Contacts of the helix formed by residues 444 - 463 (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 ASN 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438B SER 4.5 8.3 + - - -
439B GLN* 5.8 1.6 - - - +
441B ASP* 2.8 29.4 + - + +
443B ARG* 1.3 90.0 - - - +
445B LEU* 1.3 64.5 + - - +
446B SER 3.5 1.6 - - - -
447B SER* 3.3 16.7 + - - +
448B CYS* 3.0 30.2 + - - -
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Residues in contact with LEU 445 (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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150B LEU* 4.2 20.2 - - + -
151B LYS* 4.2 22.0 - - + -
154B LEU* 3.9 21.3 - - + -
393B CYS* 3.9 28.3 - - + -
396B GLU* 4.2 11.9 - - + -
397B CYS* 4.0 14.8 - - - -
400B LEU* 4.3 14.4 - - + -
442B PRO* 2.9 17.6 + - + +
443B ARG 3.3 2.4 + - - -
444B ASN* 1.3 74.9 - - - +
446B SER* 1.3 56.3 + - - +
448B CYS* 2.9 5.4 + - - +
449B PHE* 2.8 34.4 + - - +
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Residues in contact with SER 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LYS* 5.1 11.8 - - - +
150B LEU* 3.8 28.8 - - - +
444B ASN 3.5 0.4 - - - -
445B LEU* 1.3 78.1 - - - +
447B SER* 1.3 58.4 + - - +
449B PHE* 3.5 2.9 + - - +
450B ASP* 3.0 27.1 + - - +
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Residues in contact with SER 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444B ASN* 3.3 22.4 + - - +
445B LEU 3.2 0.2 - - - -
446B SER* 1.3 75.3 - - - +
448B CYS* 1.3 66.1 + - - +
450B ASP* 2.9 9.2 + - - +
451B LYS* 2.8 29.3 + - - +
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Residues in contact with CYS 448 (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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393B CYS* 4.1 4.5 - - - -
397B CYS* 3.9 16.2 - - - -
439B GLN 3.2 28.3 - - - -
440B TRP* 4.0 25.7 - - + -
444B ASN* 3.0 30.7 + - - +
445B LEU 2.9 4.8 + - - +
447B SER* 1.3 81.3 + - - +
449B PHE* 1.3 63.3 + - - +
451B LYS* 2.9 21.2 + - - +
452B LEU* 3.1 14.0 + - - +
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Residues in contact with PHE 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B LEU* 3.9 24.2 - - + -
397B CYS* 3.8 19.8 - - + -
400B LEU* 4.0 28.9 - - + -
401B MET* 3.6 39.7 - - + -
404B LEU* 4.3 7.4 - - + -
445B LEU 2.8 18.3 + - - +
446B SER 3.8 4.7 - - - +
448B CYS* 1.3 72.4 - - - +
450B ASP* 1.3 57.4 + - - +
452B LEU* 3.8 7.8 - - + +
453B LEU* 3.0 40.0 + - + +
501B PHE* 3.9 29.8 - + - -
504B PHE* 4.2 15.7 - + - -
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Residues in contact with ASP 450 (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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446B SER 3.0 13.1 + - - +
447B SER* 2.9 14.1 + - - +
449B PHE* 1.3 74.7 - - - +
451B LYS* 1.3 57.7 + - - +
453B LEU* 2.9 10.0 + - - +
454B ALA* 2.6 34.7 + - - +
497B ARG* 2.4 50.7 + - - +
501B PHE* 5.9 1.2 - - - -
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Residues in contact with LYS 451 (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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412A PHE* 3.4 35.3 - - - -
414A GLU* 5.3 2.8 + - - -
430B MET* 3.9 21.1 - - + -
433B GLN* 6.0 0.2 - - - -
434B ASP* 3.6 24.6 + - - +
439B GLN* 4.7 6.7 - - - +
440B TRP* 5.9 2.0 - - + -
447B SER 2.8 12.0 + - - +
448B CYS* 2.9 14.3 + - - +
450B ASP* 1.3 75.5 - - - +
452B LEU* 1.3 64.6 + - - +
454B ALA* 3.0 8.0 + - + +
455B PHE* 2.8 22.3 + - - +
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Residues in contact with LEU 452 (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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397B CYS* 4.0 12.6 - - + +
401B MET* 3.7 39.5 - - + -
423B VAL* 5.1 1.1 - - + +
426B ALA* 4.2 7.9 - - + -
427B ILE* 3.8 47.8 - - + +
430B MET* 3.7 30.5 - - + -
440B TRP* 5.3 4.9 - - + -
448B CYS 3.1 7.4 + - - +
449B PHE* 3.8 10.5 - - + +
451B LYS* 1.3 78.7 - - - +
453B LEU* 1.3 63.8 - - - +
455B PHE* 3.0 7.4 + - + +
456B PHE* 2.8 22.1 + - + +
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Residues in contact with LEU 453 (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* 3.5 36.6 - - + -
404B LEU* 3.8 10.5 - - + -
449B PHE* 3.0 29.3 + - + +
450B ASP* 2.9 13.5 + - - +
452B LEU* 1.3 74.3 - - - +
454B ALA* 1.3 67.1 + - - +
456B PHE* 3.0 13.2 + - - +
457B LEU* 3.0 17.8 + - + +
493B ILE* 4.5 14.3 - - + +
497B ARG* 3.7 29.8 - - + +
501B PHE* 3.5 33.4 - - + -
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Residues in contact with ALA 454 (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* 2.6 16.5 + - - +
