Contacts of the helix formed by residues 143 - 158 (chain A) in PDB entry 2E1B
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.7 27.4 - - + -
113A LEU* 3.8 16.6 - - + -
136A TYR* 3.3 23.8 + + - -
138A GLU* 2.4 37.8 + - + -
139A ASN 4.7 0.2 - - - -
140A LEU* 2.6 28.6 + - + +
141A ASN 2.6 7.3 + - - -
142A LYS* 1.3 100.8 + - + +
144A LYS* 1.3 66.7 + - - +
145A GLU 3.3 2.7 - - - -
146A GLN* 2.9 17.2 + - - +
147A ILE* 2.8 43.2 + - + +
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Residues in contact with LYS 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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140A LEU 3.6 2.7 + - - +
141A ASN* 2.7 58.6 + - + +
143A TYR* 1.3 79.8 - - - +
145A GLU* 1.3 78.0 + - - +
147A ILE* 3.0 10.5 + - - +
148A ILE* 3.0 30.4 + - + +
199A LEU* 2.8 39.2 - - + +
200A LYS* 4.7 1.0 - - - +
201A ARG* 4.2 15.5 - - + +
211A LEU* 5.6 3.6 - - + -
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Residues in contact with GLU 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 ASN 4.7 0.2 + - - -
143A TYR 3.3 0.4 - - - -
144A LYS* 1.3 93.6 + - - +
146A GLN* 1.3 62.4 + - - +
148A ILE* 4.0 19.3 - - - +
149A SER* 2.9 27.5 + - - -
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Residues in contact with GLN 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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112A VAL* 3.5 42.2 + - + +
142A LYS 5.8 0.2 - - - +
143A TYR* 2.9 21.4 + - - +
145A GLU* 1.3 78.2 - - - +
147A ILE* 1.3 60.4 + - - +
149A SER* 3.0 17.4 + - - +
150A LEU* 3.3 16.7 + - + +
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Residues in contact with ILE 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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105A LEU* 3.8 22.2 - - + -
108A VAL* 3.6 20.9 - - + +
109A LEU* 3.8 23.3 - - + -
112A VAL* 4.4 14.1 - - + -
113A LEU* 5.8 0.9 - - + -
140A LEU* 5.2 6.3 - - + +
143A TYR* 2.8 38.7 + - + +
144A LYS* 3.3 11.0 - - - +
146A GLN* 1.3 75.7 - - - +
148A ILE* 1.3 56.1 + - - +
150A LEU* 3.1 4.5 + - - +
151A PHE* 2.7 34.7 + - + +
199A LEU* 3.9 15.7 - - + -
211A LEU* 4.8 9.4 - - + -
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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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144A LYS* 3.0 17.4 + - + +
145A GLU* 4.0 23.6 - - - +
146A GLN 3.5 0.2 - - - -
147A ILE* 1.3 74.5 - - - +
149A SER* 1.3 67.3 + - - +
151A PHE* 3.0 6.4 + - - +
152A ASN* 2.9 44.6 + - - +
196A ILE* 3.7 28.0 - - + +
198A LYS* 5.4 0.9 - - - -
199A LEU* 3.8 38.1 - - + +
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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
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145A GLU 2.9 17.7 + - - -
146A GLN* 3.0 16.6 + - - +
148A ILE* 1.3 79.2 - - - +
150A LEU* 1.3 55.8 + - - +
152A ASN* 3.8 5.5 - - - +
153A LYS* 2.9 30.2 + - - +
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Residues in contact with LEU 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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108A VAL* 3.7 16.8 - - + +
111A GLU* 3.9 15.0 - - + -
112A VAL* 3.5 28.3 - - + -
146A GLN* 3.3 15.7 + - + +
147A ILE 3.1 4.8 + - - +
149A SER* 1.3 80.6 + - - +
151A PHE* 1.3 66.4 + - - +
153A LYS* 3.7 21.0 - - + +
154A TYR* 2.9 62.4 + - + +
