Contacts of the strand formed by residues 277 - 282 (chain B) in PDB entry 3A3K
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 ALA 277 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B PHE* 3.9 26.2 - - + -
223B MET* 4.0 8.5 - - - -
238B PHE 3.3 8.5 - - - +
274B PHE* 2.9 34.7 + - + +
275B GLN 3.4 1.4 - - - +
276B ALA* 1.3 79.0 - - - +
278B LYS* 1.3 70.8 + - - +
279B ILE* 6.0 0.4 - - + -
380B ASP* 4.4 3.3 - - - +
381B MET* 4.9 0.9 + - - +
388B PHE* 3.3 18.0 - - + -
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Residues in contact with LYS 278 (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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219B PHE* 4.6 0.7 - - - -
237B VAL* 4.2 8.5 - - + -
238B PHE 3.0 5.5 + - - +
239B PHE* 3.4 24.4 - - + -
240B HIS* 2.8 31.4 + - - +
275B GLN 4.9 4.4 + - - -
276B ALA 5.7 1.0 - - - -
277B ALA* 1.3 80.8 + - - +
279B ILE* 1.3 59.8 + - - +
378B LEU* 3.9 22.4 - - + -
379B TRP 3.4 11.7 - - - +
380B ASP* 2.7 34.3 + - - +
388B PHE* 4.1 1.8 - - - -
409B LEU* 5.1 2.0 - - + -
410B TYR* 2.7 29.4 + - - +
411B TRP* 3.6 36.2 - - + -
412B PRO* 5.9 0.2 - - - +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B PHE* 5.5 3.4 - - + -
240B HIS* 3.6 19.5 - - + +
242B ASP* 4.0 14.1 - - + -
247B SER* 3.9 17.7 - - - +
248B LEU* 4.2 17.0 - - + -
259B PRO* 3.9 27.8 - - + -
274B PHE* 5.1 5.2 - - + -
277B ALA 5.6 0.2 - - - -
278B LYS* 1.3 78.8 - - - +
280B ILE* 1.3 64.4 + - - +
281B THR* 3.7 22.7 - - + -
378B LEU* 3.6 3.4 - - - -
379B TRP* 2.9 47.4 + - + -
388B PHE* 4.2 16.6 - - + -
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Residues in contact with ILE 280 (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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133B LEU* 4.1 16.6 - - + -
136B PHE* 3.5 42.6 - - + -
137B VAL* 5.2 1.6 - - + -
140B LEU* 4.5 2.5 - - + -
211B TYR* 4.0 13.5 - - + -
239B PHE* 3.9 22.7 - - + -
240B HIS 2.8 14.5 + - - +
241B LEU* 4.0 22.2 - - + -
242B ASP* 2.9 30.0 + - - +
243B VAL* 3.6 3.5 + - + +
279B ILE* 1.3 75.3 - - - +
281B THR* 1.3 62.7 + - - +
376B PHE* 4.2 9.9 - - + -
377B SER 3.6 4.9 - - - +
378B LEU* 4.0 12.6 - - + -
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Residues in contact with THR 281 (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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242B ASP 3.2 22.7 - - - +
243B VAL* 3.7 2.5 - - - +
245B GLY* 4.1 5.4 - - - -
248B LEU* 3.9 11.4 - - + -
279B ILE* 3.7 17.3 - - + -
280B ILE* 1.3 74.8 - - - +
282B TYR* 1.3 72.4 + - - +
313B LEU* 3.7 12.1 - - + +
376B PHE* 3.4 12.9 - - - +
377B SER* 2.9 30.7 + - - +
379B TRP* 3.0 33.0 + - + +
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Residues in contact with TYR 282 (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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110B PRO* 5.4 0.2 - - - +
128B PRO* 3.3 33.1 - - + +
129B SER 5.3 1.1 + - - -
130B HIS* 3.9 25.6 + - - -
243B VAL* 2.9 52.9 + - + +
244B PHE* 3.7 24.7 - + - -
281B THR* 1.3 88.9 + - - +
283B LYS* 1.3 65.4 + - - +
284B GLU 3.6 1.9 + - - -
313B LEU* 3.7 13.3 - - + +
316B ILE* 3.9 29.2 - - + -
374B THR* 3.8 15.0 - - + -
375B ASP 3.7 3.4 - - - +
376B PHE* 3.6 28.9 - + - -
377B SER* 4.2 0.9 + - - -
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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
------------------------------------------------------------
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