Contacts of the helix formed by residues 390 - 395 (chain F) 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 ALA 390 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C THR* 4.0 3.1 + - - +
311C PRO* 3.7 33.2 - - + +
386F LEU* 3.4 32.1 - - + +
387F LEU* 3.5 5.6 + - + +
388F ILE 3.4 0.2 - - - -
389F PRO* 1.3 76.9 - - + +
391F ALA* 1.3 59.1 + - - +
392F SER 3.2 2.2 - - - -
393F TYR* 3.0 23.2 + - + +
394F VAL 3.0 12.0 + - - -
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Residues in contact with ALA 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C THR* 5.8 0.4 - - - +
334F LEU* 5.4 0.4 - - + -
361F VAL* 4.2 8.3 - - + -
386F LEU* 4.8 0.4 - - - -
387F LEU 3.3 9.1 + - - +
388F ILE* 3.4 22.0 - - - +
389F PRO 3.2 0.4 - - - -
390F ALA* 1.3 78.2 - - - +
392F SER* 1.3 60.0 + - - +
394F VAL* 3.5 9.7 - - + +
395F LEU* 3.2 33.9 + - + +
423F LEU* 3.8 28.9 - - + -
426F VAL* 4.7 2.5 - - + -
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Residues in contact with SER 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C GLY* 5.6 0.2 - - - -
252C HIS* 3.5 28.8 - - - -
253C THR* 3.8 15.7 + - - -
314C ASP* 2.8 28.1 + - - -
388F ILE 4.5 0.8 + - - -
389F PRO 3.0 10.7 + - - -
391F ALA* 1.3 76.8 - - - +
393F TYR* 1.3 59.8 + - - +
396F PRO* 3.4 9.1 - - - +
426F VAL* 3.9 15.1 - - - +
430F HIS* 3.4 18.5 + - - -
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Residues in contact with TYR 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B SER 5.1 0.3 - - - -
339B ARG* 2.5 86.6 + - + +
340B HIS* 5.0 2.6 + + - -
286C HIS* 3.5 44.4 - + + -
288C PHE* 3.2 33.2 - + - -
309C HIS* 5.4 8.7 - + + -
311C PRO* 4.1 15.0 - - + -
314C ASP* 5.4 3.8 - - - +
386F LEU* 5.3 3.1 - - + -
389F PRO 5.3 0.4 - - - +
390F ALA* 3.0 21.0 + - + +
392F SER* 1.3 81.7 + - - +
394F VAL* 1.3 63.2 + - + +
396F PRO* 3.5 9.1 - - - +
397F GLU* 5.3 1.6 - - - -
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Residues in contact with VAL 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B ARG* 4.1 0.7 - - - +
332F VAL* 5.8 0.2 - - + -
334F LEU* 4.0 18.4 - - + -
357F ARG* 5.7 2.5 - - - +
359F VAL* 3.9 24.7 - - + -
361F VAL* 5.0 0.7 - - + -
384F SER* 5.8 1.1 - - - +
386F LEU* 3.6 22.4 - - + -
390F ALA 3.0 11.7 + - - +
391F ALA* 3.5 15.5 - - - +
393F TYR* 1.3 79.9 - - + +
395F LEU* 1.3 56.6 + - - +
396F PRO 3.3 0.2 - - - -
397F GLU* 2.7 48.0 + - + +
398F VAL* 3.2 20.2 + - + -
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Residues in contact with LEU 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334F LEU* 4.0 8.3 - - + -
391F ALA 3.2 21.6 + - - +
394F VAL* 1.3 73.7 - - - +
396F PRO* 1.3 70.6 - - + +
397F GLU 3.2 0.2 - - - -
398F VAL* 3.3 33.4 - - + +
401F VAL* 3.9 21.3 - - + -
423F LEU* 4.6 13.2 - - + +
426F VAL* 3.7 25.1 - - + -
427F ALA* 3.8 18.4 - - + +
430F HIS* 3.7 16.2 - - + +
432F VAL* 3.6 34.0 - - + +
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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