Contacts of the strand formed by residues 179 - 185 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143D VAL* 3.8 28.7 - - + +
144D PHE* 4.1 2.5 - - - -
145D PHE* 3.6 45.7 - - + +
164D ALA* 3.5 0.7 - - - -
165D LEU* 2.8 44.1 + - + +
177D ALA* 3.8 1.8 - - - +
178D ALA* 1.3 78.0 - - - +
180D ALA* 1.3 64.1 + - - +
200D GLN* 3.7 20.6 - - + +
201D GLY 4.1 0.2 - - - -
202D ARG* 3.4 44.2 - - + +
204D LEU* 5.1 3.1 - - + -
235D LEU* 5.4 0.2 - - + -
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Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLU* 5.7 4.1 - - - +
197B PHE* 5.7 1.0 - - - +
145D PHE* 3.9 3.4 - - - -
163D LEU 3.6 10.8 - - - +
164D ALA* 4.7 1.6 - - + -
177D ALA* 4.3 15.5 - - + +
179D LEU* 1.3 76.9 - - - +
181D LEU* 1.3 61.7 + - - +
200D GLN* 2.9 31.2 + - - +
202D ARG* 5.5 0.6 - - - +
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Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197B PHE* 5.2 12.1 - - + -
145D PHE* 3.8 32.1 - - + +
147D LEU* 4.4 14.6 - - + -
162D SER* 3.2 2.4 - - - -
163D LEU* 3.1 35.3 + - + +
180D ALA* 1.3 74.1 - - - +
182D THR* 1.3 90.9 + - - +
183D VAL* 4.2 2.0 - - + -
198D GLY* 3.3 44.4 - - - +
199D PHE* 3.8 6.3 - - - +
200D GLN* 4.0 15.7 - - + +
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Residues in contact with THR 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B SER* 5.0 13.5 + - - +
197B PHE* 5.3 9.0 - - - +
160D SER* 3.3 26.9 - - - +
161D VAL 3.4 7.2 - - - +
162D SER* 3.6 12.4 + - - +
181D LEU* 1.3 90.7 + - - +
183D VAL* 1.3 69.7 + - - +
184D ASP* 4.3 8.0 + - - +
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Residues in contact with VAL 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 3.9 21.8 - - + +
149D LEU* 3.6 20.1 - - + +
160D SER* 3.5 2.4 - - - -
161D VAL* 2.9 32.6 + - - +
181D LEU* 4.2 3.6 - - + -
182D THR* 1.3 80.0 - - - +
184D ASP* 1.3 65.6 + - - +
185D LEU 3.7 0.3 + - - -
196D ALA* 3.4 33.9 - - + +
197D PHE 3.6 24.0 - - - +
198D GLY* 3.8 14.8 - - - -
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Residues in contact with ASP 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B PRO* 5.3 7.3 - - - +
193B ARG* 4.7 15.8 - - - +
195B SER 5.4 3.5 - - - +
159D GLY 3.7 7.2 - - - +
160D SER* 4.6 5.0 - - - +
182D THR* 4.6 10.4 - - - +
183D VAL* 1.3 77.5 - - - +
185D LEU* 1.3 61.3 + - - +
186D PRO* 3.6 6.2 - - + +
196D ALA* 3.6 18.9 - - - +
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Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D LEU* 6.1 2.7 - - + -
158D SER* 3.7 3.1 - - - -
159D GLY 2.8 43.8 + - - +
160D SER* 4.6 1.6 - - - +
161D VAL* 5.6 7.2 - - + -
183D VAL 3.7 1.7 + - - +
184D ASP* 1.3 73.3 - - - +
186D PRO* 1.3 69.6 - - - +
187D PRO* 3.7 1.9 - - - +
196D ALA* 5.0 1.3 - - - -
226D TRP* 3.9 33.4 - - + +
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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