Contacts of the strand formed by residues 179 - 185 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143E VAL* 5.6 9.4 - - + +
144E PHE* 6.5 0.7 - - - -
145E PHE* 6.2 3.6 - - + +
164E ALA* 3.6 0.7 - - - -
165E LEU* 2.8 50.3 + - + +
177E ALA* 3.8 2.5 - - - +
178E ALA* 1.3 79.8 - - - +
180E ALA* 1.3 63.6 + - - +
200E GLN* 4.4 12.8 - - + +
201E GLY* 6.3 1.3 - - - -
202E ARG* 5.1 9.2 - - + +
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Residues in contact with ALA 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E LEU 3.6 10.8 - - - +
164E ALA* 4.5 2.5 - - + +
177E ALA* 4.3 15.5 - - + +
179E LEU* 1.3 76.1 - - - +
181E LEU* 1.3 61.7 + - - +
200E GLN* 2.9 33.3 + - - +
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Residues in contact with LEU 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C PHE* 5.5 8.5 - - + -
145E PHE* 3.8 18.2 - - + +
146E GLN 4.8 0.2 - - - -
147E LEU* 4.3 14.8 - - + -
162E SER* 3.2 2.6 - - - -
163E LEU* 3.1 42.8 + - + +
180E ALA* 1.3 74.5 - - - +
182E THR* 1.3 90.0 + - - +
183E VAL* 4.2 2.7 - - + -
198E GLY* 3.3 43.7 - - - +
199E PHE* 3.8 7.0 - - - +
200E GLN* 4.0 17.3 - - + +
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Residues in contact with THR 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C SER* 4.9 14.3 + - - +
197C PHE* 5.4 5.0 - - - +
160E SER* 3.3 27.1 - - - +
161E VAL 3.4 7.2 - - - +
162E SER* 3.6 13.6 + - - +
181E LEU* 1.3 89.4 + - - +
183E VAL* 1.3 69.7 - - - +
184E ASP* 4.3 8.3 - - - +
198E GLY* 5.6 0.2 - - - -
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Residues in contact with VAL 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E LEU* 3.9 21.1 - - + +
149E LEU* 3.6 18.4 - - + -
160E SER* 3.5 2.3 - - - -
161E VAL* 2.9 33.2 + - - +
181E LEU* 4.2 4.3 - - + -
182E THR* 1.3 78.7 - - - +
184E ASP* 1.3 66.1 + - - +
185E LEU* 3.7 0.9 + - - +
196E ALA* 3.4 34.5 - - + +
197E PHE 3.6 24.0 - - - +
198E GLY* 3.8 15.5 - - - +
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Residues in contact with ASP 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C PRO* 5.7 1.2 - - - +
193C ARG* 3.5 28.6 - - - +
195C SER 5.7 0.9 - - - +
159E GLY 3.7 8.7 - - - +
160E SER* 4.6 5.3 - - - +
182E THR* 4.6 11.3 - - - +
183E VAL* 1.3 76.6 + - - +
185E LEU* 1.3 60.7 + - - +
186E PRO* 3.6 6.2 - - + +
196E ALA* 3.6 19.9 - - - +
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Residues in contact with LEU 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E LEU* 3.6 32.5 - - + -
158E SER* 3.7 8.2 - - - +
159E GLY 2.8 37.0 + - - +
160E SER* 4.2 9.0 - - - +
161E VAL* 3.8 23.1 - - + -
183E VAL 4.5 0.7 - - - +
184E ASP* 1.3 76.7 - - - +
186E PRO* 1.3 71.8 - - - +
187E PRO* 3.7 1.2 - - - +
196E ALA* 4.3 1.6 - - + -
218E THR* 5.8 1.3 - - - +
219E GLU 5.8 0.4 - - - +
223E ARG* 6.3 2.2 - - - -
226E TRP* 3.7 57.4 - - + +
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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