Contacts of the helix formed by residues 345 - 360 (chain A) in PDB entry 5A5J
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 MET 345 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A GLU* 3.3 24.2 - - + +
327A ILE* 3.7 34.5 - - + +
330A VAL* 4.2 8.1 - - + -
331A ILE* 3.7 22.2 - - + -
341A ASP* 3.1 33.0 - - - +
342A ARG* 3.0 17.8 + - - +
343A SER 3.2 0.4 - - - -
344A HIS* 1.3 78.2 - - - +
346A PRO* 1.3 64.7 - - - +
347A TYR 3.3 3.1 - - - -
348A THR* 3.1 18.5 + - + +
349A ASP* 3.0 21.7 + - - +
446A PHE* 4.1 11.0 - - + -
450A THR* 4.5 1.3 - - + -
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Residues in contact with PRO 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLU* 3.5 7.4 - - - +
343A SER 4.8 3.8 - - - +
344A HIS* 3.3 10.8 - - - +
345A MET* 1.3 89.5 - - - +
347A TYR* 1.3 60.6 + - + +
349A ASP* 3.8 2.4 + - + -
350A ALA* 3.3 23.4 + - - +
413A LEU* 3.8 7.0 - - - +
417A GLY 4.2 15.0 - - - +
418A ASN* 4.5 2.0 - - - -
419A PHE* 3.9 35.3 - - + +
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Residues in contact with TYR 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A VAL* 3.4 51.9 - - + +
322A LYS* 3.7 39.2 + - + +
323A VAL* 3.9 13.7 - - + -
326A GLU* 3.1 19.3 + - + +
346A PRO* 1.3 76.8 - - + +
348A THR* 1.3 63.5 + - - +
350A ALA* 3.6 4.4 + - - +
351A VAL* 3.2 24.1 + - + +
409A PRO* 3.7 21.1 - - + +
410A HIS* 4.2 18.9 + + - -
413A LEU* 4.1 16.6 - - + +
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Residues in contact with THR 348 (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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323A VAL* 3.4 33.0 + - + +
326A GLU* 2.7 23.3 + - - -
327A ILE* 4.4 0.3 - - - +
345A MET* 3.1 16.5 + - + +
347A TYR* 1.3 73.7 - - - +
349A ASP* 1.3 63.5 + - - +
351A VAL* 3.3 9.2 + - + +
352A VAL* 3.3 25.8 + - + +
446A PHE* 3.4 33.7 - - + -
450A THR* 3.9 14.4 - - + -
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Residues in contact with ASP 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 3.3 47.4 + - + +
345A MET* 3.0 16.4 + - - +
346A PRO* 4.2 4.5 - - + +
348A THR* 1.3 76.4 - - - +
350A ALA* 1.3 60.0 + - - +
352A VAL* 3.6 8.7 + - - +
353A HIS* 2.6 58.7 + - - -
419A PHE* 4.0 16.5 - - + -
446A PHE* 5.2 1.7 - - - -
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Residues in contact with ALA 350 (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 PRO 3.3 18.8 + - - +
347A TYR* 3.7 6.1 - - - +
349A ASP* 1.3 77.9 - - - +
351A VAL* 1.3 54.3 + - - +
353A HIS* 3.2 3.6 + - - +
354A GLU* 2.8 37.2 + - - +
409A PRO* 3.8 23.6 - - + +
412A PHE* 3.8 27.1 - - + +
413A LEU* 4.0 7.6 - - + -
419A PHE* 4.0 2.9 - - + -
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Residues in contact with VAL 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A LEU* 4.6 15.5 - - + -
319A VAL* 3.7 21.1 - - + -
323A VAL* 3.6 28.0 - - + -
347A TYR* 3.2 19.9 + - + +
348A THR* 3.5 10.1 - - + +
350A ALA* 1.3 76.0 - - - +
352A VAL* 1.3 59.1 + - + +
354A GLU* 3.8 2.0 - - - +
355A VAL* 2.7 44.9 + - + +
407A PHE* 4.4 5.2 - - + -
409A PRO* 3.7 15.9 - - + -
449A LEU* 5.9 4.7 - - + -
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Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A THR* 3.3 19.3 - - + +
349A ASP* 3.9 11.0 - - - +
350A ALA 3.3 0.6 - - - -
351A VAL* 1.3 76.3 - - + +
353A HIS* 1.3 70.8 + - + +
355A VAL* 3.2 9.1 + - + +
356A GLN* 2.8 28.6 + - + +
442A GLY* 5.8 2.0 - - - +
445A LEU* 4.0 34.3 - - + -
446A PHE* 4.8 21.5 - - + +
449A LEU* 4.5 19.5 - - + -
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Residues in contact with HIS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ASP* 2.6 42.0 + - - -
350A ALA 3.2 7.6 + - - +
352A VAL* 1.3 80.3 - - + +
354A GLU* 1.3 51.0 + - - +
356A GLN* 3.0 6.8 + - - +
357A ARG* 2.7 34.5 + - - +
412A PHE* 3.7 23.6 - + + -
419A PHE* 3.0 34.9 - + - -
425A PHE* 2.9 49.7 - + - -
