Contacts of the helix formed by residues 146 - 151 (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 LEU 146 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C THR 3.6 1.8 + - - -
145C ILE* 1.3 67.5 - - - +
147C TRP* 1.3 59.8 + - - +
148C LYS* 3.1 28.3 - - + -
149C ASP* 2.8 45.5 + - + +
150C ILE 3.7 0.2 + - - -
181C ARG* 3.8 37.2 - - - +
191C GLN* 2.8 32.4 + - - +
193C LEU* 4.4 6.7 - - + -
196C THR* 4.1 18.4 - - + +
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Residues in contact with TRP 147 (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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92C LEU* 4.1 20.0 - - + -
118C LEU* 4.4 3.4 - - + -
123C LEU* 5.2 1.3 - - + -
126C ILE* 4.9 5.6 - - + -
131C VAL* 3.6 26.5 - - + -
133C ILE* 3.9 8.5 - - + -
142C GLN 3.5 23.0 + - - -
143C ASP* 5.3 1.4 - - - +
145C ILE* 3.2 30.2 + - + -
146C LEU* 1.3 70.7 - - - +
148C LYS* 1.3 54.9 + - - +
150C ILE* 2.7 38.8 + - + +
151C PHE* 3.0 35.6 + + + -
160C THR* 4.1 13.7 - - + +
162C ILE* 3.2 32.3 - - + +
183C TRP* 3.8 31.4 - + - -
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Residues in contact with LYS 148 (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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146C LEU* 3.7 26.0 - - + -
147C TRP* 1.3 75.5 - - - +
149C ASP* 1.3 61.2 + - - +
151C PHE* 3.5 7.2 - - - +
156C GLN* 3.1 37.4 + - + +
195C ARG* 3.2 16.8 + - - +
196C THR* 4.4 18.8 - - - -
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Residues in contact with ASP 149 (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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124C THR* 5.1 1.4 + - - +
146C LEU* 2.8 29.7 + - + +
148C LYS* 1.3 73.3 - - - +
150C ILE* 1.3 63.9 + - - +
151C PHE 3.6 1.6 - - - +
191C GLN* 3.9 3.9 + - - +
192C SER 4.0 2.9 - - - +
193C LEU* 3.2 21.5 - - + +
194C THR* 2.7 27.5 + - - -
195C ARG* 3.0 21.8 + - - +
196C THR* 2.6 30.4 + - - -
204C ARG* 3.1 25.8 + - - -
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Residues in contact with ILE 150 (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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123C LEU* 3.4 21.3 - - + +
124C THR* 3.8 7.9 - - - -
125C GLU* 3.3 11.2 - - - +
126C ILE* 2.9 53.6 + - + +
145C ILE* 3.8 8.7 - - + -
146C LEU 4.3 1.1 - - - +
147C TRP* 2.7 22.4 + - + +
149C ASP* 1.3 72.7 - - - +
151C PHE* 1.3 64.8 + - + +
183C TRP* 3.4 38.4 - - + -
191C GLN* 3.6 23.1 - - + +
204C ARG* 3.0 11.6 + - - -
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Residues in contact with PHE 151 (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* 3.7 20.0 - - + -
129C GLY 3.8 14.4 - - - -
130C GLY* 3.9 9.2 - - - -
131C VAL* 3.8 26.7 - - + -
147C TRP* 3.0 32.2 + + + +
148C LYS* 3.5 5.0 - - - +
150C ILE* 1.3 80.2 - - + +
152C HIS* 1.3 63.4 + - - +
155C ASN* 3.4 24.0 - - - +
156C GLN* 3.2 21.1 + - - +
158C ALA* 3.7 18.6 - - + -
160C THR* 3.2 28.3 - - - -
195C ARG* 3.1 20.3 + - - -
204C ARG* 3.4 1.7 + - - -
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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