Contacts of the helix formed by residues 482 - 498 (chain A) in PDB entry 4LEY
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 ASP 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A GLN* 4.3 7.0 + - - +
481A ILE* 1.3 75.2 - - - +
483A ARG* 1.3 89.4 + - - +
484A LYS* 3.2 37.1 + - - +
485A SER* 3.2 24.7 + - - +
486A LYS* 3.3 13.2 + - - -
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Residues in contact with ARG 483 (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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463A GLU* 3.7 22.4 - - + +
478A GLN* 3.8 29.4 - - - +
481A ILE 3.8 0.4 + - - -
482A ASP* 1.3 79.3 + - - +
484A LYS* 1.3 62.4 + - + +
486A LYS* 3.6 13.3 - - - +
487A GLU* 2.9 50.3 + - + +
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Residues in contact with LYS 484 (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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482A ASP* 3.1 22.6 - - - +
483A ARG* 1.3 81.6 - - + +
485A SER* 1.3 57.4 + - - +
487A GLU* 3.8 9.0 - - - +
488A PHE* 2.9 30.6 + - - +
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Residues in contact with SER 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A GLU* 4.1 18.8 + - - -
415A LEU* 4.6 0.2 - - - +
417A ALA* 5.5 4.2 - - - +
418A PHE* 3.8 10.0 - - - -
481A ILE* 3.9 14.8 - - - +
482A ASP* 3.2 23.1 + - - +
484A LYS* 1.3 78.5 - - - +
486A LYS* 1.3 57.0 + - - +
488A PHE* 3.2 8.7 + - - +
489A LEU* 2.9 29.3 + - - +
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Residues in contact with LYS 486 (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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418A PHE* 3.9 9.4 - - + -
460A LEU* 3.8 33.9 - - + +
463A GLU* 3.6 32.8 + - + +
476A PHE* 3.1 35.7 + - + +
477A SER 3.2 6.7 + - - -
478A GLN 3.9 0.2 - - - +
481A ILE* 2.5 49.9 + - + +
482A ASP 3.3 13.3 + - - -
483A ARG* 3.6 7.6 - - + +
484A LYS 3.3 0.6 - - - -
485A SER* 1.3 78.5 - - - +
487A GLU* 1.3 54.6 + - + +
489A LEU* 3.5 2.9 + - - +
490A SER* 2.4 37.1 + - - -
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Residues in contact with GLU 487 (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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461A ARG* 5.9 5.6 - - - +
463A GLU* 5.5 0.5 - - - +
483A ARG* 2.9 41.1 + - + +
484A LYS* 3.9 6.9 - - - +
486A LYS* 1.3 74.3 - - + +
488A PHE* 1.3 59.9 + - - +
490A SER* 3.2 9.6 - - - +
491A LYS* 2.9 52.9 + - - +
436B GLN* 5.7 3.5 + - - +
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Residues in contact with PHE 488 (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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412A PHE* 4.1 14.8 - + + -
414A GLU* 3.5 45.3 - - + -
415A LEU* 3.5 24.9 - - + -
484A LYS 2.9 19.3 + - - +
485A SER* 3.2 7.8 + - - +
487A GLU* 1.3 73.8 - - - +
489A LEU* 1.3 65.1 + - - +
491A LYS* 3.1 10.7 + - + +
492A LYS* 3.0 56.0 + - + +
436B GLN* 5.5 6.5 - - + -
439B GLN* 3.6 31.4 - - + -
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Residues in contact with LEU 489 (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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405A LEU* 4.4 12.8 - - + -
408A LEU* 3.9 15.9 - - + -
415A LEU* 3.7 36.8 - - + -
418A PHE* 3.6 35.7 - - + -
456A PHE* 3.9 18.6 - - + -
460A LEU* 3.6 14.4 - - + -
485A SER 2.9 16.0 + - - +
486A LYS 3.7 4.3 - - - +
488A PHE* 1.3 76.3 - - - +
490A SER* 1.3 57.1 + - - +
492A LYS* 3.2 3.5 + - - +
493A ILE* 2.9 45.6 + - + +
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Residues in contact with SER 490 (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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457A LEU* 5.0 4.6 - - - +
460A LEU* 3.7 24.3 - - - +
461A ARG* 4.0 32.0 + - - +
486A LYS 2.4 30.3 + - - -
487A GLU* 3.2 12.1 - - - +
489A LEU* 1.3 76.9 - - - +
491A LYS* 1.3 57.1 + - - +
493A ILE* 3.8 3.6 - - - +
494A GLU* 2.9 35.9 + - - +
