Contacts of the helix formed by residues 349 - 364 (chain J) in PDB entry 5A31
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 GLU 349 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320J ARG* 4.3 8.4 + - - -
344J PHE* 3.0 33.2 + - + +
347J ALA* 4.6 17.3 - - - +
348J SER* 1.3 75.3 - - - +
350J HIS* 1.3 63.6 + - - +
351J ASP* 3.4 10.1 - - - +
352J GLN* 2.9 31.1 + - - +
353J ALA* 3.2 16.6 + - - +
389R MET 6.0 1.3 - - - +
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Residues in contact with HIS 350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345J ALA* 4.8 6.2 + - - -
348J SER* 3.2 38.4 + - - -
349J GLU* 1.3 69.8 - - - +
351J ASP* 1.3 60.1 + - - +
353J ALA* 3.3 1.2 + - - +
354J MET* 2.7 40.7 + - - +
377J GLU* 3.4 30.9 - - + +
380J LEU* 4.3 33.0 - - + +
381J THR* 3.6 30.9 - - + +
387R ILE* 4.5 4.9 - - + +
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Residues in contact with ASP 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349J GLU* 3.6 6.6 - - - +
350J HIS* 1.3 85.0 + - - +
352J GLN* 1.3 80.5 + - + +
354J MET* 3.2 9.1 - - - +
355J ALA* 3.2 18.7 + - - +
382R ASN* 5.2 9.4 - - - +
385R THR* 5.3 0.7 - - - +
387R ILE* 3.2 49.1 - - + +
388R LYS 4.8 1.4 - - - +
389R MET* 4.2 19.6 - - + +
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Residues in contact with GLN 352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320J ARG* 5.3 1.8 - - - +
344J PHE* 3.2 48.6 - - + -
349J GLU* 2.9 37.3 + - - +
350J HIS 3.3 0.6 - - - -
351J ASP* 1.3 89.9 - - + +
353J ALA* 1.3 66.4 + - - +
355J ALA* 3.0 18.7 + - - +
356J ALA* 3.1 10.9 + - - +
389R MET 5.7 0.9 - - - +
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Residues in contact with ALA 353 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341J GLY* 3.7 21.5 - - - +
344J PHE* 3.6 12.4 - - + +
345J ALA 3.9 4.3 - - - +
349J GLU 3.2 11.7 + - - +
350J HIS 3.5 3.6 - - - +
352J GLN* 1.3 76.4 - - - +
354J MET* 1.3 65.9 + - - +
356J ALA* 3.2 2.1 + - - +
357J TYR* 2.8 33.0 + - + -
377J GLU* 3.2 30.1 - - - +
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Residues in contact with MET 354 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350J HIS* 2.7 19.1 + - - +
351J ASP* 3.2 14.8 - - - +
353J ALA* 1.3 73.4 - - - +
355J ALA* 1.3 52.6 + - - +
357J TYR* 3.1 2.8 + - + +
358J PHE* 2.7 60.9 + - + -
374J ILE* 3.4 39.0 - - + +
377J GLU* 3.4 37.0 - - + +
378J TYR* 4.2 31.0 - - + +
381J THR* 6.1 1.1 - - - -
387R ILE* 6.5 0.7 - - - -
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Residues in contact with ALA 355 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761F SER* 4.4 13.9 + - - +
765F ASP* 4.6 3.3 - - - +
351J ASP 3.2 7.9 + - - +
352J GLN* 3.0 14.4 + - - +
354J MET* 1.3 79.4 - - - +
356J ALA* 1.3 58.3 + - - +
358J PHE* 3.3 1.7 + - - +
359J THR* 3.0 37.3 + - + +
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Residues in contact with ALA 356 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337J TRP* 4.2 17.4 - - + +
340J TYR* 4.2 13.2 - - + +
341J GLY* 3.6 32.1 - - - +
344J PHE* 4.8 2.7 - - + -
352J GLN 3.1 11.5 + - - +
353J ALA 3.9 1.1 - - - +
355J ALA* 1.3 72.7 - - - +
357J TYR* 1.3 61.9 + - - +
359J THR* 3.0 10.2 + - - -
360J ALA* 2.9 28.6 + - - +
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Residues in contact with TYR 357 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ARG* 4.0 3.1 - - - -
338J ILE* 3.6 35.9 - - + -
341J GLY* 3.4 10.6 + - - -
342J HIS* 2.8 38.8 + + - -
345J ALA* 4.0 0.2 - - - +
