Contacts of the helix formed by residues 146 - 163 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B SER* 1.3 67.7 + - - +
148B ALA* 3.1 15.7 - - + +
149B GLN* 3.2 33.5 + - - +
150B TYR* 3.5 16.6 + - - -
213B LYS* 5.0 10.2 - - - +
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Residues in contact with SER 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 1.3 73.1 - - - +
148B ALA* 1.3 67.5 + - - +
150B TYR* 3.1 21.1 + - - +
151B ILE* 3.3 12.0 + - - +
180B MET* 5.0 4.9 + - - +
181B ALA* 3.6 34.7 + - - +
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Residues in contact with ALA 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ALA* 4.0 10.9 - - + +
147B SER* 1.3 77.7 - - - +
149B GLN* 1.3 55.5 + - - +
151B ILE* 2.7 30.3 + - - +
152B THR* 2.9 12.8 + - - -
181B ALA* 5.2 0.8 - - - +
209B VAL* 3.4 32.9 - - + +
212B GLN* 4.8 13.0 - - - +
213B LYS* 4.4 12.3 - - + -
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Residues in contact with GLN 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TYR* 3.4 24.7 - - + +
137B GLY* 3.6 5.3 - - - -
138B ALA 2.8 47.3 + - - +
139B LEU* 4.1 3.6 - - - +
146B ALA 3.2 24.3 + - - +
148B ALA* 1.3 78.5 - - - +
150B TYR* 1.3 63.5 + - + +
152B THR* 3.2 6.8 + - - -
153B ALA* 2.9 31.3 + - + +
213B LYS* 3.8 23.9 + - - +
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 4.0 27.2 - - + +
146B ALA 3.5 24.2 + - - -
147B SER* 3.1 13.2 + - - +
148B ALA 3.1 0.2 + - - -
149B GLN* 1.3 84.1 - - + +
151B ILE* 1.3 56.9 + - - +
153B ALA* 3.3 8.1 - - + +
154B ALA* 2.8 30.0 + - - +
177B PHE* 3.2 37.7 - + + -
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Residues in contact with ILE 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B SER 3.3 6.0 + - - +
148B ALA* 2.7 16.0 + - - +
150B TYR* 1.3 69.2 - - - +
152B THR* 1.3 66.8 + - - +
153B ALA 3.1 1.6 - - - -
154B ALA* 3.7 5.6 - - - +
155B LEU* 2.8 25.2 + - + +
174B LEU* 4.4 11.9 - - + +
177B PHE* 3.5 38.6 - - + +
178B LEU* 3.6 18.2 - - + +
181B ALA* 3.7 18.4 - - + -
182B PHE* 4.1 13.9 - - + -
206B MET* 4.7 15.3 - - + -
209B VAL* 4.2 20.2 - - + -
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Residues in contact with THR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.6 18.7 - - + +
135B TYR* 3.6 31.8 - - + -
148B ALA 2.9 12.4 + - - -
149B GLN* 3.5 7.6 - - - -
151B ILE* 1.3 79.6 - - - +
153B ALA* 1.3 67.2 + - - +
155B LEU* 3.3 11.2 + - - +
156B ARG* 3.3 8.1 + - - +
209B VAL* 3.3 17.1 - - - +
210B LEU* 4.3 14.8 + - + -
213B LYS* 3.6 21.7 - - + +
214B LEU* 4.4 4.7 - - + -
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B TYR* 4.2 10.0 - - + -
149B GLN* 2.9 14.5 + - + +
150B TYR* 3.3 13.9 - - + +
152B THR* 1.3 75.3 - - - +
154B ALA* 1.3 55.6 + - - +
156B ARG* 2.6 57.9 + - - +
157B ASP* 3.4 7.0 + - - +
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Residues in contact with ALA 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B TYR 2.8 21.0 + - - +
151B ILE* 3.8 5.8 - - - +
153B ALA* 1.3 71.0 - - - +
155B LEU* 1.3 62.8 + - - +
157B ASP* 3.5 10.8 + - - +
158B LEU* 3.2 23.0 + - - +
173B ILE* 4.6 11.4 - - + -
174B LEU* 4.1 31.8 - - + +
177B PHE* 4.5 11.9 - - + -
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 4.3 10.1 - - + -
122B ILE* 4.6 7.4 - - + -
132B LEU* 4.2 11.0 - - + -
151B ILE* 2.8 21.2 + - + +
152B THR* 3.4 7.2 - - - +
153B ALA 2.7 4.6 + - - -
