Contacts of the helix formed by residues 379 - 395 (chain A) in PDB entry 5FZ9
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 LEU 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A PHE* 5.6 1.3 - - + -
76A CYS* 4.2 15.7 - - - -
78A VAL* 3.3 23.0 + - + +
81A LEU* 3.1 37.6 + - + +
83A PHE* 4.5 6.5 - - + -
378A THR* 1.3 73.5 - - - +
380A ARG* 1.3 57.4 + - - +
382A PHE* 3.9 3.3 - - + +
383A GLY* 3.0 22.5 + - - -
434A PHE* 4.4 11.9 - - + -
489A VAL* 4.1 35.7 - - + -
513A TRP* 4.4 19.1 - - + -
594A PHE* 3.7 21.6 - - + -
596A PHE* 5.1 5.2 - - + -
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Residues in contact with ARG 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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78A VAL* 3.1 40.1 + - + +
79A ASP* 2.7 40.8 + - - +
378A THR* 3.1 7.2 - - - +
379A LEU* 1.3 75.2 - - - +
381A THR* 1.3 63.4 + - + +
383A GLY* 3.2 2.5 + - - -
384A GLU* 3.0 52.3 + - + +
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Residues in contact with THR 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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376A ASP 4.8 0.3 + - - -
377A TYR* 3.5 18.4 - - - -
378A THR* 2.8 41.5 + - + +
380A ARG* 1.3 77.0 - - + +
382A PHE* 1.3 64.3 + - - +
384A GLU* 3.5 15.9 + - - +
385A MET* 3.1 23.0 + - - +
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Residues in contact with PHE 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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83A PHE* 3.6 25.4 - + + -
85A PRO* 5.1 0.4 - - + -
377A TYR* 3.5 24.9 - + + -
378A THR 3.0 17.8 + - - +
379A LEU* 3.9 3.1 - - - +
381A THR* 1.3 78.9 + - - +
383A GLY* 1.3 58.1 + - - +
385A MET* 3.1 27.1 + - + +
386A ALA* 2.8 28.3 + - + +
424A GLU* 3.5 34.3 - - + -
425A TYR* 3.9 13.7 - - - -
489A VAL* 3.7 21.3 - - + -
490A GLY 3.6 22.0 - - - -
491A MET* 4.1 11.2 - - + -
594A PHE* 3.8 7.4 - + + -
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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 LEU 3.0 11.4 + - - -
380A ARG* 3.2 3.8 + - - -
382A PHE* 1.3 78.6 - - - +
384A GLU* 1.3 60.4 + - - +
386A ALA* 3.3 0.5 + - - +
387A ASP* 3.0 34.2 + - - -
594A PHE* 3.5 35.0 - - - -
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Residues in contact with GLU 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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380A ARG* 3.0 43.4 + - + +
381A THR* 3.9 16.7 - - - +
382A PHE 3.3 0.2 - - - -
383A GLY* 1.3 75.6 - - - +
385A MET* 1.3 61.8 + - - +
387A ASP* 4.2 3.8 - - - +
388A ALA* 3.3 25.3 + - - +
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Residues in contact with MET 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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377A TYR* 3.6 30.1 - - + +
381A THR 3.1 13.8 + - - +
382A PHE* 3.1 44.9 + - + +
384A GLU* 1.3 78.1 - - - +
386A ALA* 1.3 60.9 + - - +
388A ALA* 3.8 3.8 - - - +
389A PHE* 3.0 28.8 + - + +
424A GLU* 3.7 11.7 - - + +
491A MET* 3.9 24.7 - - - +
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Residues in contact with ALA 386 (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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382A PHE* 2.8 23.1 + - + +
383A GLY 3.9 3.8 - - - +
385A MET* 1.3 85.0 - - - +
387A ASP* 1.3 61.6 + - - +
389A PHE* 3.4 7.0 + - - +
390A LYS* 3.1 23.2 + - - +
491A MET* 3.6 30.4 - - + +
492A CYS 5.2 1.9 + - - -
594A PHE* 4.1 20.3 + - + +
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Residues in contact with ASP 387 (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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383A GLY 3.0 21.3 + - - +
384A GLU* 4.2 3.9 - - - +
386A ALA* 1.3 74.3 - - - +
