Contacts of the strand formed by residues 180 - 186 (chain N) in PDB entry 5U0A
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 VAL 180 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168N LEU* 5.0 1.1 - - + -
171N ARG* 3.8 31.6 - - - +
172N ARG 4.8 10.1 - - - +
173N VAL* 6.5 0.4 - - + -
178N ALA 3.5 2.7 - - - -
179N THR* 1.3 73.3 - - - +
181N LEU* 1.3 66.6 + - - +
182N VAL* 4.7 4.9 - - + -
226N VAL* 2.7 49.5 + - + +
227N PRO 4.2 0.2 - - - +
228N ALA* 3.7 14.5 - - + +
231N VAL* 3.6 28.7 - - + -
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Residues in contact with LEU 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C ARG* 4.0 37.0 + - + +
489C PRO* 5.4 7.2 - - + -
171N ARG* 4.2 8.0 + - - -
179N THR 3.5 1.3 + - - +
180N VAL* 1.3 82.9 - - - +
182N VAL* 1.3 63.9 + - - +
223N PRO* 4.7 9.6 - - + +
224N THR 3.2 27.4 - - - +
225N GLU* 4.0 17.3 - - + -
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Residues in contact with VAL 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488C ARG* 5.4 1.1 - - - -
62N ARG* 4.1 27.6 - - + +
63N VAL 4.0 15.9 - - - +
64N ASP* 4.9 0.4 - - - +
168N LEU* 3.6 28.7 - - + -
171N ARG* 3.9 8.1 - - - +
180N VAL* 3.6 3.5 + - + +
181N LEU* 1.3 79.2 - - - +
183N ASP* 1.3 68.4 + - - +
184N LEU* 5.5 1.3 - - + -
223N PRO* 4.5 2.0 - - - -
224N THR* 2.8 41.3 + - - +
226N VAL* 3.8 27.4 - - + -
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Residues in contact with ASP 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488C ARG* 4.3 20.9 + - - +
61N VAL 3.9 0.9 - - - +
62N ARG* 3.3 1.7 - - - +
63N VAL* 3.0 48.4 + - + +
182N VAL* 1.3 73.3 - - - +
184N LEU* 1.3 73.9 + - - +
185N ILE* 5.0 3.9 - - - +
221N VAL* 3.6 27.1 - - - +
222N VAL 3.5 9.7 + - - +
223N PRO* 4.1 11.3 - - - +
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Residues in contact with LEU 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60N THR* 4.7 1.8 - - - -
61N VAL 3.8 2.5 - - - -
62N ARG* 3.8 17.9 - - + +
159N VAL* 5.0 2.9 - - + -
162N LEU* 3.8 33.2 - - + +
163N VAL* 4.2 23.8 - - + +
182N VAL* 3.5 3.2 + - + +
183N ASP* 1.3 75.2 - - - +
185N ILE* 1.3 61.0 + - - +
186N TYR* 3.8 34.9 - - + +
220N ARG 4.1 0.3 - - - +
221N VAL* 3.5 0.2 - - - -
222N VAL* 2.9 38.6 + - - +
224N THR* 3.2 32.8 - - + +
226N VAL* 5.8 1.1 - - + -
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Residues in contact with ILE 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N TYR* 3.7 44.2 - - + -
59N PHE 3.5 5.1 - - - +
60N THR* 3.1 8.5 - - - -
61N VAL* 2.8 54.8 + - + +
63N VAL* 4.2 15.3 - - + -
183N ASP* 4.5 4.0 - - - +
184N LEU* 1.3 74.2 - - - +
186N TYR* 1.3 69.7 + - - +
217N ARG* 6.1 1.8 - - - +
219N ILE* 4.6 16.4 - - + -
220N ARG 3.8 2.5 - - - +
221N VAL* 3.4 27.1 - - + -
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Residues in contact with TYR 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N PHE 4.9 1.1 - - - -
60N THR* 3.5 34.5 - - + -
159N VAL* 4.0 14.9 - - + +
163N VAL* 5.3 2.6 - - - +
184N LEU* 3.8 34.6 - - + +
185N ILE* 1.3 77.1 - - - +
187N GLU* 1.3 59.4 + - - +
219N ILE* 3.5 8.9 - - - +
220N ARG* 2.8 58.9 + - + +
222N VAL* 4.5 28.3 - - + -
224N THR* 5.1 3.2 - - + +
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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