Contacts of the helix formed by residues 141 - 166 (chain A) in PDB entry 4MBS
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 THR 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 3.8 13.6 - - - +
138A LYS 4.2 10.1 - - - +
139A ALA* 3.1 17.0 + - - +
140A ARG* 1.3 73.5 - - - +
142A VAL* 1.3 66.0 + - - +
143A THR* 3.0 18.4 + - - +
144A PHE* 3.5 19.2 + - + +
145A GLY 3.1 16.8 + - - -
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Residues in contact with VAL 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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61A LEU 4.0 10.3 - - - +
62A LYS* 3.4 35.2 - - - +
63A SER 3.9 11.7 - - - +
64A MET* 4.7 2.2 - - - +
67A ILE* 3.9 24.9 - - + +
141A THR* 1.3 71.9 + - - +
143A THR* 1.3 63.6 + - + +
145A GLY* 3.1 3.6 + - - -
146A VAL* 2.9 32.7 + - + +
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Residues in contact with THR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A THR* 3.0 18.9 + - - +
142A VAL* 1.3 76.8 - - + +
144A PHE* 1.4 51.4 + - - +
146A VAL* 3.2 10.4 + - + +
147A VAL* 2.8 42.5 + - - +
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Residues in contact with PHE 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 4.0 19.5 - - + -
68A TYR* 4.7 4.0 - - - -
139A ALA* 3.9 17.5 - - + -
141A THR* 3.5 24.7 + - + +
142A VAL 3.3 0.2 - - - -
143A THR* 1.4 79.2 + - - +
145A GLY* 1.3 51.2 + - - +
147A VAL* 3.8 10.8 - - + +
148A THR* 2.7 66.1 + - + +
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Residues in contact with GLY 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A MET* 4.3 7.0 - - - -
67A ILE* 3.7 12.6 - - - -
68A TYR* 3.6 16.3 - - - -
141A THR 3.1 11.6 + - - -
142A VAL 3.1 8.1 + - - -
144A PHE* 1.3 77.4 - - - +
146A VAL* 1.3 51.2 + - - +
148A THR* 3.0 16.7 + - - -
149A SER* 2.8 28.1 + - - -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 4.1 27.8 - - + -
142A VAL* 2.9 21.5 + - + +
143A THR* 3.2 10.3 + - - +
145A GLY* 1.3 73.4 - - - +
147A VAL* 1.4 66.8 + - + +
149A SER* 3.2 5.5 + - - -
150A VAL* 3.2 32.0 + - + +
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Residues in contact with VAL 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR* 2.8 27.3 + - - +
144A PHE* 3.8 12.1 - - + +
146A VAL* 1.4 76.6 - - + +
148A THR* 1.4 64.7 + - + +
150A VAL* 3.4 8.0 + - - +
151A ILE* 3.2 41.6 + - + +
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Residues in contact with THR 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 2.7 28.0 + - - +
121A LEU* 4.8 9.9 - - + -
144A PHE* 2.7 56.0 + - + +
145A GLY 3.0 9.2 + - - -
147A VAL* 1.4 74.3 - - + +
149A SER* 1.4 53.7 + - - +
151A ILE* 3.8 8.6 + - + +
152A THR* 2.6 37.5 + - - -
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Residues in contact with SER 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.5 5.3 - - - +
68A TYR* 3.8 4.3 - - - -
71A ASN* 3.2 34.7 + - - -
118A PHE* 3.7 16.9 - - - -
145A GLY 2.8 21.4 + - - -
146A VAL* 3.2 9.1 + - - -
148A THR* 1.4 74.1 - - - +
150A VAL* 1.3 64.2 + - - +
152A THR* 3.4 2.6 + - - -
153A TRP* 2.9 33.1 + - - -
1106A OLC 6.0 2.2 - - - -
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Residues in contact with VAL 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A VAL* 3.2 22.9 + - + +
147A VAL* 3.4 9.8 + - - +
149A SER* 1.3 71.6 - - - +
151A ILE* 1.4 69.0 + - + +
153A TRP* 3.2 10.0 + - - +
