Contacts of the helix formed by residues 156 - 166 (chain C) in PDB entry 1L0N
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 ILE 156 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ILE* 4.2 15.9 - - + -
154C PRO 2.7 16.7 + - - +
155C TYR* 1.3 83.6 - - + +
157C GLY* 1.3 62.5 + - - +
158C THR 3.5 1.8 - - - -
159C ASN* 3.3 13.3 + - + +
160C LEU* 3.0 47.3 + - + -
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Residues in contact with GLY 157 (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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150C LEU 3.4 16.8 - - - -
151C SER* 3.9 8.3 - - - -
153C ILE* 2.9 23.8 + - - +
155C TYR 3.8 0.6 - - - +
156C ILE* 1.3 75.9 - - - +
158C THR* 1.3 66.6 + - - +
160C LEU* 3.2 5.1 + - - +
161C VAL* 3.0 28.9 + - - +
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Residues in contact with THR 158 (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 SER* 4.5 12.2 + - - +
155C TYR 5.6 0.4 - - - -
156C ILE 3.4 0.8 + - - +
157C GLY* 1.3 75.5 - - - +
159C ASN* 1.3 70.0 + - - +
161C VAL* 3.2 2.8 + - - +
162C GLU* 3.0 44.1 + - + +
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Residues in contact with ASN 159 (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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155C TYR 4.4 10.7 - - - +
156C ILE* 3.3 12.2 + - + +
158C THR* 1.3 84.5 - - - +
160C LEU* 1.3 51.2 + - - +
162C GLU* 3.3 12.9 + - - +
163C TRP* 2.8 36.7 + - - +
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Residues in contact with LEU 160 (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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150C LEU* 4.6 17.3 - - + +
153C ILE* 4.0 27.4 - - + -
156C ILE* 3.0 35.6 + - + +
157C GLY* 3.2 10.5 + - - +
159C ASN* 1.3 74.6 - - - +
161C VAL* 1.3 66.7 + - + +
163C TRP* 3.0 26.8 + - + +
164C ILE* 3.0 24.3 + - + +
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Residues in contact with VAL 161 (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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147C THR* 3.9 12.6 - - + +
148C ASN* 3.9 7.0 - - - +
150C LEU* 3.8 15.3 - - + -
151C SER* 3.4 31.6 - - - +
157C GLY 3.0 16.1 + - - +
158C THR* 3.8 3.4 - - - +
160C LEU* 1.3 75.5 - - - +
162C GLU* 1.3 58.2 + - + +
164C ILE* 3.5 5.9 + - - +
165C TRP* 3.0 74.3 + - + +
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Residues in contact with GLU 162 (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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158C THR* 3.0 38.5 + - + +
159C ASN* 3.8 12.0 + - - +
161C VAL* 1.3 75.0 - - + +
163C TRP* 1.3 64.3 + - - +
165C TRP* 4.3 10.1 - - + -
166C GLY* 3.3 19.1 + - - -
167C GLY 3.8 15.5 - - - +
168C PHE* 3.3 41.1 - - + -
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Residues in contact with TRP 163 (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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159C ASN 2.8 18.2 + - - +
160C LEU* 3.0 17.9 + - + +
162C GLU* 1.3 79.6 - - - +
164C ILE* 1.3 83.1 + - + +
166C GLY* 3.6 2.3 + - - -
177C ARG* 2.9 21.8 + - - -
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Residues in contact with ILE 164 (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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128C PHE* 6.4 0.7 - - + -
129C MET* 6.2 1.8 - - + -
147C THR* 3.6 32.1 - - + +
150C LEU* 4.1 20.0 - - + -
160C LEU* 3.0 19.3 + - + +
161C VAL 4.2 3.4 - - - +
163C TRP* 1.3 97.1 - - + +
165C TRP* 1.3 64.7 + - + +
174C THR* 4.6 4.2 - - - +
177C ARG* 3.0 30.0 + - - +
178C PHE* 4.9 16.0 - - + -
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Residues in contact with TRP 165 (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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144C THR* 4.5 8.3 - - + -
147C THR* 3.4 32.0 - - + +
148C ASN* 3.3 45.3 - - + -
161C VAL* 3.0 36.3 + - + +
162C GLU* 4.0 6.7 - - + +
164C ILE* 1.3 78.5 - - + +
166C GLY* 1.3 57.6 + - - +
167C GLY 3.1 13.5 + - - +
168C PHE* 3.2 35.0 - - - -
169C SER* 3.4 17.2 - - - +
170C VAL* 3.6 25.5 - - + +
171C ASP 4.9 0.2 + - - -
173C ALA* 4.2 0.2 - - - +
174C THR* 2.3 44.0 + - + -
177C ARG* 4.3 0.2 - - - -
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Residues in contact with GLY 166 (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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162C GLU 3.3 11.5 + - - -
163C TRP 3.6 1.5 + - - -
164C ILE 3.4 2.4 - - - -
165C TRP* 1.3 77.3 - - - +
167C GLY* 1.3 57.1 + - - +
173C ALA* 3.9 14.8 - - - +
177C ARG* 3.6 25.6 - - - -
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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