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Residues in contact with LYS 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ARG* 4.9 13.1 - - - +
487A GLU* 2.9 42.0 + - - +
488A PHE* 3.1 12.8 + - + +
490A SER* 1.3 75.7 - - - +
492A LYS* 1.3 62.4 + - + +
494A GLU* 3.3 6.5 + - - +
495A TYR* 2.9 30.5 + - - +
330B GLY* 3.6 26.9 - - - +
380B ILE* 5.8 1.6 - - - -
432B THR 5.7 0.5 - - - +
433B GLN 5.5 1.8 - - - +
435B PRO* 3.7 30.7 - - + -
436B GLN* 4.3 21.9 - - + +
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Residues in contact with LYS 492 (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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408A LEU* 4.0 24.5 - - + -
412A PHE* 3.2 37.0 - - + -
415A LEU* 5.3 1.8 - - + -
488A PHE* 3.0 57.0 + - + +
489A LEU* 3.2 8.0 + - - +
491A LYS* 1.3 77.5 - - + +
493A ILE* 1.3 63.5 + - - +
495A TYR* 3.3 8.2 + - + +
496A GLU* 3.0 29.9 + - + +
433B GLN* 3.3 23.6 + - + +
434B ASP* 3.1 26.7 + - - -
435B PRO* 6.1 0.2 - - - -
439B GLN* 4.5 1.6 - - - +
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Residues in contact with ILE 493 (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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401A MET* 5.3 2.2 - - + -
404A LEU* 4.5 21.1 - - + -
408A LEU* 4.3 9.6 - - + -
453A LEU* 4.5 16.4 - - + +
456A PHE* 4.0 18.6 - - + -
457A LEU* 3.5 24.5 - - + -
460A LEU* 3.8 17.5 - - + -
489A LEU* 2.9 45.3 + - + +
490A SER 3.8 3.1 - - - +
492A LYS* 1.3 76.4 - - - +
494A GLU* 1.3 58.2 + - - +
496A GLU* 3.3 6.8 + - - +
497A ARG* 2.9 29.7 + - + +
501A PHE* 5.3 0.8 - - + -
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Residues in contact with GLU 494 (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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457A LEU* 3.1 32.0 - - + +
461A ARG* 4.1 16.7 + - - +
490A SER 2.9 20.7 + - - +
491A LYS* 3.7 5.8 - - - +
492A LYS 3.3 0.2 - - - -
493A ILE* 1.3 76.7 - - - +
495A TYR* 1.3 63.1 + - - +
497A ARG* 3.1 16.9 + - - +
498A ASN* 2.7 50.9 + - - +
330B GLY* 6.2 4.0 - - - -
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Residues in contact with TYR 495 (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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491A LYS 2.9 13.3 + - - +
492A LYS* 3.5 12.1 - - + +
494A GLU* 1.3 76.7 - - - +
496A GLU* 1.3 82.9 + - + +
498A ASN* 4.4 3.4 - - - +
499A ASN* 3.0 63.5 + - + +
502A PRO* 4.3 17.4 - - + +
429B HIS* 3.9 28.8 + - - +
432B THR* 3.9 34.3 - - + +
433B GLN* 3.4 45.8 + - + +
455B PHE* 4.7 3.8 - - - -
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Residues in contact with GLU 496 (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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404A LEU* 4.3 16.2 - - + -
408A LEU* 4.6 8.6 - - + +
492A LYS 3.0 22.7 + - - +
493A ILE* 3.7 4.7 - - - +
495A TYR* 1.3 90.6 - - + +
497A ARG* 1.3 62.3 + - - +
500A GLY 3.4 2.8 + - - -
501A PHE* 2.8 45.2 + - + +
502A PRO* 3.1 30.2 - - - +
503A ILE* 3.1 42.0 + - + +
506A LYS* 4.7 5.0 + - - -
433B GLN* 6.0 0.3 - - - -
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Residues in contact with ARG 497 (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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450A ASP* 2.6 51.7 + - - +
453A LEU* 4.2 16.4 - - + +
454A ALA* 3.9 21.4 - - - +
457A LEU* 3.5 29.2 - - - +
493A ILE* 2.9 18.4 + - + +
494A GLU* 3.1 21.8 + - - +
496A GLU* 1.3 79.9 - - - +
498A ASN* 1.3 63.7 + - - +
499A ASN 3.3 2.3 + - - -
500A GLY* 3.7 6.4 + - - -
501A PHE* 3.8 21.6 - - + -
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Residues in contact with ASN 498 (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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494A GLU* 2.7 44.2 + - - +
495A TYR* 4.4 2.2 - - - +
497A ARG* 1.3 78.4 - - + +
499A ASN* 1.3 67.9 + - - +
500A GLY 3.7 0.4 - - - -
324B GLU* 4.7 15.8 - - - +
327B PRO* 4.2 27.8 + - + +
329B GLN* 4.8 15.6 - - - +
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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