Contacts of the helix formed by residues 139 - 147 (chain A) in PDB entry 5D0A
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.7 28.9 - - - +
57A ARG* 3.4 22.3 + - - +
137A GLU 3.8 0.2 + - - -
138A LEU* 1.3 72.0 - - - +
140A ASP* 1.3 63.4 + - - +
141A ARG 3.6 0.3 + - - -
142A ALA* 3.2 17.3 + - - +
143A VAL* 3.1 24.1 + - - +
503A B12 2.5 32.9 + - - -
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Residues in contact with ASP 140 (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 MET* 4.7 2.3 - - - +
134A ASP* 2.8 25.0 + - - -
136A GLY 5.7 0.5 + - - -
138A LEU 3.7 3.3 - - - +
139A SER* 1.3 71.6 - - - +
141A ARG* 1.3 55.9 + - - +
143A VAL* 3.5 2.6 + - - +
144A ALA* 3.0 28.9 + - - +
169A LEU* 3.9 10.9 - - + +
171A GLU* 2.7 41.1 - - - +
503A B12 2.7 66.3 + - + +
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Residues in contact with ARG 141 (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 SER* 3.2 1.9 + - - +
140A ASP* 1.3 78.0 - - - +
142A ALA* 1.3 59.4 + - - +
144A ALA 3.4 0.2 + - - -
145A GLU* 2.8 30.7 + - - +
156A CYS* 2.9 27.9 + - - +
157A MET* 3.4 22.6 - - - -
158A ILE* 3.5 18.2 - - + +
169A LEU* 4.1 1.6 - - + -
503A B12 2.9 157.3 + - + +
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Residues in contact with ALA 142 (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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30A PHE* 3.6 17.9 - - + -
33A LEU* 3.9 22.0 - - + -
139A SER* 3.2 28.6 + - - +
141A ARG* 1.3 72.7 - - - +
143A VAL* 1.3 65.5 + - - +
145A GLU* 3.4 5.9 + - - +
146A ARG* 3.1 25.5 + - - +
503A B12 3.5 15.0 - - - -
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Residues in contact with VAL 143 (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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25A THR* 4.2 5.8 - - + +
30A PHE* 3.9 23.3 - - + -
70A ILE* 3.7 28.5 - - + -
72A ALA* 4.0 10.8 - - + -
138A LEU* 3.9 30.5 - - + -
139A SER 3.1 14.4 + - - +
140A ASP 3.7 6.5 - - - +
142A ALA* 1.3 75.9 - - - +
144A ALA* 1.3 62.7 + - - +
146A ARG* 3.3 3.1 + - - +
147A ALA* 3.1 22.2 + - - +
171A GLU* 3.8 20.2 - - + +
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Residues in contact with ALA 144 (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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72A ALA* 4.3 7.0 - - + -
73A ILE 6.1 0.2 - - - +
140A ASP 3.0 18.1 + - - +
141A ARG 3.8 3.1 - - - +
143A VAL* 1.3 73.7 - - - +
145A GLU* 1.3 64.3 + - - +
147A ALA 3.4 0.2 + - - -
148A GLY 3.4 2.4 + - - -
149A ILE* 3.0 54.6 + - + +
150A GLY 3.9 1.6 + - - -
158A ILE* 4.3 6.3 - - + -
169A LEU* 3.9 25.1 - - + -
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Residues in contact with GLU 145 (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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141A ARG 2.8 21.7 + - - +
142A ALA* 3.8 5.5 - - - +
144A ALA* 1.3 73.2 - - - +
146A ARG* 1.3 64.5 + - - +
147A ALA 3.1 1.3 + - - -
148A GLY* 3.2 10.7 + - - -
150A GLY 3.7 16.8 - - - +
151A PHE* 4.9 2.1 - - - +
152A SER* 3.2 30.4 + - - +
158A ILE* 4.0 8.7 - - + +
183A PRO* 3.9 20.0 - - + +
184A ILE 4.9 0.2 + - - -
503A B12 4.1 13.5 - - - +
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Residues in contact with ARG 146 (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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24A PHE 4.1 2.3 - - - +
25A THR* 2.8 25.2 + - - +
26A THR* 3.0 36.2 + - - -
27A ALA 4.2 0.4 - - - -
28A ASP* 2.8 32.5 + - - +
29A THR 3.4 11.9 + - - -
30A PHE* 3.3 41.9 - - + +
142A ALA 3.1 14.6 + - - +
143A VAL 4.0 2.9 - - - +
145A GLU* 1.3 81.7 - - - +
147A ALA* 1.3 58.8 + - - +
148A GLY 3.4 0.4 - - - -
180A PRO* 5.8 0.5 - - - +
181A ASP 4.1 10.2 - - - +
183A PRO* 4.4 18.1 - - + +
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Residues in contact with ALA 147 (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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23A GLY* 3.4 23.1 - - - -
24A PHE* 3.4 31.9 - - - +
25A THR* 4.1 5.4 - - + -
72A ALA* 3.9 16.2 - - + -
143A VAL 3.1 15.9 + - - +
144A ALA 4.1 2.2 - - - +
145A GLU 3.1 0.8 - - - -
146A ARG* 1.3 79.7 - - - +
148A GLY* 1.3 59.6 + - - +
149A ILE* 3.4 1.3 - - + -
181A ASP* 3.5 16.1 - - - +
182A VAL 4.9 0.2 - - - -
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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