Contacts of the helix formed by residues 133 - 157 (chain A) in PDB entry 1RCE
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 TYR 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LYS* 5.2 5.8 - - - -
61A HIS* 3.9 47.1 - + + -
64A LYS* 2.9 32.3 - - + +
65A LEU* 4.4 9.9 - - + -
110A LEU* 4.1 20.6 - - + +
128A PHE* 3.2 54.1 - + - -
129A LEU* 3.2 17.6 + - + +
131A SER 3.5 2.4 - - - -
132A PRO* 1.3 92.4 - - + +
134A LEU* 1.3 64.2 + - - +
136A GLU* 3.2 10.0 + - - +
137A SER* 3.0 25.2 + - - -
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Residues in contact with LEU 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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107A ASN* 4.3 8.9 - - - +
110A LEU* 3.6 35.2 - - + +
111A LEU* 4.2 27.6 - - + -
114A HIS* 4.1 17.5 - - + -
129A LEU* 3.0 23.6 + - + +
130A GLU* 3.6 28.4 + - + +
133A TYR* 1.3 73.1 - - - +
135A SER* 1.3 62.5 + - - +
137A SER* 3.2 14.2 + - - -
138A VAL* 3.2 21.0 + - + +
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLU 3.3 14.3 + - - -
131A SER* 3.7 8.3 + - - -
132A PRO* 3.3 21.1 + - - +
134A LEU* 1.3 75.6 - - - +
136A GLU* 1.3 60.0 + - - +
137A SER 3.3 0.2 + - - -
138A VAL* 3.5 8.2 + - - +
139A GLU* 3.2 39.1 + - - +
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Residues in contact with GLU 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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23A LYS* 3.8 9.5 + - - -
57A ALA* 5.8 2.3 - - + +
61A HIS* 3.2 39.1 + - + +
103A GLN* 3.8 17.9 + - - +
110A LEU* 5.0 0.7 - - - +
132A PRO* 2.8 23.9 + - + +
133A TYR* 3.3 14.3 - - - +
135A SER* 1.3 75.9 - - - +
137A SER* 1.3 68.9 + - - +
139A GLU* 3.4 9.2 + - - +
140A THR* 2.9 45.2 + - - +
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Residues in contact with SER 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 5.4 0.7 + - - -
103A GLN* 4.8 8.0 + - - +
106A VAL* 5.5 1.2 - - - +
107A ASN* 3.1 38.0 + - - +
110A LEU* 3.5 17.2 - - - +
133A TYR 3.0 14.6 + - - -
134A LEU 3.2 6.7 + - - -
136A GLU* 1.3 87.6 + - - +
138A VAL* 1.3 58.5 + - - +
140A THR* 3.2 5.0 + - - -
141A ILE* 2.9 34.1 + - - +
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Residues in contact with VAL 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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107A ASN* 4.8 9.9 - - - +
134A LEU* 3.2 16.6 + - + +
135A SER* 4.0 9.9 - - - +
136A GLU 3.5 0.2 - - - -
137A SER* 1.3 77.6 - - - +
139A GLU* 1.3 69.2 + - + +
141A ILE* 3.8 8.7 - - + +
142A LYS* 3.0 26.2 + - - +
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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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135A SER* 3.2 31.0 + - - +
136A GLU* 3.7 7.0 + - - +
138A VAL* 1.3 81.3 - - + +
140A THR* 1.3 58.2 + - - +
142A LYS* 3.5 5.6 + - - +
143A LYS* 3.0 29.8 + - - +
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Residues in contact with THR 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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54A ARG* 4.3 24.7 + - - +
103A GLN* 4.1 24.5 - - - +
136A GLU* 2.9 34.7 + - - +
137A SER 3.7 2.7 - - - -
139A GLU* 1.3 75.8 - - - +
141A ILE* 1.3 59.4 + - - +
143A LYS* 3.1 21.0 + - - +
144A LEU* 2.8 42.9 + - + +
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Residues in contact with ILE 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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100A LEU* 3.7 21.6 - - + +
