Contacts of the helix formed by residues 151 - 167 (chain A) in PDB entry 3C33
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 ILE 151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A PHE* 6.0 0.7 - - + -
149A SER* 3.1 15.1 + - - +
150A LYS* 1.3 79.3 - - + +
152A SER* 1.3 69.5 + - - +
153A THR* 4.1 12.3 - - - +
154A TYR* 3.0 31.6 + - + -
155A GLU* 2.8 20.5 + - - +
240B GLU 4.0 22.0 - - - +
241B GLY* 5.0 7.4 - - - -
245B MET* 5.5 11.4 - - + -
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Residues in contact with SER 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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150A LYS 3.5 2.8 + - - -
151A ILE* 1.3 76.2 - - - +
153A THR* 1.3 62.5 + - - +
155A GLU* 3.3 16.7 + - - +
156A LYS* 2.9 30.0 + - - +
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Residues in contact with THR 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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124A ASP* 2.6 39.2 + - + +
127A ALA* 3.8 17.8 - - + +
151A ILE* 3.3 8.3 - - - +
152A SER* 1.3 83.9 + - - +
154A TYR* 1.3 80.1 + - + +
156A LYS* 3.3 9.0 + - - +
157A MET* 3.0 35.2 + - - +
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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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123A ALA* 4.2 14.2 - - + +
145A PHE* 3.9 20.4 - + + -
146A PHE* 3.8 29.2 - + + +
149A SER* 3.6 24.7 - - - +
151A ILE* 3.0 33.9 + - + +
153A THR* 1.3 92.9 - - + +
155A GLU* 1.3 60.5 + - - +
157A MET* 3.6 7.8 - - - +
158A TRP* 2.8 29.7 + - - +
211A ILE* 3.6 38.9 + - + +
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Residues in contact with GLU 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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146A PHE 5.1 0.7 - - - -
149A SER 3.3 19.7 + - - +
150A LYS* 3.5 39.7 + - - +
151A ILE 2.8 11.1 + - - +
152A SER* 3.5 23.1 - - - +
154A TYR* 1.3 76.4 - - - +
156A LYS* 1.3 56.5 + - - +
158A TRP* 3.1 8.3 + - - +
159A ALA* 2.8 30.9 + - - +
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Residues in contact with LYS 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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127A ALA* 2.6 40.6 + - + +
128A LYS* 3.9 13.0 + - - +
129A GLN* 4.6 1.8 + - - +
130A THR* 5.9 3.4 - - - +
134A TYR* 4.2 0.8 + - - +
152A SER 2.9 13.6 + - - +
153A THR* 3.3 13.7 - - - +
154A TYR 3.3 0.2 - - - -
155A GLU* 1.3 76.4 - - - +
157A MET* 1.3 62.0 + - - +
159A ALA* 3.3 7.9 + - - +
160A PHE* 3.1 22.0 + - - +
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Residues in contact with MET 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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123A ALA* 3.8 38.8 - - + +
126A LEU* 4.7 6.5 - - + -
127A ALA* 3.6 15.3 - - + -
134A TYR* 3.5 36.9 - - + +
146A PHE* 3.8 33.9 - - + -
153A THR* 3.0 21.1 + - - +
154A TYR* 3.6 11.4 - - - +
156A LYS* 1.3 73.6 - - - +
158A TRP* 1.3 60.8 + - - +
160A PHE* 3.2 3.1 + - - +
161A MET* 2.9 35.8 + - + +
188A LEU* 4.2 14.4 - - + -
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Residues in contact with TRP 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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143A MET* 3.4 46.7 - - + -
146A PHE* 3.4 28.0 - - + +
147A LYS* 3.7 51.4 + - + +
154A TYR 2.8 13.5 + - - +
155A GLU* 3.1 6.7 + - - +
157A MET* 1.3 74.3 - - - +
159A ALA* 1.3 60.6 + - - +
161A MET* 4.0 19.9 - - + +
162A SER* 2.7 62.4 + - - -
166A GLN* 4.2 12.6 - - - -
169A LEU* 4.8 2.5 - - + -