388A ALA* 1.3 59.5 + - - +
390A LYS* 3.5 3.0 + - - +
391A SER* 2.9 32.6 + - - -
398A VAL* 4.0 21.6 - - + +
515A GLU* 4.9 5.4 - - - +
594A PHE* 3.8 25.8 + - - +
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Residues in contact with ALA 388 (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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384A GLU 3.3 17.2 + - - +
385A MET* 3.8 4.7 - - - +
387A ASP* 1.3 75.4 - - - +
389A PHE* 1.3 64.6 + - - +
391A SER* 4.3 4.5 - - - -
392A ASP* 2.9 38.9 + - - +
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Residues in contact with PHE 389 (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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385A MET* 3.0 22.8 + - - +
386A ALA 3.5 4.5 - - - +
387A ASP 3.3 0.4 - - - -
388A ALA* 1.3 77.2 - - - +
390A LYS* 1.3 68.5 + - - +
392A ASP* 3.9 3.3 - - - +
393A TYR* 3.0 44.7 + + + +
421A VAL* 4.1 16.2 - - + -
422A THR 4.5 6.5 - - - -
423A VAL* 3.9 19.7 - - + -
491A MET* 3.5 24.0 - - + -
492A CYS* 3.9 24.9 - - + -
493A PHE* 3.9 14.6 - + - -
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Residues in contact with LYS 390 (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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386A ALA 3.1 13.5 + - - +
387A ASP* 4.0 3.6 - - - +
389A PHE* 1.3 86.3 - - - +
391A SER* 1.3 62.2 - - - +
393A TYR* 3.3 3.7 + - - -
394A PHE* 3.3 31.7 + - + +
398A VAL* 3.5 30.1 + - + -
401A VAL* 3.9 28.0 + - + +
406A VAL* 4.3 7.2 - - - +
492A CYS* 4.0 24.2 - - + -
515A GLU* 3.1 31.6 + - - +
592A GLN* 2.9 33.7 + - - +
593A GLY* 4.4 2.5 - - - -
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Residues in contact with SER 391 (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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387A ASP 2.9 20.9 + - - -
388A ALA* 3.8 5.4 - - - -
390A LYS* 1.3 78.3 - - - +
392A ASP* 1.3 63.2 + - - +
395A ASN* 3.0 28.8 + - - -
396A MET 3.0 28.4 + - - -
397A PRO* 4.6 2.9 - - - +
398A VAL* 4.5 8.3 - - - +
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Residues in contact with ASP 392 (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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388A ALA* 2.9 26.5 + - - +
389A PHE* 4.0 3.6 - - - +
391A SER* 1.3 80.5 + - - +
393A TYR* 1.3 64.9 + - - +
395A ASN* 3.8 7.8 + - - +
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Residues in contact with TYR 393 (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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389A PHE* 3.0 40.4 + + + +
390A LYS* 3.3 8.0 + - - +
392A ASP* 1.3 77.3 - - - +
394A PHE* 1.3 81.9 + + + +
409A GLU* 2.5 42.8 + - + -
412A ARG* 4.0 6.1 + - - -
413A LEU* 3.3 14.0 - - - +
419A GLU* 5.0 3.3 + - - -
421A VAL* 4.4 20.2 - - + +
493A PHE* 3.8 17.9 - + - -
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Residues in contact with PHE 394 (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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390A LYS* 3.3 29.7 + - + +
393A TYR* 1.3 97.0 - + + +
395A ASN* 1.3 70.7 + - - +
396A MET* 3.3 29.7 + - + +
401A VAL* 4.0 22.7 - - + -
405A LEU* 4.1 27.1 - - + -
406A VAL* 4.2 16.4 - - + -
409A GLU* 4.3 13.5 - - + -
492A CYS* 4.2 14.8 - - - -
493A PHE* 3.8 27.4 - + - -
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Residues in contact with ASN 395 (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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391A SER 3.0 12.6 + - - -
392A ASP* 3.8 6.5 + - - +
393A TYR 3.6 2.4 - - - -
394A PHE* 1.3 78.1 - - - +
396A MET* 1.3 61.0 + - - +
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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