Contacts of the strand formed by residues 283 - 287 (chain B) in PDB entry 6PUO
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 HIS 283 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B LYS* 3.4 29.6 - - + +
162B TRP* 3.5 41.4 - + + -
164B LEU* 4.3 31.8 - - + +
237B ILE* 4.4 11.2 - - + +
238B THR 3.0 10.5 + - - +
239B ILE* 3.4 16.7 - - + -
240B GLY* 2.9 25.7 + - - -
281B HIS* 4.5 0.7 - - - +
282B SER* 1.3 106.0 + - - +
284B PHE* 1.3 69.0 + - - +
285B ILE* 6.0 0.4 - - + -
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Residues in contact with PHE 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 5.0 5.4 - - + -
132B PHE* 4.5 8.3 - + - -
140B LYS* 4.3 18.4 - - + -
141B LYS 2.9 13.8 + - - -
142B TYR* 3.1 18.6 - - + -
143B VAL 3.0 26.3 + - - -
162B TRP* 4.0 2.6 - - - -
209B GLY* 4.1 20.9 - - - -
240B GLY* 3.6 10.1 - - - -
242B ALA* 6.1 0.7 - - + -
277B LEU* 4.4 19.7 - - + -
278B ASP 3.6 24.9 - - - -
281B HIS* 3.6 42.8 - + + -
283B HIS* 1.3 79.7 - - - +
285B ILE* 1.3 66.0 + - - +
286B LEU* 4.1 14.1 - - + -
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Residues in contact with ILE 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.6 12.6 - - + -
145B VAL* 4.3 29.4 - - + -
154B ILE* 4.1 25.1 - - + -
157B LEU* 6.3 0.4 - - + -
158B MET* 4.4 18.6 - - - -
162B TRP* 4.4 11.4 - - + -
239B ILE* 4.6 16.4 - - + -
240B GLY 2.9 12.3 + - - +
241B VAL* 3.3 14.8 - - + +
242B ALA 3.0 23.9 + - - +
283B HIS 5.7 0.7 - - - -
284B PHE* 1.3 77.2 - - - +
286B LEU* 1.3 63.8 + - - +
287B VAL* 3.9 7.5 + - + +
301B LEU* 5.4 5.4 - - + -
305B LEU* 5.1 5.6 - - + -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B TYR* 4.3 18.8 - - + -
143B VAL 2.9 19.1 + - - +
144B ARG* 3.3 5.5 - - + +
145B VAL* 2.9 26.6 + - - +
240B GLY 5.2 0.2 - - - +
242B ALA* 3.0 26.7 - - + +
244B TRP* 3.6 43.7 - - + -
247B VAL* 5.0 8.1 - - + -
253B LEU* 5.2 5.2 - - + -
277B LEU* 4.6 18.8 - - + -
284B PHE* 4.5 17.3 - - + -
285B ILE* 1.3 79.7 - - - +
287B VAL* 1.3 65.4 + - - +
288B ASP 3.7 0.2 + - - -
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Residues in contact with VAL 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B VAL* 3.7 22.0 - - + -
146B SER 4.2 4.3 - - - +
147B GLN* 5.4 3.8 - - - +
241B VAL* 4.6 9.6 - - + -
242B ALA 2.9 16.3 + - - +
243B THR* 3.5 7.1 - - - +
244B TRP 2.6 32.6 + - - -
285B ILE* 3.9 4.4 + - + -
286B LEU* 1.3 73.6 - - - +
288B ASP* 1.3 56.7 + - - +
297B VAL* 4.0 12.1 - - + +
298B GLU* 3.7 30.3 - - + +
301B LEU* 3.8 33.9 - - + -
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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