Contacts of the strand formed by residues 159 - 166 (chain C) in PDB entry 4LML
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 TRP 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C LEU* 3.8 36.0 + - + +
31C ASP* 4.4 3.9 + - - -
113C LEU* 5.4 2.5 - - + -
121C ASP* 4.1 3.6 - - - -
123C GLN* 3.9 25.1 - - + -
155C PHE 3.8 8.5 - - - +
156C LEU* 3.0 36.4 + - + +
157C THR 3.9 10.5 - - - -
158C GLY* 1.3 91.4 + - - +
160C ASP* 1.3 66.5 + - - +
161C ILE* 3.9 2.0 + - - +
189C ILE* 3.4 37.9 - - + -
190C SER 3.4 8.5 - - - -
191C ARG* 3.3 72.0 - - + +
192C GLN* 3.8 8.4 + - - -
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Residues in contact with ASP 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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159C TRP* 1.3 73.0 - - - +
161C ILE* 1.3 64.3 + - - +
162C GLU* 3.5 9.4 + - - +
189C ILE* 3.3 4.2 - - - -
190C SER* 2.8 53.0 + - - +
191C ARG 4.8 2.3 - - - +
192C GLN* 2.8 40.3 + - - +
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Residues in contact with ILE 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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26C CYS* 5.0 7.0 - - + -
150C LYS* 4.3 21.6 + - + -
154C VAL* 3.8 29.2 - - + +
155C PHE 3.5 26.9 - - - +
156C LEU* 4.0 15.0 - - + -
159C TRP 3.9 1.3 + - - +
160C ASP* 1.3 73.7 - - - +
162C GLU* 1.3 70.6 + - - +
163C SER 4.7 0.7 - - - +
187C LEU* 3.8 28.3 - - + -
188C ARG 4.1 2.5 - - - +
189C ILE* 4.1 13.9 - - + -
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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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122C SER* 4.8 1.4 + - - -
150C LYS* 4.3 10.2 + - - -
160C ASP* 3.9 12.7 - - - +
161C ILE* 1.3 78.7 - - - +
163C SER* 1.3 65.3 + - - +
188C ARG* 2.8 22.9 + - + +
189C ILE 3.6 2.8 + - - -
190C SER* 3.2 41.6 + - - -
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Residues in contact with SER 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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150C LYS* 5.2 2.2 - - - +
161C ILE* 4.0 1.7 - - - +
162C GLU* 1.3 85.1 - - - +
164C PHE* 1.3 58.8 + - - +
165C THR* 4.0 14.1 + - - +
186C GLN 3.5 3.3 - - - +
187C LEU* 3.6 3.8 - - - -
188C ARG* 2.8 48.3 + - - +
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Residues in contact with PHE 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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21C ILE* 3.9 20.6 - - + -
23C LEU* 3.5 40.2 - - + -
127C ILE* 5.4 7.9 - - + -
147C LYS* 3.7 29.0 - - + +
148C VAL* 4.9 6.0 - - - +
149C GLY 3.1 24.5 - - - +
150C LYS* 5.0 13.7 - - + +
163C SER* 1.3 72.3 - - - +
165C THR* 1.3 63.1 + - - +
185C TYR* 3.7 35.7 - + + -
186C GLN 3.1 24.5 - - - -
187C LEU* 3.8 19.3 - - + +
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Residues in contact with THR 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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147C LYS* 3.4 25.6 + - - +
163C SER* 4.4 17.0 - - - +
164C PHE* 1.3 78.3 - - - +
166C ALA* 1.3 77.0 + - - +
185C TYR* 3.7 4.8 - - - +
186C GLN* 2.9 47.9 + - + +
188C ARG* 5.9 2.2 - - + -
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Residues in contact with ALA 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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142C ALA* 4.3 12.1 - - + +
144C ASP* 5.0 0.3 - - - +
147C LYS* 3.3 20.6 + - + +
165C THR* 1.3 86.5 + - - +
167C VAL* 1.3 64.8 + - - +
168C VAL* 3.3 11.8 + - - +
183C LEU* 6.4 0.4 - - + -
184C ASP 3.8 4.7 - - - +
185C TYR* 3.5 39.3 - - + -
186C GLN* 5.5 0.7 - - - -
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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