Contacts of the helix formed by residues 482 - 498 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478B GLN* 2.3 40.0 + - - +
481B ILE* 1.3 77.5 - - - +
483B ARG* 1.3 66.3 + - - +
484B LYS* 4.3 12.7 - - + +
485B SER* 3.0 31.6 + - - +
486B LYS* 3.3 5.0 + - - -
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Residues in contact with ARG 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463B GLU* 3.1 39.4 + - - +
478B GLN* 3.1 32.7 + - - +
481B ILE 3.7 0.2 + - - -
482B ASP* 1.3 72.9 + - - +
484B LYS* 1.3 58.0 + - - +
486B LYS* 3.1 11.8 + - - +
487B GLU* 2.9 46.8 + - + +
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Residues in contact with LYS 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B ASP* 3.2 12.1 - - + +
483B ARG* 1.3 77.9 - - - +
485B SER* 1.3 56.5 - - - +
487B GLU* 3.8 19.4 + - + +
488B PHE* 2.9 29.5 + - - +
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Residues in contact with SER 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLU* 4.1 16.4 + - - -
415B LEU* 4.1 1.6 - - - +
417B ALA* 5.4 4.6 - - - +
418B PHE* 3.8 21.0 - - - -
481B ILE* 3.9 7.5 - - - +
482B ASP* 3.0 23.2 + - - +
484B LYS* 1.3 75.6 - - - +
486B LYS* 1.3 59.9 + - - +
488B PHE* 3.2 7.2 + - - +
489B LEU* 2.9 29.6 + - - +
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Residues in contact with LYS 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B PHE* 4.0 9.4 - - + -
460B LEU* 3.7 32.7 - - + +
463B GLU* 3.6 27.9 + - + -
476B PHE* 3.4 47.2 + - + -
477B SER 3.5 3.0 + - - -
478B GLN* 4.3 0.6 + - - -
481B ILE* 2.6 49.4 + - + +
482B ASP 3.8 4.0 + - - +
483B ARG* 3.1 10.3 + - - +
485B SER* 1.3 75.8 - - - +
487B GLU* 1.3 53.3 + - + +
489B LEU* 3.5 2.4 + - - +
490B SER* 2.7 38.2 + - - -
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Residues in contact with GLU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B ARG* 2.9 35.4 + - + +
484B LYS* 3.8 19.7 + - + +
486B LYS* 1.3 75.6 - - + +
488B PHE* 1.3 65.9 + - - +
490B SER* 3.2 8.7 + - - -
491B LYS* 2.9 24.6 + - - +
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Residues in contact with PHE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B PHE* 3.3 43.3 - + + -
414B GLU* 3.6 35.9 - - + -
415B LEU* 3.6 26.7 - - + -
484B LYS 2.9 19.5 + - - +
485B SER* 3.3 6.1 - - - +
487B GLU* 1.3 76.4 - - - +
489B LEU* 1.3 55.9 + - - +
491B LYS* 3.1 13.6 + - + +
492B LYS* 3.0 55.3 + - + +
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Residues in contact with LEU 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405B LEU* 4.9 13.9 - - + -
408B LEU* 4.3 10.5 - - + -
415B LEU* 3.6 28.9 - - + -
418B PHE* 3.7 36.3 - - + -
456B PHE* 3.9 14.4 - - + -
460B LEU* 3.8 14.6 - - + -
485B SER 2.9 15.9 + - - +
486B LYS 3.6 5.2 - - - +
488B PHE* 1.3 73.9 - - - +
490B SER* 1.3 61.5 + - - +
492B LYS* 4.5 2.2 - - + +
493B ILE* 2.9 58.0 + - + +
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Residues in contact with SER 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LEU* 3.9 19.9 + - - +
460B LEU* 3.4 23.6 - - - +
461B ARG* 5.1 0.9 + - - -
486B LYS 2.7 23.4 + - - -
487B GLU* 3.2 8.8 + - - -
489B LEU* 1.3 75.6 - - - +