353J ALA* 2.8 32.5 + - + +
354J MET* 3.7 2.9 - - + +
356J ALA* 1.3 76.8 - - - +
358J PHE* 1.3 56.5 + - - +
360J ALA* 3.1 4.4 + - - +
361J ALA* 2.8 29.5 + - - +
370J PRO* 3.9 6.6 - - + +
373J TYR* 3.9 30.1 - + + -
374J ILE* 3.5 21.8 - - + -
377J GLU* 3.2 41.4 + - + -
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Residues in contact with PHE 358 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757F LEU* 4.1 11.0 - - + -
758F MET* 3.5 43.7 - - + -
761F SER* 3.5 36.1 - - - +
762F TRP* 3.5 10.6 + - + +
765F ASP* 5.8 0.2 - - - +
354J MET* 2.7 51.4 + - + +
355J ALA 3.7 1.3 - - - +
357J TYR* 1.3 71.9 - - - +
359J THR* 1.3 58.3 + - + +
361J ALA* 2.9 6.6 + - - +
362J GLN 2.8 26.0 + - - -
374J ILE* 3.5 35.2 - - + -
378J TYR* 4.4 8.1 - + - -
390J PHE* 3.9 17.3 - + - -
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Residues in contact with THR 359 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
762F TRP* 5.0 0.2 - - - -
765F ASP* 3.2 39.0 + - + +
337J TRP* 3.3 36.8 - - + -
355J ALA* 3.0 25.0 + - + +
356J ALA* 3.0 10.2 + - - -
358J PHE* 1.3 77.1 - - - +
360J ALA* 1.3 65.3 + - - +
362J GLN* 3.5 9.4 + - - +
363J LEU* 3.2 25.5 + - - +
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Residues in contact with ALA 360 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337J TRP* 3.6 28.0 - - + -
338J ILE* 4.1 24.5 - - + +
356J ALA 2.9 11.4 + - - +
357J TYR* 3.4 10.3 - - - +
359J THR* 1.3 81.7 + - - +
361J ALA* 1.3 58.1 + - - +
363J LEU* 3.4 1.4 + - - +
364J MET* 2.9 38.0 + - - +
370J PRO* 4.1 5.4 - - + -
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Residues in contact with ALA 361 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758F MET* 3.5 27.6 - - + -
762F TRP* 4.7 1.6 - - - -
357J TYR 2.8 13.1 + - - +
358J PHE 2.9 9.8 + - - +
360J ALA* 1.3 77.1 - - - +
362J GLN* 1.3 62.1 + - - +
364J MET 3.2 20.3 + - - +
365J LYS* 3.5 6.6 + - - +
370J PRO* 3.5 21.8 - - + -
371J MET* 4.7 9.8 - - + +
374J ILE* 4.0 7.0 - - + -
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Residues in contact with GLN 362 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740F TYR* 3.7 19.4 + - - +
762F TRP* 3.3 66.5 + - + +
765F ASP* 3.7 23.4 + - - +
766F LEU* 4.9 5.2 - - - +
144J ASP* 5.6 2.1 - - - +
146J ARG* 3.4 15.4 + - - +
358J PHE 2.8 6.6 + - - +
359J THR* 3.6 10.3 + - - +
361J ALA* 1.3 78.0 - - - +
363J LEU* 1.3 65.0 + - - +
365J LYS* 3.3 26.6 - - - +
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Residues in contact with LEU 363 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146J ARG* 3.8 39.9 - - - +
173J HIS 4.7 4.5 - - - +
175J MET* 6.1 0.3 - - - +
331J LYS* 4.3 7.9 - - + -
332J THR* 3.3 52.6 - - + +
334J GLY* 4.2 1.8 - - - -
337J TRP* 3.8 31.9 - - + +
359J THR 3.2 14.8 + - - +
360J ALA 3.7 1.1 - - - +
362J GLN* 1.3 83.2 - - + +
364J MET* 1.3 71.8 + - + +
365J LYS 3.6 1.6 + - - -
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Residues in contact with MET 364 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1G MET* 3.7 17.9 - - + -
173J HIS 4.4 9.9 - - - +
174J HIS* 3.9 19.3 - - + -
332J THR 5.5 0.4 - - - +
334J GLY* 3.3 39.3 - - - +
338J ILE* 4.0 13.5 - - + -
360J ALA* 2.9 21.2 + - - +
361J ALA 3.2 7.4 + - - +
363J LEU* 1.3 85.6 - - + +
365J LYS* 1.3 66.1 + - - +
366J GLY 3.4 0.2 + - - -
367J CYS* 3.3 55.7 + - + +
370J PRO* 4.3 5.4 - - + +
371J MET* 4.9 0.2 - - - +
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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