103A GLN* 4.0 20.6 - - + +
104A LYS* 3.9 28.7 - - + -
107A ASN* 4.0 32.1 - - + +
137A SER* 2.9 23.5 + - - +
138A VAL* 3.8 8.1 - - + +
139A GLU 3.4 0.2 - - - -
140A THR* 1.3 76.7 - - - +
142A LYS* 1.3 58.1 + - - +
144A LEU* 4.5 2.2 - - - -
145A GLY* 2.8 27.2 + - - -
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Residues in contact with LYS 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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138A VAL 3.0 17.9 + - - +
139A GLU* 3.7 5.6 - - - +
141A ILE* 1.3 73.8 - - - +
143A LYS* 1.3 61.1 + - - +
145A GLY* 3.3 1.7 + - - +
146A ASP* 2.9 70.9 + - - +
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Residues in contact with LYS 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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50A PHE* 4.2 13.2 - - + -
54A ARG* 3.5 40.3 - - - +
139A GLU 3.0 15.7 + - - +
140A THR* 3.4 20.5 + - - +
142A LYS* 1.3 77.6 - - - +
144A LEU* 1.3 55.9 + - - +
146A ASP* 3.3 10.0 + - - +
147A HIS* 3.0 55.6 + - + +
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Residues in contact with LEU 144 (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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30A TYR* 4.5 1.3 - - - +
50A PHE* 3.8 32.5 - - + -
54A ARG* 5.5 2.5 - - + -
96A LEU* 4.1 19.1 - - + +
99A ALA* 3.9 29.8 - - + +
100A LEU* 4.0 14.6 - - + +
103A GLN* 3.7 31.6 - - + -
140A THR* 2.8 30.5 + - + +
141A ILE 3.7 3.8 - - - +
143A LYS* 1.3 70.4 - - + +
145A GLY* 1.3 66.9 + - - +
147A HIS* 3.2 5.9 + - + +
148A ILE* 3.0 31.8 + - + +
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Residues in contact with GLY 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LEU* 4.3 8.2 - - - +
141A ILE 2.8 16.9 + - - -
142A LYS* 3.7 2.9 - - - -
143A LYS 3.3 0.2 - - - -
144A LEU* 1.3 77.2 - - - +
146A ASP* 1.3 63.4 + - - +
148A ILE* 3.3 11.1 + - - +
149A THR* 3.1 25.1 + - - -
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Residues in contact with ASP 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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142A LYS* 2.9 54.5 + - - +
143A LYS* 3.5 8.1 - - - +
144A LEU 3.2 0.2 - - - -
145A GLY* 1.3 76.0 - - - +
147A HIS* 1.3 66.2 + - + +
149A THR* 3.2 8.3 + - - -
150A SER* 3.1 27.3 + - - +
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Residues in contact with HIS 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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50A PHE* 4.1 24.0 - + - -
96A LEU* 4.1 13.9 - - + -
143A LYS* 3.0 42.7 + - + +
144A LEU* 3.2 8.7 + - + +
146A ASP* 1.3 76.8 - - + +
148A ILE* 1.3 66.1 + - - +
150A SER* 3.3 2.6 + - - -
151A LEU* 2.9 26.2 + - - +
166A PHE* 3.7 19.2 - + + -
170A THR* 3.6 31.0 - - + +
171A LEU* 4.2 13.5 - - + +
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Residues in contact with ILE 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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93A LEU* 4.1 15.9 - - + +
96A LEU* 3.9 29.2 - - + +
97A GLN* 4.0 16.2 - - + -
100A LEU* 3.7 40.4 - - + -
144A LEU 3.0 17.2 + - - +
145A GLY* 3.7 6.3 - - - +
147A HIS* 1.3 75.7 - - - +
149A THR* 1.3 64.0 + - - +
151A LEU* 3.3 2.0 + - - +
152A LYS* 2.9 52.1 + - - +
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Residues in contact with THR 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 GLY 3.1 13.3 + - - -
146A ASP* 3.2 10.7 + - - -
