Contacts of the helix formed by residues 366 - 381 (chain A) in PDB entry 4AY6
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 LYS 366 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A VAL* 6.2 1.4 - - - +
341A ARG* 5.1 5.7 - - - +
361A LEU* 2.8 35.8 + - + +
364A GLN* 3.6 26.2 + - + +
365A GLY* 1.3 75.8 - - - +
367A LEU* 1.3 59.5 + - - +
368A GLN* 3.5 24.7 - - - +
369A GLU* 3.4 14.3 + - - +
370A ALA* 2.9 25.5 + - - +
527A VAL* 4.2 28.3 + - + +
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Residues in contact with LEU 367 (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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362A GLN* 3.8 26.0 - - + +
365A GLY* 3.2 28.3 + - - +
366A LYS* 1.3 66.8 - - - +
368A GLN* 1.3 72.4 + - - +
369A GLU 2.7 4.2 + - - -
370A ALA* 2.8 6.9 + - - -
371A LEU* 2.7 27.1 + - - +
394A THR* 4.0 9.8 - - + +
397A GLU* 3.8 39.3 - - + +
398A MET* 3.6 31.2 - - + -
524A LYS* 6.3 0.2 - - - -
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Residues in contact with GLN 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A GLY 4.7 2.6 - - - +
366A LYS* 3.5 37.1 - - - +
367A LEU* 1.3 77.2 + - - +
369A GLU* 1.3 78.8 + - + +
371A LEU* 3.6 8.4 - - - +
372A MET* 3.6 16.0 + - - +
398A MET* 4.4 13.6 - - - +
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Residues in contact with GLU 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG* 3.1 33.7 + - - -
361A LEU* 4.0 11.4 - - + +
366A LYS* 3.7 27.4 - - - +
367A LEU 2.7 1.8 + - - -
368A GLN* 1.3 86.5 + - + +
370A ALA* 1.3 66.9 + - - +
371A LEU 2.9 1.6 - - - -
372A MET* 2.7 30.9 + - + +
373A HIS* 3.2 19.2 + - + +
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Residues in contact with ALA 370 (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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358A ALA* 3.1 31.9 - - + +
361A LEU* 3.4 21.1 - - + +
362A GLN* 3.6 13.9 - - + +
366A LYS 2.9 14.2 + - - +
367A LEU* 2.8 9.2 + - - +
369A GLU* 1.3 71.5 - - - +
371A LEU* 1.3 61.1 + - - +
373A HIS* 3.4 1.4 + - - +
374A TYR* 3.1 31.2 + - + -
394A THR* 4.9 2.7 - - + -
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Residues in contact with LEU 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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367A LEU 2.7 19.6 + - - +
368A GLN* 3.6 8.1 - - - +
369A GLU 2.8 0.4 + - - -
370A ALA* 1.3 70.1 - - - +
372A MET* 1.3 66.4 + - - +
373A HIS 3.1 0.3 + - - -
374A TYR* 3.1 7.8 + - - +
375A LYS* 2.9 44.7 + - + +
391A MET* 3.8 33.7 - - + +
394A THR* 4.5 11.6 - - + +
395A LEU* 4.1 28.5 - - + -
398A MET* 4.2 16.6 - - + -
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Residues in contact with MET 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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368A GLN 3.6 7.1 + - - +
369A GLU* 2.7 26.7 + - + +
371A LEU* 1.3 75.2 - - - +
373A HIS* 1.3 72.3 + - + +
375A LYS* 3.5 16.3 + - - +
376A GLU* 3.1 32.3 + - + +
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Residues in contact with HIS 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ARG* 4.2 10.3 + - - -
344A LEU* 4.2 5.6 - - + +
354A HIS* 3.1 50.7 + + - +
357A LEU* 3.6 32.1 - - + +
358A ALA* 4.0 6.5 - - + -
361A LEU* 4.0 12.1 - - + -
369A GLU* 3.2 22.7 + - + +
370A ALA 3.9 5.8 - - - +
371A LEU 3.1 0.8 - - - -
372A MET* 1.3 88.8 - - - +
374A TYR* 1.3 60.0 + - - +
376A GLU* 3.0 7.3 + - + +
377A ALA* 2.9 27.0 + - - +