154A VAL* 3.1 35.1 + - + +
1106A OLC 6.1 6.5 - - + -
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Residues in contact with ILE 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 3.2 40.9 + - + +
148A THR* 4.1 8.1 - - + +
150A VAL* 1.4 78.5 - - + +
152A THR* 1.4 59.1 + - - +
154A VAL* 3.1 10.2 + - - +
155A VAL* 2.9 43.0 + - + +
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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
----------------------------------------------------------
114A SER* 4.7 1.3 - - - +
117A PHE* 3.5 34.5 - - + -
118A PHE* 3.6 27.1 - - + -
121A LEU* 3.2 19.0 - - + +
148A THR 2.6 24.4 + - - -
149A SER 3.5 5.8 - - - -
150A VAL 3.3 0.2 - - - -
151A ILE* 1.4 76.8 - - - +
153A TRP* 1.4 56.0 + - - +
155A VAL* 3.4 8.6 + - - +
156A ALA* 3.0 27.7 + - - +
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Residues in contact with TRP 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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71A ASN* 2.7 43.2 + - - -
74A ILE* 4.0 14.1 - - + -
75A SER* 3.7 19.7 - - - -
78A PHE* 3.8 20.6 - + - -
110A ILE* 3.9 16.8 - - + -
114A SER* 3.3 29.2 - - - -
118A PHE* 3.5 13.9 - + - -
149A SER 2.9 29.7 + - - -
150A VAL* 3.2 8.9 + - - +
152A THR* 1.4 71.1 - - - +
154A VAL* 1.4 60.4 + - + +
156A ALA* 3.3 4.7 + - - +
157A VAL* 3.0 35.6 + - + +
1106A OLC 3.6 48.8 - - + +
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Residues in contact with VAL 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 3.1 25.7 + - + +
151A ILE* 3.1 10.6 + - - +
153A TRP* 1.4 74.4 - - + +
155A VAL* 1.4 66.8 + - + +
157A VAL* 3.3 7.6 + - - +
158A PHE* 3.1 51.9 + - + -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 3.9 12.8 - - + -
151A ILE* 2.9 35.6 + - + +
152A THR* 3.7 7.0 - - - +
154A VAL* 1.4 76.7 - - + +
156A ALA* 1.4 55.0 + - - +
158A PHE* 3.2 8.3 + - - +
159A ALA* 2.9 27.0 + - - +
1103A OLC 3.8 40.0 - - + +
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Residues in contact with ALA 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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110A ILE* 4.1 12.6 - - + +
113A PHE* 4.2 3.3 - - + -
114A SER* 3.9 34.8 - - - +
117A PHE* 3.9 12.1 - - + -
152A THR 3.0 14.2 + - - +
153A TRP* 3.6 9.0 - - - +
154A VAL 3.3 0.2 - - - -
155A VAL* 1.4 71.2 - - - +
157A VAL* 1.3 62.1 + - - +
159A ALA* 3.4 4.7 + - - +
160A SER* 2.8 33.1 + - - -
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Residues in contact with VAL 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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110A ILE* 3.9 29.2 - - + +
153A TRP 3.0 19.9 + - - +
154A VAL* 3.3 11.4 + - + +
156A ALA* 1.3 72.7 - - - +
158A PHE* 1.4 68.6 + - + +
160A SER* 3.2 5.7 + - - -
161A LEU* 3.2 37.2 + - + +
164A ILE* 4.7 1.5 - - + +
1106A OLC 4.1 33.0 - - + -
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Residues in contact with PHE 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 VAL* 3.1 45.8 + - + +
155A VAL* 3.2 10.0 + - - +
157A VAL* 1.4 80.5 - - + +
159A ALA* 1.3 62.6 + - - +
160A SER 3.5 0.5 + - - -
161A LEU* 3.5 37.1 - - + +
162A PRO* 4.0 1.4 - - - +
1103A OLC 3.1 29.9 + - + +
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Residues in contact with ALA 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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113A PHE* 3.8 20.0 - - + -
