Contacts of the strand formed by residues 179 - 185 (chain C) in PDB entry 6CU0
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 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143C VAL* 3.8 28.7 - - + +
144C PHE* 4.1 2.2 - - - -
145C PHE* 3.6 46.2 - - + +
164C ALA* 3.5 0.9 - - - -
165C LEU* 2.8 44.0 + - + +
177C ALA* 3.8 2.5 - - - +
178C ALA* 1.3 76.1 - - - +
180C ALA* 1.3 63.6 + - - +
200C GLN* 3.7 21.1 - - + +
201C GLY 4.1 0.2 - - - -
202C ARG* 3.4 43.5 - - + +
204C LEU* 5.1 2.5 - - + -
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Residues in contact with ALA 180 (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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145C PHE* 3.9 2.9 - - - -
163C LEU 3.6 11.0 - - - +
164C ALA* 4.7 2.0 - - + -
177C ALA* 4.3 16.2 - - + +
179C LEU* 1.3 77.3 - - - +
181C LEU* 1.3 61.1 + - - +
200C GLN* 2.9 32.4 + - - +
202C ARG* 5.7 0.4 - - - +
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Residues in contact with LEU 181 (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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145C PHE* 3.7 31.4 - - + +
147C LEU* 4.4 15.5 - - + -
162C SER* 3.2 2.6 - - - -
163C LEU* 3.1 34.3 + - + +
180C ALA* 1.3 74.8 - - - +
182C THR* 1.3 90.6 + - - +
183C VAL* 4.2 2.2 - - + -
198C GLY* 3.3 44.6 - - - +
199C PHE* 3.8 7.4 - - - +
200C GLN* 4.0 16.8 - - + +
197F PHE* 5.4 8.5 - - + -
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Residues in contact with THR 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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160C SER* 3.3 27.1 - - - +
161C VAL 3.4 7.4 - - - +
162C SER* 3.6 13.3 + - - +
181C LEU* 1.3 89.7 + - - +
183C VAL* 1.3 68.7 + - - +
184C ASP* 4.4 7.8 + - - +
195F SER* 4.9 14.4 - - - +
197F PHE* 4.9 8.5 - - - +
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Residues in contact with VAL 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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147C LEU* 3.9 20.6 - - + +
149C LEU* 3.6 18.4 - - + -
160C SER* 3.5 2.4 - - - -
161C VAL* 2.9 33.0 + - - +
181C LEU* 4.2 3.6 - - + -
182C THR* 1.3 79.9 - - - +
184C ASP* 1.3 66.1 + - - +
185C LEU* 3.7 1.2 + - - +
196C ALA* 3.4 35.0 - - + +
197C PHE 3.6 24.5 - - - +
198C GLY* 3.8 15.5 - - - -
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Residues in contact with ASP 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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159C GLY 3.7 7.6 - - - +
160C SER* 4.6 4.2 - - - +
182C THR* 4.6 10.7 - - - +
183C VAL* 1.3 77.6 - - - +
185C LEU* 1.3 62.2 + - - +
186C PRO* 3.6 6.6 - - + +
196C ALA* 3.6 19.2 - - - +
186F PRO* 5.3 5.7 - - - +
193F ARG* 5.0 12.1 - - - +
195F SER* 4.9 13.0 + - - +
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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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102C LEU* 4.6 2.9 - - + -
149C LEU* 3.6 31.6 - - + -
158C SER* 3.7 10.0 - - - +
159C GLY 2.8 35.8 + - - +
160C SER* 4.2 9.2 - - - +
161C VAL* 3.8 23.6 - - + -
183C VAL 4.5 0.4 - - - +
184C ASP* 1.3 76.7 - - - +
186C PRO* 1.3 68.9 - - - +
187C PRO* 3.7 2.1 - - - +
196C ALA* 4.4 1.8 - - + -
218C THR* 5.8 1.1 - - - +
219C GLU 5.8 0.7 - - - +
223C ARG* 6.3 1.6 - - - -
226C TRP* 3.7 56.1 - - + +
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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