451B LYS* 3.2 11.7 - - + +
453B LEU* 1.3 70.5 - - - +
455B PHE* 1.3 63.6 + - - +
457B LEU* 3.0 17.1 + - - +
458B GLU* 3.1 12.7 + - - +
497B ARG* 4.0 26.4 - - - +
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Residues in contact with PHE 455 (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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495A TYR* 4.7 4.5 - - - -
506A LYS* 6.6 0.4 - - - -
426B ALA* 3.2 39.0 - - + -
429B HIS* 3.5 25.8 - + + -
430B MET* 3.6 27.8 - - + -
433B GLN* 3.4 22.9 - - - -
451B LYS 2.8 13.9 + - - +
452B LEU* 3.2 8.7 - - + +
454B ALA* 1.3 71.7 - - - +
456B PHE* 1.3 66.7 + - - +
458B GLU* 3.0 16.1 + - + +
459B CYS* 3.0 41.6 + - - -
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Residues in contact with PHE 456 (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* 3.7 22.4 - - + -
405B LEU* 5.9 5.4 - - + -
418B PHE* 5.3 1.8 - + - -
422B HIS* 3.8 34.1 - - + -
423B VAL* 4.2 12.3 - - + -
426B ALA* 3.7 19.5 - - + -
452B LEU* 2.8 15.2 + - + +
453B LEU 3.0 8.5 + - - +
455B PHE* 1.3 73.8 - - - +
457B LEU* 1.3 63.5 + - + +
459B CYS* 3.0 20.8 + - + +
460B LEU* 3.0 35.7 + - + +
465B LEU* 4.6 1.1 - - + -
476B PHE* 3.9 20.9 - + - -
489B LEU* 3.9 16.8 - - + -
493B ILE* 4.1 16.8 - - + -
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Residues in contact with LEU 457 (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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453B LEU 3.0 15.8 + - - +
454B ALA* 3.0 7.1 + - - +
456B PHE* 1.3 75.1 - - + +
458B GLU* 1.3 51.9 + - - +
460B LEU* 2.9 14.0 + - + +
461B ARG* 2.7 34.7 + - - +
490B SER* 3.9 35.0 + - - +
493B ILE* 3.6 31.4 - - + -
494B GLU* 3.8 22.7 - - + +
497B ARG* 3.7 30.1 - - - +
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Residues in contact with GLU 458 (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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506A LYS* 4.1 29.2 - - + +
507A LEU 5.3 0.8 + - - -
454B ALA 3.1 9.1 + - - +
455B PHE* 3.0 18.7 + - + +
457B LEU* 1.3 75.3 - - - +
459B CYS* 1.3 51.6 + - - +
461B ARG* 2.4 52.8 + - - -
462B THR* 2.7 49.5 + - + +
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Residues in contact with CYS 459 (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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426B ALA* 5.1 0.7 - - - -
455B PHE* 3.0 50.9 + - - -
456B PHE* 3.0 14.9 + - + +
458B GLU* 1.3 76.0 - - - +
460B LEU* 1.3 55.2 + - - +
462B THR* 3.6 5.6 - - - -
463B GLU* 2.9 6.4 + - - -
464B LYS 2.8 44.1 + - - +
465B LEU* 3.8 17.0 - - + -
476B PHE* 3.4 18.7 - - + -
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Residues in contact with LEU 460 (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* 4.1 9.0 - - + -
456B PHE* 3.0 26.4 + - + +
457B LEU* 2.9 14.9 + - + +
459B CYS* 1.3 75.5 - - - +
461B ARG* 1.3 63.7 + - - +
463B GLU* 3.1 20.5 + - - +
476B PHE* 3.5 28.7 - - + -
486B LYS* 3.7 40.0 - - + +
489B LEU* 3.8 25.4 - - + -
490B SER* 3.4 29.4 - - - +
493B ILE* 4.6 0.4 - - + -
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Residues in contact with ARG 461 (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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505A ASP 3.1 23.6 + - - -
506A LYS* 4.2 5.9 - - - +
507A LEU 4.8 13.7 + - - +
457B LEU 2.7 16.5 + - - +
458B GLU* 2.4 48.1 + - - +
460B LEU* 1.3 74.2 - - - +
462B THR* 1.3 72.1 + - - +
463B GLU* 3.2 7.7 + - - +
490B SER* 5.1 1.3 + - - -
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Residues in contact with THR 462 (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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505A ASP* 4.5 13.0 - - + +
458B GLU* 2.7 36.5 + - + +
459B CYS* 3.4 10.4 + - - -
461B ARG* 1.3 102.2 - - - +
463B GLU* 1.3 68.7 + - - +
464B LYS* 3.6 20.3 + - - +
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Residues in contact with GLU 463 (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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459B CYS 2.9 9.6 + - - -
460B LEU 3.1 15.5 + - - +
461B ARG 4.1 5.5 - - - +
462B THR* 1.3 81.9 - - - +
464B LYS* 1.3 57.9 + - - +
474B ASN* 3.2 11.1 + - - -
476B PHE* 3.2 30.3 - - - +
477B SER* 4.8 0.2 - - - -
478B GLN* 4.1 7.8 + - - +
483B ARG* 3.1 55.4 + - - +
486B LYS* 3.6 15.0 - - + +
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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
------------------------------------------------------------
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