Contacts of the strand formed by residues 507 - 516 (chain B) in PDB entry 5ZF6
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 ALA 507 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488B ALA* 5.2 1.1 - - - -
489B CYS* 3.6 8.1 - - - +
506B VAL* 1.3 76.9 - - - +
508B GLY* 1.3 59.8 + - - +
548B ALA* 3.2 5.3 - - - -
549B GLY 3.0 30.7 + - - +
582B LYS* 3.9 15.4 - - + +
585B ILE* 3.7 28.7 - - + -
586B LEU* 3.7 25.3 - - + +
589B MET* 4.0 0.4 - - - -
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Residues in contact with GLY 508 (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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388B ARG* 3.1 21.5 + - - -
485B MET* 3.5 18.4 + - - -
488B ALA* 5.0 0.2 - - - +
489B CYS* 3.4 7.5 - - - +
507B ALA* 1.3 76.9 - - - +
509B VAL* 1.3 63.4 + - - +
547B ILE 3.4 11.2 - - - -
548B ALA* 3.7 9.4 - - - +
582B LYS* 6.1 1.3 - - - -
585B ILE* 3.8 9.5 - - - +
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B LEU* 4.4 0.9 - - + -
388B ARG* 4.8 5.8 - - - +
485B MET* 3.7 9.2 - - - +
508B GLY* 1.3 75.4 - - - +
510B ALA* 1.3 69.6 + - - +
511B ILE* 4.2 4.9 - - + -
531B THR* 4.7 0.7 - - + -
532B ASP* 4.0 26.9 - - + +
545B PHE 3.5 2.1 - - - +
546B LYS* 3.6 0.9 - - - -
547B ILE* 3.1 29.1 + - - +
578B ALA* 3.8 41.3 - - + +
581B ALA* 4.2 16.6 - - + -
582B LYS* 5.0 2.5 - - + +
585B ILE* 4.2 14.6 - - + -
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Residues in contact with ALA 510 (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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388B ARG* 5.9 1.0 - - - +
482B SER* 3.6 31.8 + - - +
485B MET* 4.4 0.4 - - - +
509B VAL* 1.3 77.2 - - - +
511B ILE* 1.3 61.8 + - - +
532B ASP* 3.1 29.0 + - - +
533B ILE* 3.5 14.1 + - + +
544B ASP* 3.8 17.9 - - - +
545B PHE 3.2 5.2 - - - +
546B LYS* 3.9 6.7 - - + -
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Residues in contact with ILE 511 (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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509B VAL* 4.2 8.1 - - + -
510B ALA* 1.3 77.5 - - - +
512B GLY* 1.3 67.8 + - - +
529B LEU* 4.1 12.8 - - + -
530B LEU 3.3 13.5 - - - +
531B THR* 3.9 29.6 - - + +
532B ASP 4.5 0.2 - - - +
533B ILE* 4.4 2.0 - - - -
543B MET* 3.4 13.7 - - + +
544B ASP* 4.2 0.2 - - - -
545B PHE* 2.9 46.3 + - + +
574B ALA* 3.8 24.5 - - + +
577B GLN* 4.4 4.9 - - + +
578B ALA* 3.8 30.3 - - + +
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Residues in contact with GLY 512 (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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511B ILE* 1.3 74.2 - - - +
513B LEU* 1.3 61.7 + - - -
529B LEU* 3.4 16.1 - - - +
530B LEU* 2.7 33.6 + - - -
533B ILE* 3.5 25.3 - - - +
537B GLU 5.8 1.6 - - - -
543B MET* 3.8 12.3 - - - -
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Residues in contact with LEU 513 (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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512B GLY* 1.3 75.6 - - - +
514B VAL* 1.3 74.2 + - - +
515B THR* 3.7 16.4 - - + -
527B TYR* 3.8 29.6 - - + -
528B ARG 3.3 11.7 - - - +
529B LEU* 3.9 13.0 - - + -
530B LEU* 4.4 2.6 - - - +
537B GLU 5.7 0.4 + - - -
541B GLY* 3.5 3.1 - - - -
542B ASP* 2.9 36.0 + - + +
543B MET* 3.8 29.4 + - + +
566B ILE* 3.9 25.1 - - + -
570B ILE* 3.9 20.6 - - + -
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Residues in contact with VAL 514 (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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348B PHE* 5.7 5.6 - - + -
349B ARG* 3.6 51.4 - - + +
352B VAL* 4.6 12.3 - - + -
353B LEU* 3.7 14.1 - - + +
513B LEU* 1.3 79.4 - - - +
515B THR* 1.3 62.8 - - - +
527B TYR* 3.3 2.1 - - - -
528B ARG* 2.8 43.9 + - + +
530B LEU* 3.7 25.1 - - + -
537B GLU* 5.5 0.7 - - + +
540B ASN 5.1 0.4 - - - +
541B GLY* 4.7 10.1 - - - -
542B ASP* 4.0 1.8 - - - -
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Residues in contact with THR 515 (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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349B ARG* 3.1 20.3 + - - +
353B LEU* 3.8 12.2 - - - +
513B LEU* 3.7 22.9 - - + -
514B VAL* 1.3 73.0 - - - +
516B LYS* 1.3 61.3 + - - +
517B THR* 3.9 11.8 + - - +
524B ILE* 4.0 18.4 - - + -
526B ASP 3.4 7.0 - - - -
527B TYR* 3.7 20.2 - - + -
542B ASP* 2.6 21.8 + - - -
563B LEU* 3.4 23.0 - - + +
570B ILE* 4.8 0.7 - - + -
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Residues in contact with LYS 516 (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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353B LEU* 3.9 23.6 - - + -
515B THR* 1.3 73.1 - - - +
517B THR* 1.3 61.3 + - - +
524B ILE* 3.7 1.0 - - - -
525B GLU* 2.9 67.1 + - + +
526B ASP* 2.9 23.8 + - + +
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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