Contacts of the helix formed by residues 146 - 166 (chain A) in PDB entry 2AYN
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 ALA 146 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A SER* 1.3 68.4 + - - +
148A ALA* 3.0 15.8 + - + +
149A GLN* 3.3 30.1 + - - +
150A TYR* 3.6 17.3 - - - -
213A LYS* 5.2 8.6 - - - +
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Residues in contact with SER 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 1.3 72.7 - - - +
148A ALA* 1.3 69.1 + - - +
150A TYR* 3.2 19.8 + - - +
151A ILE* 3.3 13.9 + - - +
180A MET* 4.8 5.4 + - - +
181A ALA* 3.7 32.0 + - - +
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Residues in contact with ALA 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 3.9 10.7 - - + +
147A SER* 1.3 77.7 - - - +
149A GLN* 1.3 54.4 + - - +
151A ILE* 2.5 33.9 + - - +
152A THR* 3.0 9.5 + - - -
181A ALA* 5.3 0.6 - - - +
209A VAL* 3.4 33.7 - - + -
212A GLN* 5.0 12.6 - - - +
213A LYS* 4.5 12.8 - - + -
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Residues in contact with GLN 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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135A TYR* 3.4 23.8 + - + +
137A GLY* 3.9 4.1 - - - -
138A ALA 3.1 44.3 + - - +
139A LEU* 4.1 3.8 - - - +
146A ALA 3.3 21.8 + - - +
148A ALA* 1.3 77.3 - - - +
150A TYR* 1.3 67.3 + - + +
152A THR* 3.1 10.7 + - - -
153A ALA* 2.8 31.8 + - + +
213A LYS* 3.7 25.4 + - - +
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Residues in contact with TYR 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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139A LEU* 3.9 30.3 - - + +
146A ALA 3.6 24.7 + - - -
147A SER* 3.2 11.3 + - - +
148A ALA 2.9 2.2 + - - -
149A GLN* 1.3 84.5 - - + +
151A ILE* 1.3 53.2 + - - +
153A ALA* 3.3 8.5 - - + +
154A ALA* 2.8 34.5 + - - +
177A PHE* 3.2 37.2 - + + -
100B MET* 5.7 9.2 - - + -
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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 SER 3.9 7.4 - - - +
148A ALA* 2.5 16.5 + - - +
150A TYR* 1.3 70.2 - - - +
152A THR* 1.3 65.5 + - - +
153A ALA 3.2 0.2 - - - -
154A ALA* 3.8 5.9 - - - +
155A LEU* 2.9 24.2 + - + +
174A LEU* 4.2 7.1 - - + +
177A PHE* 3.4 28.0 - - + +
178A LEU* 3.8 14.4 - - + +
181A ALA* 3.4 34.3 - - + -
182A PHE* 4.0 13.5 - - + -
206A MET* 4.4 22.9 - - + -
209A VAL* 4.4 18.4 - - + -
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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
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132A LEU* 3.8 12.5 - - + +
135A TYR* 3.8 27.8 - - + -
148A ALA 3.0 11.1 + - - -
149A GLN* 3.1 7.1 + - - -
151A ILE* 1.3 79.9 - - - +
153A ALA* 1.3 66.5 + - - +
155A LEU* 3.3 10.7 + - - +
156A ARG* 3.4 9.2 + - - +
209A VAL* 3.5 16.6 - - - +
210A LEU* 4.0 24.7 + - + -
213A LYS* 3.7 24.7 - - + +
214A LEU* 4.5 4.0 - - + -
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Residues in contact with ALA 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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135A TYR* 4.3 8.0 - - + -
149A GLN* 2.8 13.3 + - + +
150A TYR* 3.3 13.7 - - + +
152A THR* 1.3 76.2 - - - +
154A ALA* 1.3 65.6 + - - +
156A ARG* 2.8 49.5 + - - +
157A ASP* 3.2 9.3 - - - +
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Residues in contact with ALA 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 TYR 2.8 20.2 + - - +
151A ILE* 3.8 6.7 - - - +
153A ALA* 1.3 72.6 - - - +
155A LEU* 1.3 63.2 - - - +
157A ASP* 3.4 10.5 + - - +
158A LEU* 3.0 23.2 + - - +
173A ILE* 4.7 10.1 - - + -
174A LEU* 4.0 32.1 - - + +
177A PHE* 4.5 12.1 - - + -
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Residues in contact with LEU 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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119A VAL* 4.0 18.6 - - + -
122A ILE* 4.7 7.6 - - + -
132A LEU* 4.3 11.0 - - + -
151A ILE* 2.9 18.0 + - + +
152A THR* 3.5 5.6 - - - +
153A ALA 2.9 1.2 + - - -
154A ALA* 1.3 77.8 - - - +
156A ARG* 1.3 61.4 + - - +
158A LEU* 3.2 8.1 + - + +
159A PHE* 3.0 45.5 + - + -
174A LEU* 4.1 20.8 - - + +
206A MET* 4.0 24.0 - - + -
210A LEU* 4.2 29.8 - - + -
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Residues in contact with ARG 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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132A LEU* 4.0 33.9 + - + +
133A LYS* 4.5 6.8 + - + +
135A TYR* 3.3 44.6 + - + +
136A ALA* 4.8 6.5 - - - +
137A GLY 5.4 1.6 - - - +
