Contacts of the helix formed by residues 149 - 164 (chain A) in PDB entry 2AGA
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 SER 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A GLN* 3.1 11.4 + - - +
147A LEU* 4.1 8.3 + - - +
148A ILE* 1.3 73.9 - - - +
150A ASP* 1.3 57.7 + - - +
151A THR* 3.0 11.6 - - - +
152A TYR* 2.7 27.4 + - - +
153A LEU* 2.6 34.4 + - - +
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Residues in contact with ASP 150 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ILE* 3.1 53.4 - - + +
130A LYS* 5.6 4.3 + - - -
133A LYS 3.2 10.8 - - - +
134A GLN* 2.5 40.5 + - - +
135A TRP* 4.3 6.3 + - - -
149A SER* 1.3 73.6 + - - +
151A THR* 1.3 60.2 + - - +
152A TYR 3.5 0.3 + - - -
154A ALA* 3.6 7.6 + - - +
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Residues in contact with THR 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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149A SER* 3.0 12.5 - - - +
150A ASP* 1.3 78.5 - - - +
152A TYR* 1.3 62.5 + - + +
154A ALA* 4.8 2.8 - - - +
155A LEU* 3.1 24.1 + - - +
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Residues in contact with TYR 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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147A LEU 5.6 2.2 - - - -
148A ILE* 3.7 13.2 - - + -
149A SER* 2.7 33.0 + - - +
151A THR* 1.3 82.1 - - + +
153A LEU* 1.3 54.9 - - - +
154A ALA 3.2 1.6 - - - -
155A LEU* 3.0 23.4 - - + +
156A PHE* 2.4 49.3 + + + +
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Residues in contact with LEU 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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111A PRO 3.6 15.9 - - - +
112A ILE* 3.6 22.2 - - + -
117A PHE* 4.7 3.1 - - + -
128A VAL* 4.3 17.5 - - + -
135A TRP* 3.4 33.2 - - + -
148A ILE* 3.1 19.0 - - + +
149A SER 2.6 15.6 + - - +
152A TYR* 1.3 72.1 - - - +
154A ALA* 1.3 57.6 + - - +
156A PHE* 3.4 9.6 - - + +
157A LEU* 2.8 67.9 + - + +
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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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111A PRO* 3.4 21.7 - - + +
112A ILE* 3.4 30.5 - - + -
150A ASP 3.6 8.2 + - - +
151A THR* 4.8 3.1 - - - +
152A TYR 3.2 0.4 - - - -
153A LEU* 1.3 76.5 - - - +
155A LEU* 1.3 61.1 + - - +
157A LEU* 3.4 2.1 + - - +
158A ALA* 2.9 30.1 + - - +
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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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151A THR 3.1 18.9 + - - +
152A TYR* 3.0 38.6 + - + +
154A ALA* 1.3 79.8 - - - +
156A PHE* 1.3 72.5 + - - +
158A ALA* 3.3 8.4 + - + +
159A GLN* 2.6 72.9 + - + +
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Residues in contact with PHE 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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119A CYS* 3.9 27.8 - - + -
126A PHE* 5.3 5.2 - + - -
128A VAL* 4.9 3.1 - - + -
137A ASN* 3.6 23.3 - - - -
148A ILE* 4.2 11.7 - - + -
152A TYR* 2.4 35.9 + + + +
153A LEU* 3.4 12.1 - - + +
155A LEU* 1.3 74.8 - - + +
157A LEU* 1.3 82.2 + - + +
159A GLN* 2.9 10.0 + - + +
160A LEU* 2.9 35.6 + - + -
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Residues in contact with LEU 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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99A PHE* 4.2 7.9 - - + -
111A PRO* 3.2 17.9 - - + -
117A PHE* 3.1 43.1 - - + -
119A CYS* 5.3 2.7 - - + -
128A VAL* 5.8 1.6 - - + -
153A LEU* 2.8 44.8 + - + +
154A ALA 3.9 3.6 - - - +
156A PHE* 1.3 92.9 - - + +
158A ALA* 1.3 52.2 + - - +
160A LEU* 3.2 15.7 - - + +
161A GLN* 2.7 40.9 + - - +
167A ILE* 3.6 15.5 - - + -
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Residues in contact with ALA 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 ALA 2.9 18.4 + - - +
155A LEU* 3.3 10.3 - - + +
156A PHE 3.0 0.2 - - - -
157A LEU* 1.3 75.8 - - - +
159A GLN* 1.3 55.5 + - + +
161A GLN* 3.4 7.3 - - - +
162A GLN* 2.7 44.6 + - - +
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Residues in contact with GLN 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 LEU* 2.6 50.3 - - + +
156A PHE* 2.9 11.0 + - + +
158A ALA* 1.3 77.7 - - + +
160A LEU* 1.3 57.3 + - - +
162A GLN* 3.4 5.0 + - - +
163A GLU* 2.8 30.0 + - - +
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Residues in contact with LEU 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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119A CYS* 3.7 26.0 - - + -
120A ASN 4.9 1.3 - - - +
156A PHE* 2.9 20.2 + - + +
157A LEU* 3.2 31.9 - - + +
159A GLN* 1.3 73.5 - - - +
161A GLN* 1.3 63.3 + - - +
163A GLU* 3.0 15.7 - - + +
164A GLY 2.8 24.6 + - - -
165A TYR 3.5 2.8 + - - -
166A SER* 3.6 26.5 - - - +
167A ILE* 3.0 41.1 - - + -
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Residues in contact with GLN 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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99A PHE* 3.4 14.5 - - - -
100A ASN* 3.0 31.5 + - - +
105A GLN* 3.1 31.9 - - - +
157A LEU 2.7 28.0 + - - +
158A ALA* 3.4 9.4 - - - +
160A LEU* 1.3 75.5 - - - +
162A GLN* 1.3 59.8 + - + +
164A GLY 2.7 23.9 - - - +
165A TYR* 2.8 33.1 + - + -
167A ILE* 3.2 9.2 - - + -
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Residues in contact with GLN 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 ALA* 2.7 26.3 + - - +
159A GLN* 3.9 4.9 - - - +
161A GLN* 1.3 73.5 - - + +
163A GLU* 1.3 63.2 + - - +
164A GLY* 3.5 0.3 + - - -
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Residues in contact with GLU 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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121A TYR* 5.9 2.3 - - - -
122A LYS* 4.3 25.0 + - - +
159A GLN 2.8 15.6 + - - +
160A LEU* 3.0 24.5 - - + +
161A GLN 3.2 0.4 - - - -
162A GLN* 1.3 80.9 - - - +
164A GLY* 1.3 58.2 + - - +
165A TYR 5.1 0.4 + - - +
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Residues in contact with GLY 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 LEU 2.8 5.8 + - - -
161A GLN 2.7 7.1 - - - +
162A GLN 3.2 1.6 - - - -
163A GLU* 1.3 85.5 - - - +
165A TYR* 1.3 82.3 + - - +
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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