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Residues in contact with GLU 354 (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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350A ALA 2.8 17.3 + - - +
351A VAL* 3.8 3.4 - - - +
353A HIS* 1.3 74.2 - - - +
355A VAL* 1.3 66.9 + - - +
357A ARG* 2.7 38.3 + - - +
358A TYR* 2.7 27.9 + - - +
406A MET 3.7 1.0 - - - +
407A PHE* 3.7 15.0 - - + -
408A ASP 3.0 34.0 + - - +
409A PRO* 3.9 6.1 - - + -
411A HIS* 2.6 30.7 + - - +
412A PHE* 3.3 16.0 - - + -
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Residues in contact with VAL 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A THR* 4.1 17.5 - - + -
308A TYR 4.6 2.7 - - - -
309A ALA* 3.7 46.2 - - + +
312A LEU* 4.1 12.3 - - + -
313A LEU* 5.5 1.8 - - + -
351A VAL* 2.7 31.6 + - + +
352A VAL* 3.4 9.2 - - + +
354A GLU* 1.3 72.5 - - - +
356A GLN* 1.3 58.2 + - + +
359A ILE* 3.1 34.5 + - + +
407A PHE* 3.6 23.3 - - + -
445A LEU* 6.1 0.2 - - + -
449A LEU* 5.7 1.3 - - + -
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Residues in contact with GLN 356 (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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305A THR* 4.5 7.5 + - + +
352A VAL* 2.8 24.7 + - + +
353A HIS* 3.0 9.9 + - - +
355A VAL* 1.3 73.1 - - - +
357A ARG* 1.3 59.7 + - - +
359A ILE* 4.1 10.0 - - - +
360A ASP* 4.0 10.6 + - - -
361A LEU* 4.7 2.8 + - - +
395A LEU* 4.3 4.7 - - - +
425A PHE* 4.0 15.5 - - + -
427A PRO* 3.1 41.5 - - + +
428A PHE* 3.6 25.3 - - - -
442A GLY* 5.4 3.1 - - - -
445A LEU* 3.5 28.3 - - + +
1493A HEM 4.0 14.8 - - - +
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Residues in contact with ARG 357 (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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353A HIS 2.7 17.6 + - - +
354A GLU* 2.7 43.5 + - - +
356A GLN* 1.3 75.8 - - - +
358A TYR* 1.3 70.6 + - - +
360A ASP 3.8 4.0 + - - -
395A LEU* 3.0 56.6 + - + +
396A HIS* 2.9 36.6 + - - -
401A PHE* 3.8 29.0 - - + +
404A PRO* 3.1 35.9 + - - +
406A MET 3.3 12.5 + - - -
411A HIS* 3.7 10.7 + - - -
412A PHE* 4.0 10.1 - - + -
425A PHE* 4.7 5.8 - - + -
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Residues in contact with TYR 358 (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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48A LYS* 5.8 0.9 - - - -
308A TYR* 4.8 11.1 + + - -
312A LEU* 3.7 38.9 - - + +
354A GLU* 2.7 21.7 + - - +
355A VAL 4.2 0.4 - - - +
357A ARG* 1.3 85.2 - - - +
359A ILE* 1.3 71.3 + - + +
360A ASP* 3.9 1.2 - - - +
396A HIS* 3.1 29.2 + + - -
405A GLU 3.3 26.1 + - - -
406A MET* 4.2 3.6 - - - -
407A PHE* 3.9 32.5 - + + -
469A THR* 3.6 17.1 + - - -
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Residues in contact with ILE 359 (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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48A LYS* 4.3 3.5 - - - +
305A THR* 3.7 36.1 - - + +
308A TYR* 3.3 59.7 + - + -
312A LEU* 3.7 14.6 - - + -
355A VAL* 3.1 24.5 - - + +
356A GLN* 4.1 7.2 - - - +
358A TYR* 1.3 81.9 - - + +
360A ASP* 1.3 63.1 + - - +
361A LEU* 3.7 20.6 - - + +
471A PRO* 5.6 0.9 - - - +
478A SER* 2.9 27.4 + - - -
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Residues in contact with ASP 360 (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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48A LYS* 3.3 19.9 + - - +
356A GLN 4.0 2.2 + - - -
357A ARG 3.8 9.6 + - - +
358A TYR 3.2 9.2 - - - +
359A ILE* 1.3 82.2 - - - +
361A LEU* 1.3 68.2 + - - +
362A LEU 2.7 7.7 + - - +
363A PRO* 3.2 24.0 - - - +
391A LEU 4.3 0.2 - - - -
392A THR* 2.5 41.1 + - + +
395A LEU* 3.8 22.7 - - + +
396A HIS* 4.6 6.7 - - + +
478A SER* 3.2 6.7 + - - +
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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
------------------------------------------------------------
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