Contacts of the strand formed by residues 336 - 341 (chain T) in PDB entry 6O81
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 LEU 336 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83T TYR* 3.7 39.9 - - + +
281T GLY 3.5 9.4 - - - +
323T ALA* 4.5 14.0 - - - +
324T GLU 5.1 2.1 + - - -
335T GLY* 1.3 67.8 - - - -
337T ILE* 1.3 62.6 + - - +
338T GLY 3.5 3.1 + - - -
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Residues in contact with ILE 337 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280T GLY* 3.5 1.4 - - - -
281T GLY 2.9 37.0 + - - +
282T SER 5.3 0.4 - - - -
283T ILE* 4.8 16.4 - - + +
323T ALA* 5.7 2.2 - - - -
331T ALA* 5.3 11.9 - - + -
332T ALA 5.1 7.9 - - - +
335T GLY 3.0 8.6 + - - +
336T LEU* 1.3 69.3 - - - +
338T GLY* 1.3 60.3 + - - +
339T VAL* 4.1 1.8 + - + +
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Residues in contact with GLY 338 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279T ALA 3.4 10.3 - - - -
280T GLY* 4.1 3.8 - - - -
321T LEU* 3.2 5.4 - - - +
322T PHE* 2.6 50.9 + - - +
323T ALA* 4.6 1.0 - - - +
336T LEU 3.5 5.5 + - - -
337T ILE* 1.3 72.5 - - - +
339T VAL* 1.3 56.7 + - - -
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Residues in contact with VAL 339 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277T GLY 3.4 2.8 - - - +
278T VAL* 4.4 1.3 - - - -
279T ALA* 2.9 36.6 + - + +
280T GLY* 4.8 0.2 - - - -
318T ILE* 5.4 9.6 - - + -
320T SER 3.5 9.0 - - - +
321T LEU* 4.4 3.8 - - + +
337T ILE* 4.1 2.1 + - + +
338T GLY* 1.3 73.6 - - - -
340T GLY* 1.3 60.5 + - - +
341T THR* 3.8 4.7 + - - +
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Residues in contact with GLY 340 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276T GLY 5.4 0.2 - - - -
277T GLY 3.6 7.4 - - - -
278T VAL* 3.9 12.5 - - - +
318T ILE 5.0 0.2 - - - -
319T VAL* 3.1 7.9 + - - +
320T SER* 2.9 42.4 + - - -
322T PHE* 4.9 3.6 - - - +
338T GLY 4.2 1.4 + - - -
339T VAL* 1.3 70.1 - - - +
341T THR* 1.3 62.2 + - - -
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Residues in contact with THR 341 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276T GLY 2.9 20.1 + - - +
277T GLY 3.3 10.9 + - - -
294T ILE* 5.6 3.8 - - - -
316T SER* 4.0 18.4 - - - -
317T LYS 3.4 16.4 - - - -
318T ILE* 4.0 9.9 - - - -
319T VAL* 3.7 7.3 - - - +
339T VAL* 3.8 4.4 + - - -
340T GLY* 1.3 74.9 - - - +
342T LYS* 1.3 57.9 + - - +
343T ILE* 3.2 7.2 - - - -
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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