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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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155A GLU 2.8 12.4 + - - +
156A LYS* 3.5 11.9 - - - +
158A TRP* 1.3 77.8 - - - +
160A PHE* 1.3 62.1 + - - +
162A SER* 3.6 5.6 + - - -
163A SER* 3.1 24.9 + - - -
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Residues in contact with PHE 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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129A GLN 4.9 0.4 - - - -
130A THR* 4.1 40.8 - - + -
132A ILE 4.5 2.0 - - - -
133A GLU* 3.4 36.1 - - - -
134A TYR* 3.3 66.0 - + - +
156A LYS 3.1 10.7 + - - +
157A MET 3.6 2.2 - - - +
158A TRP 3.2 0.2 - - - -
159A ALA* 1.3 74.1 - - - +
161A MET* 1.3 67.1 + - - +
163A SER* 2.8 26.5 + - - +
164A ARG* 3.5 25.8 + - - -
168A ALA* 4.0 1.6 - - + -
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Residues in contact with MET 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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134A TYR* 3.7 30.1 - - + +
135A GLY* 3.9 13.5 - - - -
136A ALA* 4.5 4.7 - - - -
143A MET* 5.3 1.6 - - - -
146A PHE* 3.7 42.8 - - + -
157A MET* 2.9 33.8 + - + +
158A TRP* 3.8 20.4 - - + +
160A PHE* 1.3 79.2 - - - +
162A SER* 1.3 61.1 + - - +
163A SER 3.6 1.4 + - - +
166A GLN* 3.5 18.9 - - - -
168A ALA* 4.1 9.3 - - - +
169A LEU* 3.9 28.3 - - + +
188A LEU* 4.7 5.6 - - + -
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Residues in contact with SER 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 TRP* 2.7 57.7 + - - -
159A ALA* 3.6 6.4 + - - -
161A MET* 1.3 74.4 - - - +
163A SER* 1.3 67.6 + - - +
164A ARG 3.8 0.2 + - - -
165A GLN* 4.0 2.8 + - - -
166A GLN* 3.4 23.6 + - - +
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Residues in contact with SER 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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159A ALA 3.1 17.7 + - - -
160A PHE* 2.8 21.6 + - - +
161A MET 4.0 1.9 - - - +
162A SER* 1.3 78.7 - - - +
164A ARG* 1.3 94.5 + - - +
166A GLN* 3.0 10.9 + - - -
167A SER 3.6 5.2 + - - -
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Residues in contact with ARG 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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133A GLU* 2.8 42.2 + - - -
160A PHE* 3.5 28.2 + - - -
162A SER 3.8 0.2 + - - -
163A SER* 1.3 90.1 + - - +
165A GLN* 1.3 75.5 + - - +
167A SER* 3.1 35.5 + - - +
168A ALA* 4.1 4.8 - - - +
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Residues in contact with GLN 165 (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 ARG* 4.5 3.8 + - - -
162A SER 4.0 3.2 + - - -
163A SER 3.3 0.6 - - - -
164A ARG* 1.3 79.7 + - - +
166A GLN* 1.3 70.7 + - - +
167A SER* 3.4 1.2 + - - -
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Residues in contact with GLN 166 (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 ARG* 2.8 51.3 + - - +
139A ASP* 5.5 1.8 + - - -
143A MET* 4.5 5.3 - - - +
158A TRP* 4.2 17.6 - - - -
161A MET 3.5 13.5 - - - -
162A SER* 3.4 18.8 + - - +
163A SER 3.0 5.6 + - - -
165A GLN* 1.3 78.7 - - - +
167A SER* 1.3 65.3 + - - +
168A ALA 3.1 3.1 - - - -
169A LEU* 2.9 35.9 + - + +
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Residues in contact with SER 167 (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 GLU* 4.6 1.4 + - - -
163A SER 3.6 1.8 + - - -
164A ARG* 3.1 45.4 + - - +
165A GLN 3.2 1.7 - - - -
166A GLN* 1.3 77.2 - - - +
168A ALA* 1.3 58.4 + - - +
169A LEU 3.5 2.9 + - - +
179A ARG* 3.0 25.4 + - - -
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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