Contacts of the helix formed by residues 152 - 156 (chain C) in PDB entry 1N8Z
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 HIS 152 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125C GLU* 3.4 26.7 - - - +
126C ILE 2.9 21.0 + - - +
127C LEU* 3.7 27.5 + - + +
150C ILE 3.4 1.0 + - - -
151C PHE* 1.3 74.8 - - - +
153C LYS* 1.3 65.4 + - + +
154C ASN* 3.1 45.6 + - + +
155C ASN* 2.9 10.7 + - + +
156C GLN* 2.6 23.5 + - - +
203C ALA* 5.6 8.2 - - + +
204C ARG* 3.8 6.5 - - + +
219C ALA* 6.1 0.2 - - - -
234C LEU* 4.1 24.5 - - + +
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Residues in contact with LYS 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C PHE 3.9 0.2 + - - -
152C HIS* 1.3 87.0 - - + +
154C ASN* 1.3 73.2 + - - +
155C ASN 3.4 0.5 + - - -
156C GLN* 2.8 18.9 + - - +
195C ARG* 3.9 24.6 - - + +
202C CYS 6.3 0.4 - - - -
203C ALA* 5.1 20.2 - - + -
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Residues in contact with ASN 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LEU 5.0 1.6 - - - +
128C LYS* 6.1 1.2 - - - +
152C HIS* 3.0 30.1 + - + +
153C LYS* 1.3 96.4 + - - +
155C ASN* 1.3 58.2 + - - +
156C GLN 3.9 0.4 - - - -
157C LEU 5.7 0.2 - - - -
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Residues in contact with ASN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C ILE* 3.3 17.8 + - - +
127C LEU 3.3 22.2 + - - +
128C LYS* 3.3 5.3 - - - +
129C GLY 2.9 40.4 + - - +
151C PHE* 3.4 24.1 - - - +
152C HIS* 2.9 15.1 + - + +
154C ASN* 1.3 76.5 - - - +
156C GLN* 1.4 58.5 + - - +
157C LEU* 3.2 4.7 - - - +
158C ALA* 2.7 40.1 - - - +
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Residues in contact with GLN 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C LYS* 3.1 30.5 + - + +
151C PHE* 3.2 26.6 + - - +
152C HIS 2.6 19.4 + - - +
153C LYS* 2.8 18.9 + - - +
154C ASN 3.9 0.2 - - - -
155C ASN* 1.4 68.3 - - - +
157C LEU* 1.3 56.6 + - + +
158C ALA* 2.7 21.5 + - - +
195C ARG* 2.7 34.0 - - - +
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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