Contacts of the helix formed by residues 148 - 156 (chain D) in PDB entry 5NC5
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 THR 148 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D HIS* 4.0 3.4 - - - -
139D VAL 4.1 7.2 - - - -
140D ASN* 3.7 31.6 - - + +
141D ALA 3.6 7.0 - - - +
142D GLN* 4.2 11.0 - - + +
146D GLY 4.5 1.3 - - - +
147D LYS* 1.3 77.0 - - - +
149D ALA* 1.3 69.7 + - - +
150D PHE* 3.5 12.2 + - - +
151D ASP* 2.9 32.2 + - - +
152D ILE* 3.0 22.9 + - - +
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Residues in contact with ALA 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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117D LEU* 3.8 35.2 - - + +
118D HIS* 3.9 13.4 - - + -
121D ALA* 4.0 14.1 - - + +
139D VAL* 4.2 6.8 + - + +
141D ALA 4.5 0.6 + - - -
148D THR* 1.3 76.0 - - - +
150D PHE* 1.3 56.7 + - - +
152D ILE* 3.4 9.8 + - - +
153D SER* 3.0 22.3 + - - -
165D LEU* 3.6 23.9 - - + +
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Residues in contact with PHE 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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139D VAL* 5.1 2.1 + - + +
148D THR* 3.0 10.7 + - - +
149D ALA* 1.3 77.3 - - - +
151D ASP* 1.3 74.8 + - - +
153D SER* 2.8 25.8 + - - -
154D ILE* 3.0 34.0 + - + +
162D ALA* 3.9 19.5 - - + -
165D LEU* 3.8 27.6 - - + +
166D GLN 4.2 18.4 - - - -
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Residues in contact with ASP 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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259A ARG* 4.9 9.5 + - - +
146D GLY 4.0 4.0 - - - +
147D LYS* 3.6 27.3 + - + +
148D THR* 2.9 39.1 + - - +
150D PHE* 1.3 83.6 - - - +
152D ILE* 1.3 62.2 + - - +
154D ILE* 3.2 17.8 - - - +
155D ASN* 3.1 23.4 + - - +
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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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118D HIS* 3.8 44.0 - - + +
121D ALA* 4.1 5.6 - - + +
122D ASN* 3.7 29.6 - - + +
143D ASP* 5.5 2.9 - - - +
147D LYS* 5.1 9.9 - - + -
148D THR 3.0 10.4 + - - +
149D ALA* 3.4 9.4 - - - +
150D PHE 3.1 0.2 - - - -
151D ASP* 1.3 75.9 - - - +
153D SER* 1.3 58.1 + - - +
155D ASN* 3.2 5.4 + - - -
156D ASN* 2.8 53.9 + - - +
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Residues in contact with SER 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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121D ALA 5.5 0.2 - - - -
149D ALA 3.0 10.8 + - - -
150D PHE* 2.8 19.5 + - - -
152D ILE* 1.3 79.1 - - - +
154D ILE* 1.3 61.7 + - - +
156D ASN* 3.4 4.4 + - - -
157D GLY 2.9 3.1 + - - -
158D ASN* 2.9 33.8 + - - +
161D LEU* 3.8 28.9 - - - -
162D ALA* 3.5 31.8 - - - +
165D LEU* 4.6 1.3 - - - +
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Residues in contact with ILE 154 (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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259A ARG* 4.1 26.0 - - - +
263A ARG* 3.6 9.0 + - - -
150D PHE* 3.0 40.8 + - + +
151D ASP* 3.2 22.0 - - - +
153D SER* 1.3 83.4 + - - +
155D ASN* 1.4 60.5 + - - +
157D GLY* 2.6 26.8 + - - -
158D ASN 5.4 0.2 - - - -
162D ALA* 4.6 8.3 - - + -
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Residues in contact with ASN 155 (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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248A LYS* 3.8 30.4 + - - +
259A ARG* 3.4 36.1 + - - +
261A LEU* 4.2 15.1 - - - +
263A ARG* 2.6 23.8 + - - +
151D ASP 3.1 18.1 + - - +
152D ILE* 3.7 5.4 - - - +
154D ILE* 1.4 77.5 - - - +
156D ASN* 1.3 62.8 + - - +
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Residues in contact with ASN 156 (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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244A GLU* 3.3 28.3 - - - +
248A LYS* 3.2 32.6 + - - +
263A ARG* 4.1 2.0 - - - -
121D ALA 4.3 2.8 + - - +
122D ASN* 2.9 43.9 + - - +
152D ILE* 2.8 30.0 + - - +
153D SER* 3.9 5.2 - - - +
155D ASN* 1.3 83.4 + - - +
157D GLY* 1.3 62.8 + - - +
158D ASN* 3.3 6.4 + - + +
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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