Contacts of the strand formed by residues 181 - 187 (chain C) in PDB entry 1K4R
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 ASP 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173C ILE* 3.9 23.4 - - + +
174C LEU 3.2 6.1 - - - +
175C THR* 2.7 36.5 + - - +
180C GLY* 1.3 76.7 - - - -
182C VAL* 1.3 61.4 + - - +
293C GLY 4.5 1.0 - - - +
296C LYS* 3.2 44.0 + - + +
297C LEU* 3.7 6.3 + - - +
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Residues in contact with VAL 182 (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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41C MET* 4.2 8.1 - - + -
143C VAL* 4.7 8.1 - - + -
172C THR 4.0 0.2 - - - +
173C ILE* 3.4 4.1 - - - +
174C LEU* 2.8 53.2 + - + +
176C MET* 3.7 24.2 - - + -
180C GLY 4.1 0.4 + - - -
181C ASP* 1.3 73.7 - - - +
183C SER* 1.3 64.7 + - - +
184C LEU* 5.3 3.7 - - + +
292C VAL* 3.6 24.9 - - + -
293C GLY 3.4 15.5 - - - +
294C LEU* 4.6 0.2 - - + -
297C LEU* 4.2 21.8 - - + -
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Residues in contact with SER 183 (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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20C ARG* 5.9 0.7 + - - -
171C LYS* 4.3 14.8 - - - -
172C THR 3.5 4.7 - - - -
173C ILE* 3.8 22.9 - - - +
182C VAL* 1.3 74.0 - - - +
184C LEU* 1.3 62.1 - - - +
185C LEU 4.2 0.2 - - - -
291C GLU 3.5 0.9 + - - +
292C VAL* 3.4 7.4 - - - +
293C GLY* 2.9 46.8 + - - -
295C GLU* 4.2 6.8 + - - -
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Residues in contact with LEU 184 (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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43C VAL* 4.9 6.7 - - + -
141C VAL* 4.1 16.6 - - + -
143C VAL* 3.9 26.5 - - + -
163C ALA* 4.0 23.8 - - + -
165C PHE* 3.5 16.4 - - + -
171C LYS* 3.3 6.1 - - - +
172C THR* 2.8 40.9 + - - +
174C LEU* 4.1 8.5 - - + -
182C VAL* 5.3 4.9 - - + +
183C SER* 1.3 76.0 - - - +
185C LEU* 1.3 61.0 + - - +
186C CYS* 3.9 2.7 - - - -
290C CYS* 4.5 11.2 - - + -
291C GLU 3.5 2.2 - - - +
292C VAL* 3.8 31.9 - - + -
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Residues in contact with LEU 185 (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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20C ARG* 4.5 12.8 - - - +
170C GLU* 3.2 28.7 - - + +
171C LYS* 4.3 25.8 - - + +
183C SER 4.2 0.2 - - - -
184C LEU* 1.3 74.4 - - - +
186C CYS* 1.3 62.0 + - - +
187C ARG* 3.7 51.4 + - + +
289C THR 4.0 0.7 - - - +
290C CYS* 3.1 2.1 - - - -
291C GLU* 2.8 53.3 + - + +
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Residues in contact with CYS 186 (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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139C TYR* 6.1 0.7 - - + -
141C VAL* 4.1 4.5 - - - -
165C PHE* 3.5 46.6 - - + +
166C THR 5.3 0.2 - - - +
170C GLU* 3.0 25.9 + - - +
184C LEU* 3.9 6.5 - - - -
185C LEU* 1.3 76.5 - - - +
187C ARG* 1.3 64.7 + - - +
188C VAL* 3.6 2.8 + - - +
288C VAL* 4.4 9.6 - - + -
289C THR 3.5 4.7 - - - +
290C CYS* 2.0 46.4 - - - -
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Residues in contact with ARG 187 (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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170C GLU* 4.0 20.2 + - - +
185C LEU* 3.7 34.6 + - + +
186C CYS* 1.3 71.0 - - - +
188C VAL* 1.3 59.9 + - - +
189C ALA* 3.1 8.5 - - + +
190C SER* 2.6 45.0 + - - +
288C VAL* 3.3 6.4 - - - +
289C THR* 3.3 15.7 + - - +
291C GLU* 3.2 30.9 + - - +
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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