117A PHE* 5.0 2.5 - - + -
155A VAL 2.9 16.0 + - - +
156A ALA* 3.7 8.5 - - - +
157A VAL 3.4 0.2 - - - -
158A PHE* 1.3 76.1 - - - +
160A SER* 1.3 55.7 + - - +
161A LEU 3.5 0.2 - - - -
163A ASN* 3.5 2.1 + - - -
197A LYS* 2.8 33.7 + - + +
201A LEU* 4.4 11.9 - - + -
1103A OLC 3.8 28.4 - - + -
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Residues in contact with SER 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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109A PHE* 3.3 23.2 - - - +
110A ILE* 3.3 29.8 + - - -
113A PHE* 3.4 6.4 - - - -
156A ALA 2.8 17.4 + - - -
157A VAL 3.2 5.1 + - - -
159A ALA* 1.3 74.1 - - - +
161A LEU* 1.3 64.2 + - - +
163A ASN* 3.2 20.2 + - - +
164A ILE* 3.3 23.7 + - - +
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Residues in contact with LEU 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 VAL* 3.2 21.3 + - + +
158A PHE* 3.5 37.7 - - + +
160A SER* 1.3 72.0 - - - +
162A PRO* 1.4 74.7 - - + +
164A ILE* 3.2 28.0 + - + +
165A ILE* 3.2 33.5 + - + +
1103A OLC 5.5 0.4 - - - +
1106A OLC 6.5 0.7 - - + -
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Residues in contact with PRO 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 PHE 4.0 7.4 - - - +
161A LEU* 1.4 92.1 - - + +
163A ASN* 1.3 55.7 + - - +
165A ILE* 3.2 14.0 + - + +
166A PHE* 3.1 43.9 + - + -
190A TRP* 5.3 5.6 - - + -
193A PHE* 5.7 2.5 - - + -
194A GLN* 3.9 17.0 - - - +
197A LYS* 3.5 25.4 - - - +
1103A OLC 4.8 15.0 - - - +
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Residues in contact with ASN 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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105A THR* 4.8 2.5 - - - -
109A PHE* 3.4 44.8 - - + -
113A PHE* 5.6 0.2 - - - -
159A ALA 3.5 7.1 + - - -
160A SER* 3.2 17.8 + - - +
161A LEU 3.2 0.2 - - - -
162A PRO* 1.3 75.1 - - - +
164A ILE* 1.4 54.2 - - - +
166A PHE* 3.5 9.3 + - - +
167A THR* 2.7 33.4 + - - -
180A SER* 5.0 2.2 + - - -
182A PHE* 5.7 1.0 - - - -
194A GLN* 2.6 31.3 + - - +
197A LYS* 3.2 25.7 - - - +
198A ILE* 5.6 0.2 - - - +
1101A MRV 5.4 0.9 - - - +
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Residues in contact with ILE 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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102A GLN* 3.0 42.1 - - + +
105A THR* 4.8 3.6 - - - +
106A GLY* 3.6 30.7 - - - +
109A PHE* 5.7 0.9 - - + -
110A ILE* 4.6 9.4 - - + -
157A VAL* 4.7 1.6 - - + +
160A SER* 3.4 30.3 - - - +
161A LEU* 3.2 22.8 + - + +
163A ASN* 1.4 75.4 - - + +
165A ILE* 1.3 63.0 + - + +
167A THR* 3.5 15.2 + - - +
1106A OLC 3.9 28.3 - - + +
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 4.1 7.1 - - - +
161A LEU* 3.2 39.4 + - + +
162A PRO* 3.2 11.6 + - + +
164A ILE* 1.3 80.3 - - + +
166A PHE* 1.4 63.9 + - + +
167A THR 3.2 5.9 + - - +
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO* 3.1 38.6 + - + +
163A ASN* 3.8 9.2 - - - +
164A ILE 3.4 0.4 - - - -
165A ILE* 1.4 78.3 - - + +
167A THR* 1.3 59.5 + - - +
168A ARG* 4.1 1.8 + - - +
180A SER* 4.0 13.0 - - - +
181A HIS* 2.8 50.5 + - - +
182A PHE* 3.8 20.0 - + - -
183A PRO* 3.5 24.7 - - + -
190A TRP* 3.5 50.0 - + - -
194A GLN* 4.3 4.3 - - + -
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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
------------------------------------------------------------
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