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Residues in contact with TYR 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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355A SER* 3.8 21.1 - - - -
358A ALA* 3.5 26.8 - - + +
359A SER* 3.3 21.6 - - - -
362A GLN* 3.3 15.9 + - - -
370A ALA* 3.1 24.4 + - + -
371A LEU* 3.1 8.9 + - - +
373A HIS* 1.3 76.2 - - - +
375A LYS* 1.3 61.6 - - - +
377A ALA* 3.2 5.5 + - - +
378A ILE* 3.1 29.5 + - - +
387A ALA* 4.1 19.5 - - + +
390A ASN* 3.3 29.4 - - + +
391A MET* 4.1 25.6 - - + -
394A THR* 3.4 26.7 - - - -
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Residues in contact with LYS 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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371A LEU* 2.9 46.8 + - + +
372A MET* 3.5 16.6 - - - +
374A TYR* 1.3 75.2 - - - +
376A GLU* 1.3 62.5 + - + +
378A ILE* 3.6 8.6 + - - +
379A ARG* 3.2 22.0 + - - +
391A MET* 4.1 11.9 - - + -
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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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348A PRO 4.9 0.9 - - - +
349A GLU* 4.8 1.7 - - - +
354A HIS* 3.5 30.4 + - + +
372A MET* 3.1 20.4 + - + +
373A HIS* 3.0 11.7 + - + +
375A LYS* 1.3 74.8 - - + +
377A ALA* 1.3 67.5 + - - +
379A ARG* 2.8 58.4 + - - +
380A ILE* 3.2 21.5 + - + +
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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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351A ALA* 4.0 20.2 - - - +
354A HIS* 4.0 10.9 - - + +
355A SER* 4.1 15.3 - - - +
373A HIS 2.9 15.2 + - - +
374A TYR* 3.2 12.8 + - - +
376A GLU* 1.3 73.8 - - - +
378A ILE* 1.3 63.4 + - - +
380A ILE* 3.2 8.4 + - - +
381A SER* 3.0 22.7 + - - -
384A PHE* 4.4 11.7 - - + -
387A ALA* 4.5 4.7 - - + -
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Residues in contact with ILE 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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374A TYR 3.1 15.8 + - - +
375A LYS* 3.7 8.5 - - - +
376A GLU 3.3 0.2 - - - -
377A ALA* 1.3 73.7 - - - +
379A ARG* 1.3 66.8 + - - +
381A SER 2.9 28.9 + - - +
382A PRO* 3.2 8.4 - - + +
384A PHE* 4.1 3.6 - - + +
387A ALA* 3.2 35.9 - - + +
388A TYR* 3.2 61.0 - - + +
391A MET* 4.7 10.5 - - + -
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Residues in contact with ARG 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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349A GLU* 3.4 28.1 + - - -
375A LYS 3.2 9.4 + - - +
376A GLU* 2.8 48.3 + - - +
378A ILE* 1.3 78.8 - - - +
380A ILE* 1.3 86.1 + - - +
382A PRO* 4.3 9.1 - - - +
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Residues in contact with ILE 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A PRO 4.4 0.4 - - - +
349A GLU* 3.8 38.4 - - + +
350A PHE 4.6 2.2 - - - +
351A ALA* 3.9 15.3 - - + -
354A HIS* 4.2 18.6 - - + -
376A GLU* 3.2 26.5 - - - +
377A ALA* 3.2 7.6 + - - +
378A ILE 3.0 0.4 - - - -
379A ARG* 1.3 110.2 - - - +
381A SER* 1.3 60.6 + - - +
382A PRO* 3.4 7.7 - - - +
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Residues in contact with SER 381 (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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351A ALA* 3.8 18.3 - - - +
377A ALA 3.0 8.6 + - - -
378A ILE* 2.9 11.5 + - - +
380A ILE* 1.3 77.6 + - - +
382A PRO* 1.3 68.6 - - - +
383A THR* 3.1 4.5 - - - -
384A PHE* 3.0 33.1 + - - +
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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