Contacts of the helix formed by residues 469 - 482 (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 HIS 469 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465B ASN 3.1 16.2 + - - -
466B GLN 3.7 15.6 + - - -
467B LYS 3.8 13.6 + - - -
468B PHE* 1.4 77.2 - - - +
470B TYR* 1.4 58.4 + - - +
471B ARG 3.4 2.2 - - - -
472B ASP* 3.2 21.3 - - + +
473B VAL* 2.8 32.1 + - + +
529B MET 5.0 1.5 + - - -
530B ASN* 3.3 43.2 + - + +
534B ASN* 3.4 30.4 + - + +
535B SER* 6.3 0.7 - - - -
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Residues in contact with TYR 470 (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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415B TYR* 3.2 33.3 + - - -
464B LEU* 3.0 61.3 + - + +
465B ASN* 3.5 5.7 + - + +
468B PHE* 3.1 19.9 + + + -
469B HIS* 1.4 75.3 - - - +
471B ARG* 1.4 63.3 + - - +
473B VAL* 3.0 15.3 + - + +
474B VAL* 3.1 21.3 + - + +
565B TYR* 3.5 30.1 - + - -
567B PRO* 3.2 29.8 - - + +
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Residues in contact with ARG 471 (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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461B ASN* 5.8 2.2 + - - +
465B ASN* 3.3 38.2 + - - +
469B HIS 3.4 0.2 - - - -
470B TYR* 1.4 76.5 - - - +
472B ASP* 1.3 58.5 + - - +
474B VAL* 3.1 27.2 - - + +
475B PHE* 3.3 39.4 - - + -
668B LEU* 5.7 1.2 + - - +
669B GLN* 3.8 42.4 - - - +
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Residues in contact with ASP 472 (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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469B HIS* 3.2 28.5 - - + +
471B ARG* 1.3 76.7 - - - +
473B VAL* 1.3 58.1 + - + +
475B PHE* 3.6 12.7 + - - +
476B ALA* 3.0 29.6 + - - +
530B ASN 5.3 0.9 - - - +
531B SER* 4.9 15.1 + - - -
532B PRO* 5.6 4.5 - - - +
535B SER* 6.1 4.0 - - - -
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Residues in contact with VAL 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B PHE 4.2 7.6 - - - +
469B HIS* 2.8 27.0 + - + +
470B TYR* 3.0 10.5 + - + +
472B ASP* 1.3 75.2 - - + +
474B VAL* 1.4 59.4 + - + +
476B ALA* 3.3 4.3 + - - +
477B LEU* 2.9 29.5 + - + +
535B SER* 6.2 0.4 - - - -
536B SER* 3.2 30.2 - - - +
562B TYR* 4.2 10.5 - - + +
565B TYR* 3.6 28.5 - - + +
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B TYR* 3.1 13.1 + - + +
471B ARG* 3.1 25.8 - - + +
473B VAL* 1.4 76.8 - - + +
475B PHE* 1.3 71.4 + - + +
477B LEU* 3.1 14.6 + - + +
478B LYS* 3.0 21.7 + - - +
565B TYR* 5.7 2.7 - - - +
661B PHE* 4.2 13.5 - - + -
724B LEU* 4.8 19.3 - - + -
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Residues in contact with PHE 475 (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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471B ARG* 3.3 41.9 + - + -
472B ASP* 3.6 13.7 - - - +
474B VAL* 1.3 84.1 - - + +
476B ALA* 1.4 56.8 + - - +
478B LYS* 3.2 10.3 + - - +
479B ASN* 2.9 37.1 + - - +
661B PHE* 4.8 14.4 - + - -
665B THR* 4.5 16.8 - - + -
669B GLN* 5.0 11.4 - - - -
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Residues in contact with ALA 476 (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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472B ASP* 3.0 21.7 + - - +
473B VAL* 3.4 9.6 - - - +
475B PHE* 1.4 71.3 - - - +
477B LEU* 1.4 61.7 + - - +
479B ASN* 3.3 13.1 + - - +
480B ILE* 2.9 32.0 + - + +
