Contacts of the helix formed by residues 374 - 385 (chain A) in PDB entry 1O6K
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 SER 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249A GLU* 2.6 36.6 + - - -
372A THR 3.4 3.9 + - - -
373A LEU* 1.3 74.7 - - - +
375A PRO* 1.4 71.2 - - - +
376A GLU* 3.3 23.2 - - - +
377A ALA* 3.1 13.0 + - - +
378A LYS* 3.0 21.2 + - - +
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Residues in contact with PRO 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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373A LEU 3.7 2.2 - - - +
374A SER* 1.4 84.5 - - - +
376A GLU* 1.3 65.7 + - - +
378A LYS* 3.4 13.1 + - + +
379A SER* 3.0 30.0 + - - -
407A ARG* 4.1 15.2 + - - +
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Residues in contact with GLU 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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249A GLU* 4.7 1.8 - - - +
253A ARG* 4.9 8.2 + - - +
374A SER* 3.3 25.7 + - - +
375A PRO* 1.3 90.4 - - - +
377A ALA* 1.3 56.6 + - - +
379A SER* 4.4 1.8 - - - -
380A LEU* 3.1 22.5 + - - +
406A HIS* 3.4 11.3 - - - -
407A ARG* 4.1 23.7 + - + +
408A PHE* 3.7 35.2 - - + +
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Residues in contact with ALA 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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249A GLU* 3.6 13.9 - - - +
344A MET* 4.0 9.2 - - + -
373A LEU* 3.8 19.1 - - + -
374A SER* 3.1 22.9 + - - +
376A GLU* 1.3 76.5 - - - +
378A LYS* 1.3 65.0 + - - +
379A SER 3.2 0.2 - - - -
380A LEU* 3.2 2.9 + - - +
381A LEU* 3.0 30.5 + - - +
408A PHE* 3.8 18.2 - - + -
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Residues in contact with LYS 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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369A PHE* 3.6 32.5 + - + -
370A PRO 3.4 18.9 + - - -
371A ARG* 3.4 22.4 + - - +
373A LEU* 3.2 35.5 + - + +
374A SER 3.0 13.2 + - - +
375A PRO* 3.4 13.6 + - + +
377A ALA* 1.3 75.7 - - - +
379A SER* 1.3 56.7 + - - +
382A ALA* 2.9 31.8 + - - +
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Residues in contact with SER 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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375A PRO 3.0 17.8 + - - -
376A GLU 3.8 3.8 - - - -
378A LYS* 1.3 74.9 - - - +
380A LEU* 1.3 59.2 + - - +
382A ALA* 3.9 5.4 - - - +
383A GLY* 3.0 25.3 + - - -
406A HIS* 3.0 23.1 + - - -
407A ARG* 3.5 24.7 + - - -
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Residues in contact with LEU 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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340A MET* 3.9 23.8 - - + -
344A MET* 4.5 7.9 - - + -
376A GLU 3.1 18.9 + - - +
377A ALA 3.2 4.0 + - - +
379A SER* 1.3 75.4 - - - +
381A LEU* 1.3 59.5 + - + +
383A GLY* 3.2 2.3 + - - -
384A LEU* 2.9 47.2 + - + +
393A LEU* 3.9 19.5 - - + +
403A VAL* 4.8 1.1 - - + -
406A HIS* 3.5 26.9 - - + +
408A PHE* 3.6 26.9 - - + -
409A PHE* 3.8 23.3 - - + -
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A GLY* 3.7 11.0 - - - +
340A MET* 3.7 18.6 - - + +
341A TYR* 3.6 50.9 - - + +
344A MET* 4.1 15.9 - - + -
345A CYS* 4.1 4.0 - - - -
369A PHE* 3.6 17.5 - - + -
373A LEU* 3.9 23.6 - - + -
377A ALA 3.0 18.4 + - - +
380A LEU* 1.3 76.6 - - + +
382A ALA* 1.3 58.4 + - - +
384A LEU* 4.7 2.0 - - + -
385A LEU* 2.8 37.9 + - + +
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Residues in contact with ALA 382 (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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367A ILE* 3.9 15.2 - - + +
369A PHE* 3.8 13.2 - - + -
378A LYS 2.9 20.3 + - - +
379A SER* 4.0 5.8 - - - +
381A LEU* 1.3 74.3 - - - +
383A GLY* 1.3 61.1 + - - +
385A LEU 3.7 1.4 - - - -
386A LYS* 3.4 29.5 + - + +
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Residues in contact with GLY 383 (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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379A SER 3.0 15.3 + - - -
380A LEU 3.6 3.1 - - - -
381A LEU 3.2 0.2 - - - -
382A ALA* 1.3 75.6 - - - +
384A LEU* 1.3 62.2 + - - +
385A LEU 3.5 0.2 + - - -
386A LYS* 3.6 8.3 + - - +
391A GLN 5.6 1.3 - - - -
392A ARG* 3.4 9.0 - - - +
393A LEU* 2.9 36.5 + - - -
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Residues in contact with LEU 384 (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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333A TRP* 3.5 19.1 - - + +
334A TRP* 3.6 11.6 - - - -
336A LEU* 4.0 20.6 - - + +
337A GLY* 3.7 31.4 - - - +
340A MET* 4.6 3.8 - - + -
380A LEU* 2.9 44.1 + - + +
381A LEU* 4.2 2.2 - - - +
383A GLY* 1.3 75.9 - - - +
385A LEU* 1.3 59.3 + - - +
386A LYS 3.4 0.4 - - - -
392A ARG* 3.2 28.0 + - - -
393A LEU* 3.6 28.9 - - + +
403A VAL* 4.1 15.5 - - + -
409A PHE* 6.1 0.2 - - + -
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Residues in contact with LEU 385 (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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334A TRP* 3.3 54.3 - - + +
337A GLY* 3.8 15.7 - - - +
338A VAL* 3.8 19.7 - - + +
341A TYR* 3.9 29.8 - - + -
349A PRO* 4.3 7.2 - - + -
350A PHE* 5.4 0.8 - - + -
367A ILE* 3.9 32.6 - - + +
381A LEU* 2.8 22.6 + - + +
382A ALA 3.7 4.9 - - - -
383A GLY 3.3 0.2 - - - -
384A LEU* 1.3 76.3 - - - +
386A LYS* 1.3 61.9 + - - +
387A LYS* 3.5 5.7 + - - +
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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