Contacts of the helix formed by residues 146 - 153 (chain D) in PDB entry 5HMG
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 ASN 146 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26D HIS* 3.1 16.2 + - - -
28D ASN* 2.8 33.6 + - - +
30D GLU* 3.2 33.7 + - - +
31D GLY 4.5 0.3 - - - +
145D ASP* 1.3 75.8 - - - +
147D ALA* 1.3 57.0 + - - +
149D ILE* 3.4 5.3 + - - +
150D GLU* 2.9 27.1 + - - +
153D ARG* 5.5 1.4 + - - -
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Residues in contact with ALA 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D GLU* 4.9 0.6 + - - -
145D ASP* 3.1 11.5 + - - +
146D ASN* 1.3 74.6 - - - +
148D CYS* 1.3 61.4 + - - +
150D GLU* 3.2 10.0 + - - +
151D SER* 2.9 26.5 + - - -
401D NAG 3.6 21.2 - - - +
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Residues in contact with CYS 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D HIS* 3.8 15.3 - - - -
144D CYS* 2.0 48.5 - - - -
145D ASP* 2.9 20.3 + - - +
147D ALA* 1.3 77.3 - - - +
149D ILE* 1.3 60.5 + - - +
151D SER* 2.8 24.4 + - - -
152D ILE* 3.0 11.5 + - - +
157D TYR* 4.0 13.0 - - - -
162D TYR* 3.8 20.4 - - + +
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Residues in contact with ILE 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA* 4.8 2.7 - - + -
12C THR 4.9 0.4 - - - +
13C LEU* 4.2 12.6 - - + -
26D HIS* 3.3 52.3 - - + +
28D ASN* 3.5 26.5 - - + +
140D ILE* 4.1 17.5 - - + -
144D CYS* 3.7 18.2 - - + -
145D ASP 3.0 4.8 + - - +
146D ASN 3.6 7.6 - - - +
148D CYS* 1.3 73.6 - - - +
150D GLU* 1.3 61.5 + - - +
152D ILE* 3.2 6.1 + - + +
153D ARG* 3.1 44.5 + - + +
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Residues in contact with GLU 150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D ASN 2.9 14.6 + - - +
147D ALA* 3.4 9.6 - - - +
148D CYS 3.2 0.2 - - - -
149D ILE* 1.3 76.1 - - - +
151D SER* 1.3 56.3 + - - +
153D ARG* 2.6 39.0 + - - +
154D ASN* 2.8 49.9 + - - +
401D NAG 3.7 24.9 + - - +
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Residues in contact with SER 151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ALA 2.9 13.9 + - - -
148D CYS* 2.8 22.4 + - - -
150D GLU* 1.3 73.7 - - - +
152D ILE* 1.3 64.2 + - - +
154D ASN* 3.1 11.1 - - - +
155D GLY 3.1 0.3 + - - -
156D THR* 2.8 43.8 + - - -
157D TYR* 3.1 22.0 + - - +
162D TYR* 4.9 2.8 + - - -
401D NAG 3.9 8.9 + - - -
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Residues in contact with ILE 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 3.9 22.0 - - + -
24D PHE* 5.2 3.4 - - + -
122D THR* 4.3 11.3 + - + -
125D GLN* 2.8 32.0 + - + +
126D LEU* 3.5 31.0 - - + -
140D ILE* 3.6 24.0 - - + -
144D CYS* 4.2 7.9 - - - -
148D CYS 3.0 11.6 + - - +
149D ILE* 3.7 10.1 - - + +
151D SER* 1.3 74.0 - - - +
153D ARG* 1.3 64.1 + - + +
155D GLY* 3.2 3.5 + - - -
157D TYR* 3.4 35.4 - - + -
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Residues in contact with ARG 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C LEU* 5.3 2.0 - - + -
24D PHE* 3.5 56.2 - - + +
26D HIS* 4.1 14.3 + - - -
33D GLY 5.7 0.2 - - - -
34D GLN 4.9 2.6 + - - -
35D ALA* 3.6 30.3 - - - +
36D ALA 5.9 0.9 - - - -
37D ASP* 4.9 6.4 - - - +
146D ASN 5.5 1.0 + - - -
149D ILE* 3.1 38.3 + - + +
150D GLU* 2.6 48.1 + - - +
152D ILE* 1.3 79.8 - - + +
154D ASN* 1.3 57.2 + - - +
155D GLY 3.3 0.6 + - - -
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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