148A ILE* 1.3 76.1 - - - +
150A SER* 1.3 64.0 + - - +
152A LYS* 3.2 10.3 + - - +
153A LYS* 3.2 42.1 + - + +
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Residues in contact with SER 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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146A ASP* 3.1 14.0 + - - +
147A HIS* 3.8 3.6 + - - -
149A THR* 1.3 81.3 - - - +
151A LEU* 1.3 61.3 + - - +
153A LYS* 3.5 13.5 + - - +
154A LEU* 3.4 23.6 + - - +
166A PHE* 3.8 23.6 - - - -
170A THR* 5.3 2.2 - - - -
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Residues in contact with LEU 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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47A PHE* 4.1 11.9 - - + -
92A GLY 3.9 3.1 - - - -
93A LEU* 3.7 35.4 - - + +
96A LEU* 3.8 21.8 - - + -
147A HIS 2.9 17.8 + - - +
148A ILE* 3.9 3.1 - - - +
150A SER* 1.3 74.1 - - - +
152A LYS* 1.3 60.7 + - - +
154A LEU* 3.4 3.3 + - + +
155A TRP* 2.8 52.9 + - + +
162A ALA* 4.0 15.7 - - + +
163A GLU* 4.4 2.0 - - - +
166A PHE* 3.9 30.0 - - + -
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Residues in contact with LYS 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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93A LEU* 4.1 17.3 - - + -
97A GLN* 3.7 22.8 + - - -
148A ILE* 2.9 34.6 + - + +
149A THR* 3.2 8.3 + - - +
151A LEU* 1.3 72.7 - - - +
153A LYS* 1.3 69.0 + - - +
155A TRP* 3.2 7.9 + - - +
156A SER* 3.2 20.1 + - - -
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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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149A THR* 3.2 30.4 + - + +
150A SER* 3.6 14.8 - - - +
152A LYS* 1.3 77.2 - - - +
154A LEU* 1.3 62.0 + - + +
156A SER* 2.6 27.4 + - - -
157A SER* 4.1 3.8 + - - -
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Residues in contact with LEU 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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150A SER* 3.4 13.2 + - - +
151A LEU* 3.4 6.6 + - + +
152A LYS 3.4 0.4 - - - -
153A LYS* 1.3 80.3 - - + +
155A TRP* 1.3 63.0 + - - +
157A SER* 3.1 18.6 + - - +
158A HIS 3.2 13.9 + - - +
162A ALA* 3.6 33.2 - - + +
165A LEU* 4.1 29.6 - - + -
166A PHE* 4.3 19.5 - - + +
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Residues in contact with TRP 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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91A ASN* 3.8 32.8 - - + -
93A LEU* 4.2 26.5 - - + +
151A LEU* 2.8 35.6 + - + +
152A LYS* 3.4 11.0 - - - +
154A LEU* 1.3 78.2 - - - +
156A SER* 1.3 64.2 + - - +
157A SER 3.1 1.0 + - - -
159A PRO* 3.4 54.7 - - + +
162A ALA* 3.8 15.9 - - + +
163A GLU* 3.3 41.7 - - + -
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Residues in contact with SER 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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152A LYS 3.2 7.9 + - - -
153A LYS* 2.6 22.7 + - - -
155A TRP* 1.3 77.8 - - - +
157A SER* 1.3 65.1 + - - +
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Residues in contact with SER 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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153A LYS 4.2 2.8 + - - -
154A LEU* 3.1 11.7 + - - +
155A TRP 3.7 0.7 - - - -
156A SER* 1.3 87.3 + - - +
158A HIS* 1.3 85.9 + - - +
159A PRO* 4.3 2.1 - - - +
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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