152A THR 3.4 5.8 + - - +
153A ALA* 2.8 41.5 + - - +
155A LEU* 1.3 70.9 - - - +
157A ASP* 1.3 84.4 + - - +
159A PHE* 2.8 14.8 + - - +
160A ASP* 2.7 47.2 + - - +
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Residues in contact with ASP 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 ALA* 3.2 10.4 + - - +
154A ALA* 3.5 11.9 - - - +
156A ARG* 1.3 111.0 + - - +
158A LEU* 1.3 64.6 + - - +
160A ASP* 3.1 8.1 + - - +
161A SER* 2.9 28.7 + - - +
173A ILE* 6.2 4.7 - - + -
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Residues in contact with LEU 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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106A LEU* 3.7 14.4 - - + -
119A VAL* 4.2 16.6 - - + -
154A ALA 3.0 14.0 + - - +
155A LEU* 3.2 10.5 - - + +
156A ARG 3.0 0.2 - - - -
157A ASP* 1.3 76.9 - - - +
159A PHE* 1.3 65.4 + - + +
161A SER* 3.3 4.8 + - - -
162A MET* 2.9 53.0 + - + +
169A ILE* 4.8 10.3 - - + -
171A PRO* 3.8 23.3 - - + -
174A LEU* 3.5 33.2 - - + -
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Residues in contact with PHE 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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119A VAL* 3.7 24.7 - - + -
122A ILE* 4.5 5.4 - - + -
123A ARG* 3.3 64.2 - - + +
128A LEU* 5.6 0.7 - - + -
129A LYS* 4.7 14.8 - - + -
132A LEU* 3.1 38.8 - - + -
155A LEU* 3.0 32.3 + - + -
156A ARG* 2.8 13.1 + - - +
158A LEU* 1.3 74.3 - - + +
160A ASP* 1.3 63.2 + - - +
162A MET* 2.8 19.3 + - - +
163A ASP* 2.8 21.5 + - - +
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Residues in contact with ASP 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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133A LYS* 5.0 19.0 - - - +
156A ARG* 2.7 35.9 + - - +
157A ASP* 3.3 11.5 - - - +
159A PHE* 1.3 72.0 - - - +
161A SER* 1.3 55.5 + - - +
163A ASP* 2.7 41.5 + - - +
164A LYS* 3.8 25.6 + - - +
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Residues in contact with SER 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 ASP* 2.9 18.9 + - - +
158A LEU* 3.8 5.4 - - - -
160A ASP* 1.3 72.9 - - - +
162A MET* 1.3 60.4 + - - +
164A LYS* 3.4 9.0 + - - +
165A THR* 3.0 34.9 + - - -
169A ILE* 3.7 16.6 - - - -
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Residues in contact with MET 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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104A CYS* 3.0 62.3 + - + +
106A LEU* 3.6 25.6 - - + -
119A VAL* 5.2 1.3 - - - -
120A GLN* 3.4 19.3 - - - +
123A ARG* 3.3 31.4 + - - +
158A LEU* 2.9 44.2 + - + +
159A PHE* 2.8 20.2 + - - +
161A SER* 1.3 73.3 - - - +
163A ASP* 1.3 57.1 + - - +
164A LYS* 2.8 14.3 + - - -
166A SER* 4.3 1.6 + - - -
169A ILE* 4.1 2.9 - - + -
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Residues in contact with ASP 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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123A ARG* 2.9 23.3 + - - -
129A LYS* 4.9 9.6 + - - +
133A LYS* 4.2 22.2 + - - -
159A PHE* 2.8 22.1 + - - +
160A ASP* 2.7 14.9 + - - +
162A MET* 1.3 74.4 - - - +
164A LYS* 1.3 70.3 + - + +
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Residues in contact with LYS 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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160A ASP* 3.8 36.2 + - - +
161A SER* 3.8 8.5 - - - +
162A MET 2.8 5.1 + - - -
163A ASP* 1.3 91.8 - - - +
165A THR* 1.3 55.2 - - - +
166A SER* 2.2 32.8 + - - -
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Residues in contact with THR 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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104A CYS* 4.6 2.2 - - - -
161A SER* 3.0 18.9 + - - -
164A LYS* 1.3 75.7 - - - +
166A SER* 1.3 56.8 + - - +
167A SER* 2.7 54.8 + - - +
168A SER 3.6 19.1 - - - +
169A ILE* 3.7 16.3 - - + +
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Residues in contact with SER 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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100A MET 5.0 10.0 + - - +
101A GLU* 5.9 0.5 - - - -
102A LEU* 4.3 16.7 + - - +
103A PRO 5.2 1.0 - - - +
104A CYS* 4.6 14.6 - - - +
162A MET 4.3 5.5 + - - -
164A LYS 2.2 24.9 + - - -
165A THR* 1.3 68.0 - - - +
167A SER* 1.3 57.1 + - - +
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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
------------------------------------------------------------
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