0 21.0 + - - +
170A HIS 5.5 1.6 - - - +
171A LYS 4.3 7.5 + - - -
172A LEU* 3.7 15.5 - - + +
173A ASP* 2.5 37.1 + - - +
174A ASN* 3.9 24.1 - - - +
379A PHE* 4.7 2.9 - - + -
380A VAL* 3.4 21.5 - - + +
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Residues in contact with LYS 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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128A MSE 3.0 14.1 + - - +
129A ALA 3.2 7.6 + - - +
131A LYS* 1.4 72.6 - - - +
133A ALA* 1.3 65.5 + - - +
135A ASN* 3.0 22.9 + - - +
136A LEU* 3.1 39.5 + - - +
356A GLU 6.0 0.9 - - - -
359A LEU* 4.1 17.0 - - + -
379A PHE* 3.9 13.2 - - + -
380A VAL* 3.0 32.8 + - + +
381A GLU 3.3 8.7 + - - -
382A GLY* 3.0 23.3 + - - +
383A LYS* 5.2 6.3 - - - +
401A PHE* 4.5 3.1 - - + -
407A PHE* 3.8 21.5 - - + -
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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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129A ALA 2.7 20.6 + - - +
130A ALA 3.2 4.9 + - - +
132A LYS* 1.3 71.7 - - - +
134A GLN* 1.3 56.2 + - - +
136A LEU* 3.2 3.9 + - - +
137A LEU* 2.8 34.6 + - + +
142A ILE* 3.9 14.1 - - + -
404A TYR* 3.7 28.3 - - + +
406A ILE* 3.8 18.2 - - + -
407A PHE* 3.7 6.0 - - - -
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Residues in contact with GLN 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 ALA 2.8 17.0 + - - +
131A LYS* 3.6 33.6 + - - +
132A LYS 3.2 0.2 - - - -
133A ALA* 1.3 76.5 - - - +
135A ASN* 1.3 58.9 + - - +
138A GLY* 2.9 29.2 + - - -
139A SER* 3.8 26.7 - - - +
142A ILE* 2.9 36.3 - - + +
143A ASP* 4.4 5.7 - - - +
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Residues in contact with ASN 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 LYS 3.0 13.8 + - - +
132A LYS* 3.0 36.4 - - - +
134A GLN* 1.3 79.1 - - - +
136A LEU* 1.3 67.1 + - - +
138A GLY 4.7 0.7 + - - -
313A LYS* 5.9 0.3 + - - -
380A VAL* 3.5 23.2 + - + +
381A GLU* 3.6 24.5 + - - +
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Residues in contact with LEU 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 LYS* 3.1 28.8 + - - +
133A ALA 3.6 6.7 - - - +
135A ASN* 1.3 91.9 - - - +
137A LEU* 1.3 65.9 + - + +
138A GLY 3.6 0.2 - - - -
313A LYS* 3.5 20.7 + - - -
316A LEU* 3.5 25.6 - - + +
320A LEU* 4.5 17.7 - - + -
356A GLU* 4.4 19.1 - - + +
406A ILE* 4.5 2.0 - - + -
407A PHE* 4.0 26.0 - - + -
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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
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56A LEU* 4.0 26.5 - - + -
133A ALA 2.8 18.0 + - - +
136A LEU* 1.3 82.6 - - + +
138A GLY* 1.3 60.6 + - - +
140A ASP* 3.9 2.8 - - - +
141A LEU* 3.6 24.8 - - + +
142A ILE* 4.1 17.7 - - + -
304A TRP* 6.0 1.1 - - + -
311A SER* 4.5 0.3 + - - -
313A LYS* 3.3 41.7 - - + +
316A LEU* 4.1 16.6 - - + -
317A LEU* 4.2 18.8 - - + -
320A LEU* 4.2 14.1 - - + -
406A ILE* 4.3 13.5 - - + -
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Residues in contact with GLY 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 GLN* 2.9 19.9 + - - -
135A ASN 4.6 0.6 + - - -
136A LEU 3.6 1.2 - - - -
137A LEU* 1.3 77.7 - - - +
139A SER* 1.3 59.8 + - - -
140A ASP* 3.2 10.3 - - - -
141A LEU 3.1 4.0 + - - -
142A ILE* 3.0 26.3 + - - +
313A LYS* 5.0 1.7 - - - +
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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