Contacts of the strand formed by residues 277 - 282 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A PHE* 3.7 33.0 - - + -
223A MET* 4.1 8.1 - - - -
238A PHE* 3.2 4.3 - - - -
274A PHE* 3.1 36.0 + - + +
275A GLN 3.3 1.9 - - - +
276A ALA* 1.3 79.0 - - - +
278A LYS* 1.3 68.7 + - - +
279A ILE* 5.9 0.4 - - + -
380A ASP* 4.3 4.0 - - - +
381A MET* 4.8 0.9 + - - +
388A PHE* 3.5 12.7 - - + -
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Residues in contact with LYS 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A PHE* 4.7 0.5 - - - -
237A VAL* 4.3 10.5 - - + +
238A PHE 2.9 6.9 + - - +
239A PHE* 3.3 24.3 - - + -
240A HIS* 2.8 25.6 + - - +
275A GLN 5.1 4.2 + - - -
276A ALA 5.2 0.8 - - - +
277A ALA* 1.3 79.0 + - - +
279A ILE* 1.3 65.2 + - - +
378A LEU* 3.8 23.8 - - + -
379A TRP 3.3 10.5 - - - +
380A ASP* 2.9 30.9 + - + +
388A PHE* 4.4 1.3 - - - -
409A LEU* 4.7 4.0 - - + -
410A TYR* 2.7 30.6 + - - +
411A TRP* 3.6 35.8 - - + -
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 5.5 4.7 - - + -
240A HIS* 3.6 17.9 - - + +
242A ASP* 4.3 7.4 - - + -
247A SER* 4.0 22.4 - - - +
248A LEU* 4.1 14.1 - - + -
259A PRO* 3.9 21.3 - - + -
274A PHE* 5.2 4.0 - - + -
277A ALA* 5.5 0.4 - - + -
278A LYS* 1.3 77.9 - - - +
280A ILE* 1.3 65.0 + - - +
281A THR* 3.8 21.1 - - + -
378A LEU* 3.5 4.0 - - - -
379A TRP* 2.8 49.7 + - + -
388A PHE* 3.6 29.4 - - + -
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.9 20.4 - - + -
136A PHE* 3.6 37.2 - - + -
137A VAL* 5.1 1.8 - - + -
140A LEU* 4.7 2.2 - - + -
211A TYR* 4.0 11.0 - - + -
239A PHE* 3.8 32.1 - - + -
240A HIS 2.8 14.2 + - - +
241A LEU* 3.9 20.0 - - + -
242A ASP* 3.0 29.8 + - - +
243A VAL* 3.7 3.2 + - + -
279A ILE* 1.3 72.0 - - - +
281A THR* 1.3 64.4 + - - +
376A PHE* 4.2 8.5 - - + -
377A SER 3.7 3.4 - - - +
378A LEU* 3.9 13.0 - - + -
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Residues in contact with THR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ASP 3.5 17.5 - - - +
243A VAL* 3.8 2.9 - - - +
245A GLY* 4.1 10.8 - - - -
248A LEU* 4.2 4.0 - - + -
279A ILE* 3.8 12.6 - - + -
280A ILE* 1.3 77.7 - - - +
282A TYR* 1.3 76.2 + - - +
313A LEU* 3.7 14.9 - - + +
376A PHE* 3.4 15.2 - - - -
377A SER* 3.0 29.8 + - - +
379A TRP* 3.2 35.6 + - + +
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Residues in contact with TYR 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO* 5.2 0.9 - - - +
128A PRO* 3.5 32.3 - - + +
129A SER 5.4 1.7 + - - -
130A HIS* 3.9 21.8 + - - -
243A VAL* 2.8 54.4 + - + +
244A PHE* 3.7 29.1 - + - -
281A THR* 1.3 88.0 + - - +
283A LYS* 1.3 64.4 + - - +
284A GLU 3.6 2.3 + - - -
313A LEU* 3.6 14.5 - - + +
316A ILE* 3.8 26.9 - - + -
374A THR* 3.8 13.2 - - + -
375A ASP 3.8 3.1 - - - +
376A PHE* 3.6 30.7 - + - -
377A SER* 4.1 1.1 + - - -
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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