Contacts of the helix formed by residues 485 - 502 (chain B) in PDB entry 5FLZ
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 LYS 485 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B ALA* 5.5 1.2 - - - +
479B ASN* 3.5 42.6 - - - +
480B ILE* 4.7 7.2 - - - +
483B MET 3.1 5.1 + - - -
484B GLY* 1.4 77.7 - - - +
486B SER* 1.4 64.2 - - - +
487B ASP* 3.3 3.0 + - + -
488B PHE* 3.4 27.6 - - + +
489B MET* 3.3 27.9 + - + +
523B SER* 3.7 18.2 - - - +
525B LEU* 3.7 31.9 - - + +
537B VAL* 4.3 20.3 - - - +
248D MET* 3.5 14.5 - - + +
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Residues in contact with SER 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B MET 5.1 0.9 - - - -
485B LYS* 1.4 74.7 + - - +
487B ASP* 1.3 63.4 + - - +
489B MET* 3.2 9.6 + - - +
490B ASP* 3.1 26.3 + - - +
594B LYS* 4.5 10.6 + - - +
245D PRO 5.2 0.2 - - - -
248D MET* 3.5 39.9 + - - +
249D TYR* 5.0 0.5 - - - -
251D SER* 3.8 23.0 + - - -
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Residues in contact with ASP 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LYS* 3.3 0.8 - - + -
486B SER* 1.3 76.9 - - - +
488B PHE* 1.3 63.2 - - - +
490B ASP* 3.6 5.5 + - - +
491B ALA* 3.3 19.4 + - - +
522B LEU* 3.2 34.8 - - - +
523B SER* 3.6 17.3 - - - +
524B SER* 5.6 1.1 - - - -
1D MET* 5.4 0.6 - - - +
2D GLY* 3.8 24.4 + - - -
245D PRO* 4.3 30.4 + - + +
251D SER* 5.0 1.2 + - - -
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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
----------------------------------------------------------
480B ILE* 5.5 12.6 - - + -
485B LYS* 3.4 26.2 + - + +
487B ASP* 1.3 80.9 + - - +
489B MET* 1.3 87.0 + - + +
491B ALA* 3.1 6.5 + - - +
492B LEU* 2.8 45.4 + - + +
516B LEU* 3.8 27.1 - - + -
519B ALA* 3.5 38.2 - - + +
520B VAL* 3.8 20.0 - - + -
523B SER* 3.5 19.6 + - - +
525B LEU* 5.3 0.9 - - + -
537B VAL* 4.9 8.7 - - + -
541B LEU* 5.6 0.7 - - + -
560B LEU* 6.0 4.9 - - + -
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Residues in contact with MET 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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479B ASN 4.0 9.0 - - - +
480B ILE* 4.3 9.2 - - + +
483B MET* 3.6 61.0 - - + +
485B LYS* 3.3 24.9 + - + +
486B SER* 3.2 8.8 + - - +
488B PHE* 1.3 101.7 - - + +
490B ASP* 1.4 64.5 + - - +
492B LEU* 3.3 9.5 + - - +
493B ILE* 3.0 39.3 + - + +
587B PHE* 6.0 0.2 - - + -
594B LYS* 4.7 14.6 - - + -
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Residues in contact with ASP 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B SER 3.1 15.8 + - - +
487B ASP* 3.8 5.6 - - - +
489B MET* 1.4 76.0 - - - +
491B ALA* 1.3 59.4 + - - +
493B ILE* 3.5 2.6 + - - +
494B GLU* 3.0 28.1 + - - +
598B TYR* 3.5 34.9 + - - -
601B GLN* 5.8 2.3 - - - +
253D SER* 5.9 2.6 - - - -
254D SER* 4.3 13.3 + - - -
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Residues in contact with ALA 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B ASP 3.3 11.1 + - - +
488B PHE* 3.1 10.6 + - - +
490B ASP* 1.3 80.6 + - - +
492B LEU* 1.4 56.5 + - - +
494B GLU* 3.0 7.0 + - - +
495B LYS* 3.0 57.5 + - + +
519B ALA* 4.7 3.6 - - - -
522B LEU* 3.7 27.4 - - + -
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B PHE* 2.8 35.2 + - + +
489B MET* 3.3 12.3 + - - +
491B ALA* 1.4 67.7 - - - +
493B ILE* 1.3 69.1 + - + +
496B ALA* 2.9 38.7 + - + +
500B LEU* 6.3 2.0 - - + -
512B LEU* 5.6 2.7 - - + +
515B VAL* 4.0 14.5 - - + +
516B LEU* 3.6 38.4 - - + +
519B ALA* 4.3 11.6 - - + +
558B PHE* 4.2 27.1 - - + -
560B LEU* 5.9 2.7 - - + -
591B TRP* 5.7 6.5 - - + +
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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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489B MET* 3.0 22.5 + - + +
490B ASP 4.0 0.2 - - - +
492B LEU* 1.3 86.4 - - + +
494B GLU* 1.4 60.6 + - - +
496B ALA* 4.5 3.6 - - - -
497B ASN* 3.1 36.1 + - - +
555B TRP* 3.9 19.1 - - + -
591B TRP* 6.3 2.9 - - + +
594B LYS* 3.6 32.8 - - + +
