Contacts of the helix formed by residues 149 - 157 (chain A) in PDB entry 2POD
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 ASP 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLY* 4.8 2.1 - - - -
124A PRO* 4.3 16.4 - - - +
126A TYR* 5.7 0.5 + - - -
146A ALA 4.5 11.8 + - - +
147A ARG* 3.4 3.5 + - - -
148A TYR* 1.3 71.6 - - - +
150A ASP* 1.3 58.9 + - - +
151A LEU* 3.3 3.1 + - - +
152A ASN* 3.4 33.2 + - - +
153A ALA* 2.9 27.5 + - - +
157A ARG* 4.7 14.5 + - - +
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Residues in contact with ASP 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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119A ASN* 3.5 13.1 + - - -
121A CYS* 3.3 23.5 - - + +
122A ALA 3.7 11.1 + - - +
123A GLY* 4.3 1.2 - - - -
147A ARG 5.1 0.2 - - - +
148A TYR* 3.0 20.7 + - - +
149A ASP* 1.3 73.4 + - - +
151A LEU* 1.3 60.1 + - - +
153A ALA* 3.8 6.6 - - - +
154A PHE* 2.9 30.1 + - - -
161A LEU* 3.4 20.1 - - + +
347A VAL* 5.8 0.2 - - - +
348A ARG* 3.0 44.0 + - - +
349A ALA 5.0 0.9 + - - -
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Residues in contact with LEU 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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121A CYS 3.1 13.4 + - - +
123A GLY* 3.8 17.9 - - - +
149A ASP* 6.1 0.4 - - - +
150A ASP* 1.3 76.4 - - - +
152A ASN* 1.3 68.6 + - - +
154A PHE* 3.3 20.2 + - + -
155A LEU* 3.1 43.0 + - + +
176A TRP* 3.6 37.9 - - + +
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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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149A ASP* 3.4 33.4 + - - +
151A LEU* 1.3 85.6 - - - +
153A ALA* 1.3 64.0 + - - +
155A LEU* 4.0 17.1 - - - +
156A HIS* 3.1 43.3 + - + +
157A ARG* 4.5 7.1 + - - +
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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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149A ASP 2.9 18.2 + - - +
150A ASP* 3.6 13.9 - - - +
151A LEU 3.2 0.2 - - - -
152A ASN* 1.3 78.3 - - - +
154A PHE* 1.3 57.0 + - - +
157A ARG* 2.8 64.9 + - + +
158A ALA* 3.4 0.2 - - - -
161A LEU* 3.9 22.9 - - + -
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Residues in contact with PHE 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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121A CYS* 3.7 19.1 - - + -
150A ASP 2.9 27.9 + - - -
151A LEU* 3.3 29.1 + - + -
153A ALA* 1.3 71.7 - - - +
155A LEU* 1.3 78.8 + - + +
156A HIS 3.3 0.9 + - - -
158A ALA* 3.6 15.4 - - + +
161A LEU* 3.6 12.9 - - + +
173A MSE 5.0 0.2 - - + -
175A ILE* 3.6 35.4 - - + -
176A TRP* 3.4 43.7 - + - -
177A PRO* 3.7 24.2 - - + -
201A PRO* 3.4 18.0 - - - +
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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 LEU* 3.1 37.2 + - + +
152A ASN* 3.8 20.9 - - - +
153A ALA 3.3 1.0 - - - -
154A PHE* 1.3 97.3 - - + +
156A HIS* 1.3 82.0 + - + +
176A TRP 5.6 0.2 - - - +
177A PRO* 4.8 13.0 - - + +
180A PRO* 5.0 15.3 - - + -
201A PRO* 4.9 8.1 - - + +
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Residues in contact with HIS 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* 3.1 36.0 + - + +
154A PHE 3.3 0.2 - - - -
155A LEU* 1.3 101.2 + - + +
157A ARG* 1.4 70.5 + - + +
158A ALA* 3.7 2.5 - - - -
204A LYS* 3.6 24.3 + - - -
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Residues in contact with ARG 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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149A ASP* 4.7 15.6 + - - +
152A ASN* 4.5 4.8 + - - +
153A ALA* 2.8 47.6 + - - +
156A HIS* 1.4 83.4 - - + +
158A ALA* 1.3 59.8 + - - +
159A ASP* 3.3 11.4 - - - -
160A GLU* 2.9 52.2 + - + +
161A LEU* 3.1 10.1 + - - +
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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
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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