491B LYS* 1.3 57.0 + - - +
494B GLU* 2.9 38.7 + - - +
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Residues in contact with LYS 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487B GLU 2.9 12.6 + - - +
488B PHE* 3.2 16.2 - - + +
490B SER* 1.3 74.6 - - - +
492B LYS* 1.3 65.7 + - + +
494B GLU* 3.3 5.6 + - - +
495B TYR* 2.9 29.7 + - - +
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Residues in contact with LYS 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B LEU* 4.3 20.2 - - + -
412B PHE* 3.5 35.9 - - + -
415B LEU* 5.4 1.1 - - + -
488B PHE* 3.0 55.5 + - + +
489B LEU* 4.0 5.6 - - + +
491B LYS* 1.3 80.3 - - + +
493B ILE* 1.3 63.2 + - - +
495B TYR* 3.2 12.6 + - + +
496B GLU* 3.0 28.6 + - - +
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Residues in contact with ILE 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B MET* 5.0 4.9 - - + -
404B LEU* 4.7 13.0 - - + -
405B LEU* 6.3 0.9 - - + -
408B LEU* 3.8 16.6 - - + -
453B LEU* 4.5 20.0 - - + -
456B PHE* 4.1 25.6 - - + -
457B LEU* 3.6 26.2 - - + -
460B LEU* 4.6 4.0 - - + -
489B LEU* 2.9 48.1 + - + +
490B SER 4.0 2.2 - - - +
492B LYS* 1.3 72.7 - - - +
494B GLU* 1.3 58.8 + - - +
496B GLU* 3.2 6.9 + - - +
497B ARG* 2.9 27.3 + - + +
501B PHE* 5.2 0.9 - - - -
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Residues in contact with GLU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LEU* 3.8 23.7 - - + +
490B SER* 2.9 26.1 + - - +
491B LYS* 3.7 4.7 - - - +
493B ILE* 1.3 75.4 - - - +
495B TYR* 1.3 63.7 + - - +
497B ARG* 3.1 23.1 + - - -
498B ASN* 2.9 53.6 + - - +
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Residues in contact with TYR 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491B LYS 2.9 13.2 + - - +
492B LYS* 3.2 17.5 - - + +
494B GLU* 1.3 75.6 - - - +
496B GLU* 1.3 77.6 + - - +
498B ASN* 3.0 15.4 + - - +
499B ASN* 3.1 50.1 + - + +
502B PRO* 4.2 23.0 - - + +
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Residues in contact with GLU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404B LEU* 4.5 6.7 - - + -
408B LEU* 4.2 15.8 - - + +
492B LYS 3.0 18.6 + - - +
493B ILE* 3.6 7.6 - - - +
495B TYR* 1.3 87.5 - - + +
497B ARG* 1.3 60.2 - - - +
499B ASN 3.4 3.3 + - - -
501B PHE* 3.0 46.1 + - + -
502B PRO* 3.1 33.9 - - - +
503B ILE* 3.2 46.4 + - + +
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Residues in contact with ARG 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450B ASP* 2.4 43.5 + - - +
453B LEU* 3.7 25.9 - - + +
454B ALA* 4.0 22.7 - - - +
457B LEU* 3.7 24.8 - - - +
493B ILE 2.9 16.9 + - - +
494B GLU* 3.4 23.9 + - - +
495B TYR 3.1 0.2 - - - -
496B GLU* 1.3 76.4 - - - +
498B ASN* 1.3 65.1 + - - +
499B ASN 3.6 0.5 + - - -
500B GLY 4.5 2.8 + - - -
501B PHE* 3.8 16.1 - - + -
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Residues in contact with ASN 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494B GLU* 2.9 40.2 + - - +
495B TYR* 3.0 5.2 + - - +
497B ARG* 1.3 87.1 - - - +
499B ASN* 1.3 68.5 + - - +
500B GLY 3.8 0.9 - - - -
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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