595B LYS* 3.9 13.5 - - + +
598B TYR* 3.4 39.3 - - + -
599B PHE* 4.9 2.2 - - + -
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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
----------------------------------------------------------
490B ASP* 3.0 21.3 + - - +
491B ALA* 3.0 4.8 + - - +
493B ILE* 1.4 75.4 - - - +
495B LYS* 1.3 97.3 + - - +
497B ASN* 3.8 8.3 + - - +
498B ASP* 3.9 8.8 - - - +
598B TYR* 4.2 22.8 - - + +
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Residues in contact with LYS 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B ALA* 3.0 39.4 + - + +
492B LEU 4.9 0.2 - - - +
494B GLU* 1.3 105.2 + - - +
496B ALA* 1.3 62.5 + - - +
497B ASN 3.5 0.5 + - - -
498B ASP* 3.6 11.3 - - - +
499B ILE* 4.6 9.7 - - - +
515B VAL* 3.4 33.3 - - + +
518B GLU* 3.7 39.5 - - + +
519B ALA 4.8 0.7 - - - +
522B LEU* 3.9 19.9 - - - +
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Residues in contact with ALA 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 2.9 27.3 + - + +
493B ILE* 4.1 3.4 - - - +
495B LYS* 1.3 78.9 - - - +
497B ASN* 1.4 63.6 + - - +
498B ASP 3.2 0.9 - - - -
499B ILE* 3.0 21.9 + - - +
500B LEU* 3.1 32.8 + - + +
512B LEU* 4.0 18.6 - - + -
515B VAL* 4.6 6.3 - - + -
555B TRP* 5.5 0.2 - - + -
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Residues in contact with ASN 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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493B ILE* 3.1 24.9 + - - +
494B GLU* 3.8 8.3 + - - +
495B LYS 3.4 1.8 - - - -
496B ALA* 1.4 73.4 - - - +
498B ASP* 1.3 62.3 + - - +
500B LEU 3.5 0.5 + - - -
501B ALA* 3.2 30.1 + - - +
555B TRP* 3.3 37.0 - - - -
598B TYR* 4.3 7.6 - - + -
599B PHE* 3.5 19.2 - - - -
602B LYS* 3.7 23.3 + - - +
770B TYR* 5.5 0.3 + - - -
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Residues in contact with ASP 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 3.9 9.7 - - - +
495B LYS 3.6 14.6 - - - +
496B ALA 3.1 0.2 + - - -
497B ASN* 1.3 80.2 - - - +
499B ILE* 1.4 61.2 + - + +
501B ALA* 3.6 13.5 - - - +
502B THR* 3.0 18.2 + - - -
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Residues in contact with ILE 499 (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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495B LYS 4.6 10.3 - - - +
496B ALA* 3.0 11.6 + - - +
498B ASP* 1.4 78.9 - - + +
500B LEU* 1.4 59.1 + - + +
502B THR* 2.9 28.1 - - - +
508B PRO* 4.1 30.6 - - + +
511B LYS* 3.6 39.5 - - + -
512B LEU* 4.6 16.6 - - + +
515B VAL* 5.1 9.4 - - + -
554B GLY* 5.0 0.2 - - - -
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Residues in contact with LEU 500 (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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492B LEU* 6.3 1.6 - - + -
496B ALA* 3.1 31.1 + - + +
497B ASN 4.0 0.4 - - - +
499B ILE* 1.4 73.4 - - + +
501B ALA* 1.3 62.2 + - - +
502B THR 3.2 3.2 - - - +
508B PRO* 6.4 0.2 - - + -
512B LEU* 4.1 29.4 - - + -
553B VAL* 3.7 0.3 - - - -
554B GLY* 2.8 51.3 + - - +
555B TRP* 3.4 57.8 - - + +
558B PHE* 4.8 17.0 - - + -
591B TRP* 5.8 0.7 - - + +
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Residues in contact with ALA 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B ASN* 3.2 19.3 + - - +
498B ASP* 3.6 9.9 - - - +
500B LEU* 1.3 79.3 - - - +
502B THR* 1.4 56.2 + - - +
503B PRO* 3.9 1.0 - - - +
552B SER 3.6 14.0 - - - +
553B VAL* 3.9 7.6 - - - +
555B TRP* 3.5 11.1 - - - +
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Residues in contact with THR 502 (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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498B ASP 3.0 16.5 + - - -
499B ILE* 2.9 25.9 + - - +
500B LEU 3.2 8.2 - - - +
501B ALA* 1.4 69.8 - - - +
503B PRO* 1.3 82.7 - - + +
504B SER* 3.6 0.9 + - - -
505B ASP* 6.1 0.2 - - - +
508B PRO* 6.5 0.7 - - - -
554B GLY* 3.6 3.3 + - - -
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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