Contacts of the helix formed by residues 387 - 398 (chain A) in PDB entry 5Y7G
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 ASN 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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385A VAL 3.8 2.6 + - - -
386A GLU* 1.3 89.0 + - - +
388A GLY* 1.3 58.6 + - - +
389A LEU 3.3 2.6 - - - +
390A ILE* 4.3 0.8 - - - +
391A ASN* 3.0 36.1 + - - +
466A TYR* 3.8 7.3 + - + +
502A ARG 3.4 22.6 + - - +
503A ALA* 3.3 9.6 - - - +
504A GLY 3.2 11.4 + - - -
505A LEU* 3.0 59.3 + - + +
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Residues in contact with GLY 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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386A GLU 2.5 15.7 + - - +
387A ASN* 1.3 74.4 - - - +
389A LEU* 1.3 60.1 + - - +
392A SER* 2.7 34.1 + - - -
466A TYR* 3.5 18.4 - - - -
469A LEU* 3.5 24.9 - - - +
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Residues in contact with LEU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A VAL* 4.2 20.5 - - + +
387A ASN* 3.3 1.2 - - - +
388A GLY* 1.3 77.8 - - - +
390A ILE* 1.3 65.6 + - + +
392A SER* 3.2 1.7 + - - -
393A LEU* 2.9 51.1 + - + +
469A LEU* 5.3 0.2 - - - -
470A LEU* 3.8 23.1 - - + -
474A LEU* 3.8 35.0 - - + -
478A ALA* 4.0 15.9 - - + -
482A LEU* 4.4 4.5 - - + -
509A ILE* 3.8 35.0 - - + -
511A PHE* 4.2 0.2 - - + -
520A MET* 5.9 0.4 - - + -
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Residues in contact with ILE 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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387A ASN* 4.1 1.6 + - - +
389A LEU* 1.3 85.4 - - + +
391A ASN* 1.3 68.9 + - - +
393A LEU* 4.9 5.6 - - + -
394A PHE* 3.0 22.5 + - - +
482A LEU* 6.1 2.0 - - + -
487A LEU* 5.8 1.6 - - + -
490A TRP* 3.9 48.5 - - + -
491A PHE* 3.9 10.4 - - + -
494A LEU* 4.2 17.7 - - + -
505A LEU* 3.6 30.7 - - + -
509A ILE* 5.7 1.1 - - + -
520A MET* 3.7 30.7 - - + -
537A TRP* 5.5 5.2 - - + +
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Residues in contact with ASN 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ASN* 3.0 24.2 + - - +
390A ILE* 1.3 78.5 - - - +
392A SER* 1.3 58.7 + - - +
394A PHE* 3.6 4.1 - - - +
395A GLY 2.8 22.9 + - - -
463A PRO 5.4 0.4 + - - -
464A PHE* 3.1 39.4 - - + +
466A TYR* 3.8 20.0 + - + -
494A LEU* 3.3 23.0 - - - +
502A ARG* 3.7 39.1 + - - +
505A LEU* 5.2 0.8 - - - +
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Residues in contact with SER 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 GLY 2.7 24.8 + - - -
389A LEU* 3.8 3.1 - - - -
390A ILE 3.1 0.2 - - - -
391A ASN* 1.3 73.7 - - - +
393A LEU* 1.3 68.3 + - - +
395A GLY* 2.9 12.0 + - - -
396A LEU* 2.9 19.3 + - - +
464A PHE 3.2 7.1 + - - -
465A VAL* 4.2 3.3 - - - +
466A TYR* 2.9 32.3 + - - +
469A LEU* 5.8 0.2 - - - +
470A LEU* 3.8 26.7 - - - -
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Residues in contact with LEU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A LEU* 2.9 39.3 + - + +
390A ILE* 4.2 4.3 - - + +
392A SER* 1.3 75.3 - - - +
394A PHE* 1.3 62.5 + - - +
396A LEU* 3.2 8.1 + - + +
397A LEU* 3.0 25.1 + - - +
450A ILE* 4.5 12.9 - - + +
470A LEU* 4.7 3.8 - - + -
475A LEU* 3.9 27.8 - - + -
478A ALA* 4.7 7.4 - - + -
479A LEU* 5.0 9.6 - - + -
482A LEU* 3.8 21.1 - - + -
487A LEU* 3.5 32.1 - - + -
491A PHE* 3.8 12.3 - - + -
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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 ILE 3.0 17.7 + - - +
391A ASN 3.6 2.5 - - - +
393A LEU* 1.3 76.1 - - - +
395A GLY* 1.3 65.6 + - - +
396A LEU 3.1 0.3 + - - -
397A LEU* 3.2 1.1 + - - -
398A CYS* 3.0 48.5 + - + +
402A ILE* 4.6 3.8 - - + -
426A PHE* 6.1 0.9 - + - -
434A PHE* 4.0 21.8 - + - -
438A LEU* 5.2 0.9 - - + -
464A PHE* 3.6 39.7 - + - -
491A PHE* 3.5 52.3 - + + -
494A LEU* 4.3 20.6 - - + -
495A LEU* 4.0 21.1 - - + -
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Residues in contact with GLY 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 ASN 2.8 17.4 + - - -
392A SER 2.9 3.7 + - - -
394A PHE* 1.3 73.4 - - - +
396A LEU* 1.3 62.3 + - - +
399A TRP* 3.1 30.3 + - - +
402A ILE* 4.0 11.8 - - - +
464A PHE* 3.8 10.5 - - - -
465A VAL* 3.6 20.9 - - - -
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Residues in contact with LEU 396 (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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392A SER 2.9 17.5 + - - +
393A LEU* 3.6 7.6 - - + +
395A GLY* 1.3 75.6 - - - +
397A LEU* 1.3 67.0 + - - +
399A TRP* 3.1 21.7 + - + +
450A ILE* 3.7 35.4 - - + +
453A ARG* 3.3 19.1 - - + +
454A TYR* 3.9 24.9 - - + +
465A VAL* 3.9 9.6 - - + -
467A TRP* 3.7 33.4 - - + -
470A LEU* 3.8 24.9 - - + -
475A LEU* 4.5 4.0 - - + -
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Residues in contact with LEU 397 (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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393A LEU 3.0 17.0 + - - +
394A PHE 4.0 2.0 - - - +
396A LEU* 1.3 77.8 - - - +
398A CYS* 1.3 60.9 + - - +
399A TRP 3.3 0.7 + - - -
437A CYS* 3.3 48.5 - - - +
438A LEU* 4.6 4.0 - - + -
440A ARG* 4.3 11.3 + - - -
441A LEU* 3.5 26.5 - - + -
446A TYR* 3.9 22.4 - - + +
449A ALA* 4.4 4.7 - - + -
450A ILE* 3.6 27.8 - - + +
453A ARG* 4.0 10.3 + - - +
491A PHE* 3.9 17.5 - - + -
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Residues in contact with CYS 398 (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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394A PHE* 3.0 34.4 + - + +
395A GLY 3.9 1.8 - - - -
397A LEU* 1.3 80.9 - - - +
399A TRP* 1.3 65.6 + - - +
400A GLU 3.2 3.1 - - - -
401A ALA* 2.9 4.9 + - + -
402A ILE* 2.8 27.2 + - + +
434A PHE* 3.6 37.5 - - + -
437A CYS* 4.0 17.3 - - - -
438A LEU* 4.0 15.5 - - - -
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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