154B ALA* 1.3 73.0 - - - +
156B ARG* 1.3 62.2 + - - +
158B LEU* 3.4 5.4 + - + +
159B PHE* 3.2 43.8 + - + -
174B LEU* 4.0 20.6 - - + +
206B MET* 3.9 29.6 - - + -
210B LEU* 3.9 33.0 - - + -
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Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B LEU* 3.8 38.3 + - + +
133B LYS* 4.5 6.8 + - + +
135B TYR* 3.3 45.3 + - + +
136B ALA* 4.6 8.9 - - - +
137B GLY 5.2 2.6 - - - +
152B THR 3.3 5.1 + - - +
153B ALA* 2.6 40.1 + - - +
155B LEU* 1.3 72.0 - - - +
157B ASP* 1.3 79.5 + - - +
159B PHE* 2.8 9.8 + - + +
160B ASP* 2.6 50.0 + - - +
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Residues in contact with ASP 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ALA* 3.4 6.5 + - - +
154B ALA* 3.7 13.9 - - - +
156B ARG* 1.3 108.3 + - - +
158B LEU* 1.3 53.1 + - - +
160B ASP* 3.1 9.8 + - - +
161B SER* 2.8 39.7 + - - +
173B ILE* 6.1 5.6 - - + -
191C GLN* 3.5 36.1 - - - +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU* 3.7 15.5 - - + -
119B VAL* 4.0 21.1 - - + -
154B ALA 3.2 10.0 + - - +
155B LEU* 3.4 9.9 - - + +
156B ARG 3.0 0.2 - - - -
157B ASP* 1.3 76.0 - - - +
159B PHE* 1.3 69.4 + - + +
161B SER* 3.1 5.6 + - - -
162B MET* 2.6 50.6 + - + +
169B ILE* 4.2 15.7 - - + -
171B PRO* 4.1 20.0 - - + -
174B LEU* 3.8 29.8 - - + -
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Residues in contact with PHE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B VAL* 3.8 24.5 - - + -
122B ILE* 4.6 5.2 - - + -
123B ARG* 3.2 66.0 - - + +
128B LEU* 5.4 0.9 - - + -
129B LYS* 4.7 15.0 - - + -
132B LEU* 3.2 38.4 - - + -
155B LEU* 3.2 25.5 + - + -
156B ARG* 2.8 10.9 + - - +
158B LEU* 1.3 76.7 - - + +
160B ASP* 1.3 56.9 + - - +
162B MET* 2.6 30.1 + - - +
163B ASP* 2.8 19.4 + - - +
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Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LYS* 4.9 19.2 - - - +
156B ARG* 2.6 37.8 + - - +
157B ASP* 3.2 12.1 - - - +
159B PHE* 1.3 70.2 - - - +
161B SER* 1.3 57.1 + - - +
163B ASP* 2.7 40.8 + - - +
164B LYS* 3.8 25.1 + - - +
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ASP* 2.8 20.9 + - - +
158B LEU* 3.7 3.6 - - - -
160B ASP* 1.3 73.6 - - - +
162B MET* 1.3 62.4 + - - +
164B LYS* 3.3 9.0 + - - +
165B THR* 3.2 32.5 + - - -
169B ILE* 3.6 19.3 - - - -
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Residues in contact with MET 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B CYS* 3.1 61.0 + - - +
106B LEU* 3.5 26.2 - - + -
119B VAL* 5.1 1.1 - - - -
120B GLN* 3.5 17.9 - - - +
123B ARG* 3.3 30.7 + - - +
158B LEU* 2.6 44.9 + - + +
159B PHE* 2.6 27.7 + - - +
161B SER* 1.3 68.3 - - - +
163B ASP* 1.3 55.9 + - - +
164B LYS 3.0 12.1 + - - -
166B SER* 4.5 1.4 + - - -
169B ILE* 3.9 2.0 - - + -
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Residues in contact with ASP 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A LEU* 4.8 3.3 - - - +
170A PRO* 4.8 6.9 - - - +
172A ILE* 3.8 10.2 - - - +
123B ARG* 2.8 24.8 + - - -
129B LYS* 4.6 10.2 + - - +
133B LYS* 4.0 23.5 + - - +
159B PHE* 2.8 19.6 + - - +
160B ASP* 2.7 20.5 + - - +
162B MET* 1.3 70.6 - - - +
164B LYS* 1.3 70.3 + - + +
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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
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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