Contacts of the strand formed by residues 289 - 292 (chain B) in PDB entry 7UUT
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 THR 289 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TYR* 5.4 3.1 + - - -
289A THR* 3.6 28.7 - - + -
290A ILE 3.5 7.4 - - - +
291A LYS* 3.9 21.0 - - + +
163B ASP* 5.9 0.2 - - - +
259B GLY 5.7 0.2 + - - -
260B GLY 3.1 11.4 + - - -
261B THR* 3.4 9.8 - - + -
262B ILE* 2.6 35.0 + - - +
287B HIS* 3.4 6.6 + - - -
288B LYS* 1.3 73.1 - - - +
290B ILE* 1.3 58.1 + - - +
291B LYS* 4.0 20.9 - - + -
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Residues in contact with ILE 290 (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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276A VAL* 5.8 0.4 - - + -
281A TRP* 3.8 26.0 - - + -
288A LYS 4.0 2.3 - - - +
289A THR* 3.6 2.9 - - - -
290A ILE* 2.9 53.5 + - + +
249B MET* 4.1 18.6 - - + -
253B VAL* 4.4 9.4 - - + -
262B ILE* 3.4 18.8 - - + +
276B VAL* 3.9 31.2 - - + -
281B TRP* 3.9 22.2 - - + +
288B LYS 3.8 7.4 - - - +
289B THR* 1.3 77.2 - - - +
291B LYS* 1.3 63.2 + - - +
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Residues in contact with LYS 291 (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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281A TRP* 4.2 5.6 - - - -
289A THR* 3.8 29.2 - - + +
291A LYS* 6.1 1.3 - - - +
161B LEU* 3.2 54.1 + - + +
163B ASP* 2.8 35.0 + - - -
261B THR* 4.4 3.8 - - + -
262B ILE 2.7 13.5 + - - +
263B ALA* 4.6 1.1 - - - -
264B ASN* 2.7 34.9 + - - +
289B THR* 4.0 17.7 - - + -
290B ILE* 1.3 77.1 - - - +
292B GLY* 1.3 54.0 + - - +
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Residues in contact with GLY 292 (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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281A TRP* 3.9 17.0 - - - -
284A GLY 3.2 16.4 - - - +
285A MET 4.0 0.2 + - - -
286A ALA 3.4 5.5 + - - -
287A HIS* 2.6 35.5 + - - +
288A LYS 4.0 3.8 + - - -
161B LEU* 4.5 1.3 - - - -
264B ASN 3.2 11.7 - - - -
291B LYS* 1.3 76.9 - - - +
293B GLY* 1.3 51.9 + - - -
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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