485B LYS* 5.2 1.9 + - - +
535B SER* 6.0 3.1 - - - -
536B SER* 4.4 18.8 - - - +
537B VAL* 4.9 12.7 - - + +
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Residues in contact with LEU 477 (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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473B VAL* 2.9 17.3 + - + +
474B VAL* 3.1 17.0 + - + +
476B ALA* 1.4 75.5 - - - +
478B LYS* 1.3 56.8 + - - +
480B ILE* 4.0 10.3 - - + -
481B LEU* 2.7 66.5 + - + +
482B LEU* 5.7 2.0 - - + -
536B SER* 6.4 0.4 - - - -
562B TYR* 5.8 10.5 - - + -
583B TYR* 4.2 26.5 - - + +
724B LEU* 5.6 10.3 - - + -
728B HIS* 6.6 0.4 - - + -
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Residues in contact with LYS 478 (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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474B VAL 3.0 11.9 + - - +
475B PHE* 3.3 8.5 - - - +
477B LEU* 1.3 76.5 - - - +
479B ASN* 1.3 76.8 + - - +
482B LEU* 3.3 47.3 + - + +
483B MET 3.5 2.3 + - - -
484B GLY* 3.5 11.5 + - - -
653B LEU* 6.0 4.9 - - - +
657B ILE* 5.7 7.6 - - + -
658B GLU* 5.8 9.4 + - - +
661B PHE* 3.8 42.0 - - + -
731B PHE* 5.9 0.4 - - + -
248D MET* 4.0 22.8 - - - +
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Residues in contact with ASN 479 (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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475B PHE* 2.9 24.9 + - - +
476B ALA* 3.5 11.6 - - - +
478B LYS* 1.3 92.3 + - - +
480B ILE* 1.3 54.5 + - - +
483B MET* 3.2 5.9 - - - -
484B GLY 2.8 47.0 + - - +
485B LYS* 3.5 35.9 - - - +
489B MET* 4.0 0.5 - - - +
248D MET* 4.1 11.7 - - - +
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Residues in contact with ILE 480 (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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476B ALA 2.9 23.8 + - - +
477B LEU* 3.7 14.1 - - + +
479B ASN* 1.3 71.6 - - - +
481B LEU* 1.4 68.7 + - + +
483B MET* 3.2 21.1 + - - +
485B LYS* 5.0 8.7 - - - +
488B PHE* 5.5 10.1 - - + -
489B MET* 4.3 10.2 - - + +
536B SER* 6.3 2.2 - - - -
537B VAL* 4.9 11.7 - - + -
541B LEU* 2.4 52.7 - - + -
560B LEU* 5.3 13.2 - - + -
587B PHE* 3.7 6.8 - - + -
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Residues in contact with LEU 481 (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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477B LEU* 2.7 40.9 + - + +
480B ILE* 1.4 75.2 - - + +
482B LEU* 1.4 68.6 + - + +
483B MET* 3.6 0.9 + - - +
583B TYR* 3.5 66.4 - - + +
584B LEU* 4.8 2.7 - - + +
586B ILE* 5.7 5.6 - - + -
587B PHE* 3.3 37.5 + - + +
590B LEU* 3.5 11.4 - - - +
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Residues in contact with LEU 482 (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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477B LEU* 4.5 2.7 - - + +
478B LYS* 3.3 34.5 + - + +
481B LEU* 1.4 91.2 - - + +
483B MET* 1.4 65.8 + - - +
484B GLY* 3.3 3.2 + - - +
586B ILE* 4.0 18.6 - - + -
590B LEU* 3.3 35.8 - - + +
594B LYS* 5.2 1.2 - - - -
653B LEU* 5.2 8.4 - - + +
657B ILE* 4.2 29.1 - - + +
661B PHE* 5.8 0.9 - - + -
731B PHE* 3.9 34.3 - - + -
735B ILE* 4.8 6.3 - - + -
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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
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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