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Residues in contact with PHE 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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101A GLY* 3.8 16.2 - - - -
104A LEU* 3.3 42.0 - - + -
105A LEU* 4.5 9.6 - - + -
108A VAL* 3.9 15.7 - - + +
147A ILE* 2.7 19.8 + - + +
148A ILE* 3.4 11.2 - - - +
150A LEU* 1.3 74.5 - - - +
152A ASN* 1.3 74.5 + - - +
154A TYR* 3.1 6.2 + - - +
155A VAL* 3.0 24.3 + - + +
193A ILE* 3.9 22.0 - - + -
194A GLY 3.5 20.2 - - - -
196A ILE* 3.2 39.0 - - + -
213A MET* 4.5 4.5 - - + -
215A LEU* 4.0 5.4 - - + -
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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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148A ILE* 2.9 27.9 + - - +
149A SER* 3.8 5.8 - - - +
151A PHE* 1.3 82.6 - - - +
153A LYS* 1.3 59.2 + - - +
155A VAL* 2.6 37.2 + - - +
156A ASP* 3.0 10.4 + - - +
195A HIS* 3.2 40.4 + - + +
196A ILE* 3.0 27.7 + - - +
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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 SER 2.9 22.5 + - - +
150A LEU* 3.7 23.7 - - + +
151A PHE 3.4 0.2 - - - -
152A ASN* 1.3 71.9 - - - +
154A TYR* 1.3 68.5 + - + +
156A ASP* 3.5 10.6 + - - +
157A GLU* 3.0 50.2 + - + +
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Residues in contact with TYR 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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104A LEU* 4.0 17.7 - - + -
107A HIS* 3.8 14.0 + + - -
108A VAL* 3.5 22.9 - - + -
111A GLU* 3.6 22.2 + - - +
150A LEU* 2.9 52.5 + - + +
151A PHE 3.1 6.0 + - - +
152A ASN 3.1 0.8 - - - -
153A LYS* 1.3 81.5 - - + +
155A VAL* 1.3 67.8 + - - +
157A GLU* 3.3 15.0 + - - +
158A GLY 2.8 18.9 + - - +
175A ARG* 3.5 21.5 + - - +
177A PHE* 3.7 19.1 - + - -
190A ILE* 3.5 14.7 - - + +
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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
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104A LEU* 4.4 8.1 - - + -
151A PHE* 3.0 28.3 - - + +
152A ASN* 2.6 21.2 + - - +
154A TYR* 1.3 70.9 - - - +
156A ASP* 1.3 56.7 + - - +
158A GLY* 2.6 28.4 + - - -
190A ILE* 3.8 19.3 - - - +
191A LYS* 3.4 17.0 - - - +
193A ILE* 5.2 0.7 - - + -
194A GLY* 3.6 44.0 - - - +
195A HIS* 3.9 10.5 - - + -
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Residues in contact with ASP 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 ASN* 3.0 9.3 + - - +
153A LYS* 3.8 10.0 - - - +
155A VAL* 1.3 80.8 - - - +
157A GLU* 1.3 66.5 + - + +
158A GLY* 3.0 2.3 + - - -
191A LYS* 4.4 8.5 + - - +
195A HIS* 2.7 37.4 + - - -
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Residues in contact with GLU 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* 3.0 51.6 + - + +
154A TYR* 3.5 8.8 - - - +
156A ASP* 1.3 76.5 - - + +
158A GLY* 1.3 69.4 + - - +
175A ARG* 3.0 29.7 + - - +
191A LYS* 4.1 9.5 + - - -
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Residues in contact with GLY 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 TYR 2.8 7.1 + - - +
155A VAL 2.6 24.0 + - - -
157A GLU* 1.3 85.2 - - - +
159A GLY* 1.3 58.8 + - - -
175A ARG* 4.0 10.9 + - - -
189A ASP* 3.5 4.5 - - - -
190A ILE* 3.8 9.0 - - - -
191A LYS* 3.5 20.4 - - - -
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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