Contacts of the helix formed by residues 370 - 380 (chain A) in PDB entry 4FO9
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 370 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A LEU* 3.9 14.8 - - + -
308A LEU* 4.4 6.3 - - + -
355A ILE* 2.8 36.4 + - + +
357A CYS* 3.9 23.1 - - + -
368A PHE 3.4 2.2 + - - -
369A ASP* 1.3 72.3 - - - +
371A ALA* 1.3 64.5 + - - +
373A TYR* 3.7 3.8 - - - +
374A LEU* 3.1 30.1 + - - +
397A LEU* 6.4 0.4 - - - -
399A LEU* 4.3 5.4 - - + -
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Residues in contact with ALA 371 (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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301A SER* 4.9 1.4 - - - -
305A LEU* 3.7 28.0 - - + +
354A THR* 6.2 2.0 - - + -
355A ILE* 5.1 5.0 - - + +
369A ASP* 3.2 11.5 + - - +
370A ALA* 1.3 79.4 - - - +
372A LEU* 1.3 57.8 + - - +
374A LEU* 3.5 5.3 + - - +
375A GLN* 2.9 43.8 + - + +
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Residues in contact with LEU 372 (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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346A CYS* 4.4 3.1 - - - -
348A LEU* 4.4 13.5 - - + -
349A GLY* 3.6 34.1 - - - +
351A MET* 4.0 21.5 - - + -
369A ASP* 3.3 18.4 + - + +
370A ALA 3.2 0.4 - - - -
371A ALA* 1.3 77.2 - - - +
373A TYR* 1.3 64.0 + - - +
375A GLN* 3.4 23.6 + - + +
376A MET* 3.1 34.4 + - + +
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Residues in contact with TYR 373 (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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348A LEU* 4.0 22.5 - - + +
357A CYS* 5.4 0.7 - - - -
368A PHE* 3.4 29.6 - + + -
369A ASP 3.1 18.7 + - - +
370A ALA* 3.7 3.8 - - - +
372A LEU* 1.3 78.4 - - - +
374A LEU* 1.3 58.8 + - + +
376A MET* 3.5 3.8 + - + +
377A ASN* 3.0 54.5 + - - -
383A TRP* 3.3 25.9 - + - -
384A ILE 3.3 19.7 + - - -
386A PRO* 4.1 7.2 - - + -
392A ALA* 2.7 42.2 + - + +
397A LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 374 (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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153A PHE* 3.5 6.4 - - + -
301A SER* 4.0 15.6 - - - +
304A LEU* 3.9 12.3 - - + -
305A LEU* 3.6 42.0 - - + +
308A LEU* 4.4 11.2 - - + -
370A ALA* 3.1 18.6 + - - +
371A ALA* 3.8 3.8 - - - +
373A TYR* 1.3 78.6 - - + +
375A GLN* 1.3 60.4 + - - +
377A ASN* 4.5 2.9 - - - +
378A GLU* 2.9 29.3 + - - +
383A TRP* 4.1 18.8 - - + -
394A TYR* 3.8 27.6 - - + -
397A LEU* 4.5 8.7 - - + -
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Residues in contact with GLN 375 (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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301A SER* 4.0 17.5 - - - +
371A ALA* 2.9 41.0 + - - +
372A LEU* 3.6 23.6 - - + +
373A TYR 3.3 0.2 - - - -
374A LEU* 1.3 76.7 - - - +
376A MET* 1.3 61.7 + - + +
378A GLU* 3.3 22.5 + - - +
379A LYS* 3.5 8.8 + - - +
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Residues in contact with MET 376 (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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348A LEU* 3.3 43.7 - - + +
372A LEU* 3.1 28.9 + - + +
373A TYR* 3.7 5.4 - - + +
374A LEU 3.3 0.2 - - - -
375A GLN* 1.3 77.1 - - - +
377A ASN* 1.3 61.9 + - - +
379A LYS* 3.3 6.0 + - - +
380A LYS* 3.0 29.4 + - - +
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Residues in contact with ASN 377 (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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153A PHE* 3.7 5.8 - - - -
373A TYR* 3.0 57.2 + - - +
374A LEU 4.3 2.5 - - - +
376A MET* 1.3 78.6 - - - +
378A GLU* 1.3 64.3 + - - +
379A LYS 3.2 0.9 + - - -
380A LYS 3.7 4.7 - - - -
381A PRO* 3.2 25.7 - - + +
382A THR* 2.8 17.2 + - - -
383A TRP* 2.5 60.2 + - + +
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Residues in contact with GLU 378 (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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153A PHE* 3.4 24.0 - - + -
199A PRO* 4.2 36.7 - - + +
298A GLN* 5.5 3.6 + - - +
299A LEU 4.0 3.2 - - - +
300A THR* 3.2 16.1 - - - +
301A SER* 3.1 37.5 + - - -
374A LEU 2.9 19.4 + - - +
375A GLN* 3.4 11.4 - - - +
376A MET 3.3 0.4 - - - -
377A ASN* 1.3 77.1 - - - +
379A LYS* 1.3 59.7 + - + +
381A PRO* 5.0 1.7 - - - +
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Residues in contact with LYS 379 (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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199A PRO* 6.2 3.6 - - + -
375A GLN 3.5 6.7 + - - +
376A MET* 3.3 7.9 + - - +
377A ASN 3.2 0.4 - - - -
378A GLU* 1.3 81.7 - - + +
380A LYS* 1.3 61.8 + - + +
381A PRO* 3.8 6.2 - - - +
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Residues in contact with LYS 380 (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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376A MET 3.0 16.4 + - - +
377A ASN* 3.7 4.5 - - - +
379A LYS* 1.3 79.7 - - + +
381A PRO* 1.3 61.8 - - + +
382A THR* 2.9 27.7 + - + +
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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