Contacts of the strand formed by residues 572 - 579 (chain D) in PDB entry 4BUR
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 VAL 572 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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568D LEU* 3.4 4.7 - - - -
569D ARG 3.0 35.5 + - - +
570D ASP* 4.6 4.7 - - + +
571D LYS* 1.3 84.8 - - - +
573D VAL* 1.3 74.6 + - - +
574D VAL* 3.5 9.5 + - + +
595D GLY* 3.6 41.3 - - - +
596D GLU 3.8 5.8 - - - +
597D GLN* 4.3 18.4 - - + +
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Residues in contact with VAL 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D LEU* 5.5 0.2 - - - +
566D PHE* 4.0 14.1 - - + -
567D TYR 3.6 6.1 - - - +
568D LEU* 3.7 14.1 - - + -
571D LYS 5.2 0.9 - - - +
572D VAL* 1.3 83.0 - - - +
574D VAL* 1.3 59.1 + - - +
575D GLY 3.4 24.7 - - - +
576D ILE* 3.8 23.1 - - + -
591D ILE* 4.1 16.5 - - + +
592D ILE* 3.7 17.5 - - + +
596D GLU 4.3 1.4 + - - +
598D HIS* 4.0 25.6 - - + -
601D LEU* 4.3 12.8 - - + -
604D VAL* 6.1 0.2 - - + -
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Residues in contact with VAL 574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D LEU* 3.7 18.9 - - + +
496D GLY* 3.4 6.1 - - - -
497D LEU* 2.7 57.0 + - + +
502D LEU* 4.7 7.0 - - + -
567D TYR 2.8 19.7 + - - +
568D LEU 4.4 0.7 - - - -
569D ARG* 3.8 36.3 - - + +
572D VAL* 3.7 19.5 - - + +
573D VAL* 1.3 77.7 - - - +
575D GLY* 1.3 52.1 + - - +
592D ILE* 3.4 9.4 - - - +
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Residues in contact with GLY 575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495D ILE 3.4 11.4 - - - -
497D LEU 3.3 18.8 - - - -
498D VAL* 4.5 0.2 - - - -
567D TYR* 2.8 35.0 + - - -
573D VAL* 3.4 2.8 - - - +
574D VAL* 1.3 80.6 - - - +
576D ILE* 1.3 68.0 + - - +
592D ILE* 3.5 3.3 - - - +
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Residues in contact with ILE 576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D ALA* 3.5 3.8 - - - +
495D ILE* 3.0 37.2 + - + +
498D VAL* 3.9 1.6 - - - +
564D VAL* 3.8 21.8 - - + -
565D ILE 3.4 4.7 - - - -
566D PHE* 3.7 22.0 - - + -
567D TYR* 4.3 0.6 - - - -
573D VAL* 3.8 8.3 - - + -
575D GLY* 1.3 76.2 - - - +
577D VAL* 1.3 73.7 + - - +
578D LEU* 3.9 17.3 - - + -
588D ALA* 3.9 24.7 - - + +
591D ILE* 4.4 11.9 - - + -
592D ILE* 3.7 30.1 - - + -
608D PHE* 4.8 3.6 - - + -
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Residues in contact with VAL 577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D ILE* 5.4 0.4 - - + -
344D LEU* 4.7 7.9 - - + -
492D TYR* 3.9 25.8 - - + -
493D GLU 3.5 3.6 - - - -
494D ALA* 3.8 17.0 - - + -
498D VAL* 4.1 12.1 - - + -
564D VAL* 3.5 3.6 - - - +
565D ILE* 3.0 53.6 + - + +
567D TYR* 3.9 24.7 - - + +
576D ILE* 1.3 79.2 - - - +
578D LEU* 1.3 63.7 + - - +
579D TRP* 4.1 14.1 - - + -
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Residues in contact with LEU 578 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492D TYR* 2.9 23.6 - - - +
493D GLU* 2.8 34.5 + - + +
495D ILE* 5.8 0.9 - - + -
563D GLY 4.2 2.7 - - - -
564D VAL* 4.4 6.7 - - + -
576D ILE* 3.9 13.7 - - + -
577D VAL* 1.3 70.7 - - - +
579D TRP* 1.3 59.9 + - - +
580D ASN 3.7 0.9 + - - -
581D ILE* 4.1 28.4 + - + +
584D ARG* 4.4 1.6 - - + -
585D MET* 4.1 42.6 - - + +
588D ALA* 4.4 7.6 - - + -
608D PHE* 3.3 39.3 - - + -
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Residues in contact with TRP 579 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D LEU* 4.0 16.2 - - + -
348D LEU* 3.7 34.5 - - + -
351D TRP* 3.4 32.0 - + - -
352D THR* 3.6 18.2 - - - -
490D VAL* 3.7 20.9 - - + -
491D GLY 5.2 0.7 - - - -
492D TYR* 3.7 36.3 - + + -
508D PHE* 4.6 2.0 - + + -
560D TYR 2.8 28.6 + - - -
561D GLY 3.6 5.8 - - - -
562D LYS* 3.5 3.9 - - - -
563D GLY* 2.9 41.1 + - - +
565D ILE* 4.0 10.3 - - + -
577D VAL* 3.8 8.0 + - + -
578D LEU* 1.3 69.6 - - - +
580D ASN* 1.3 89.7 + - - +
581D ILE* 3.4 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
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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