Contacts of the strand formed by residues 548 - 552 (chain D) in PDB entry 6PB4
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 548 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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522D GLY 3.4 19.7 - - - +
523D GLU* 3.7 7.0 - - - +
524D GLY* 3.7 9.2 - - - +
525D MET* 2.9 62.4 - - + +
527D LEU* 5.7 0.2 - - + -
546D ALA* 3.0 15.7 + - + +
547D ARG* 1.3 86.3 - - - +
549D LYS* 1.3 66.9 + - - +
550D VAL* 3.8 6.0 + - + +
570D LYS 3.7 0.3 - - - +
571D ASP* 2.7 9.5 + - - -
572D THR 2.8 27.7 + - - +
574D VAL* 5.2 7.2 - - + -
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Residues in contact with LYS 549 (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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524D GLY* 5.3 2.4 - - - +
525D MET 3.2 11.6 + - - +
526D VAL* 3.2 37.3 + - + -
527D LEU* 3.2 1.6 + - - +
548D VAL* 1.3 81.7 - - - +
550D VAL* 1.3 70.2 + - - +
569D LEU* 4.9 13.9 - - + +
570D LYS* 3.2 8.2 - - - +
571D ASP* 3.8 34.9 - - + +
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Residues in contact with VAL 550 (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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527D LEU* 3.6 41.5 - - + +
529D GLY* 5.5 1.6 - - - +
530D PRO* 6.3 1.1 - - + -
533D ALA* 5.7 0.2 - - + -
548D VAL* 4.2 7.2 - - + +
549D LYS* 1.3 85.8 - - - +
551D ARG* 1.3 71.2 + - - +
552D ILE* 4.6 9.0 - - + -
569D LEU* 3.1 14.8 - - - +
570D LYS* 2.9 34.9 + - + +
572D THR* 4.1 19.3 - - + +
574D VAL* 6.3 3.4 - - + -
577D ALA* 4.4 20.2 - - + -
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Residues in contact with ARG 551 (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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527D LEU 3.6 11.5 + - - +
528D THR* 3.5 24.5 + - - +
529D GLY* 4.1 8.8 - - - -
530D PRO* 4.8 4.3 - - - +
550D VAL* 1.3 78.0 - - - +
552D ILE* 1.3 69.2 + - - +
553D THR* 5.0 0.9 - - - +
567D THR* 2.7 53.1 + - - +
568D SER* 3.1 27.7 - - - +
569D LEU* 3.7 19.1 - - + +
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Residues in contact with ILE 552 (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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530D PRO* 6.1 3.6 - - + -
550D VAL* 4.6 11.4 - - + -
551D ARG* 1.3 79.9 - - - +
553D THR* 1.3 61.7 + - - +
554D GLU* 3.6 42.0 - - + +
566D LYS* 5.3 2.7 - - - +
567D THR* 2.5 25.9 + - - -
568D SER* 2.8 34.6 + - - +
570D LYS* 4.4 24.9 - - + +
577D ALA* 6.0 3.4 - - + -
580D TRP* 5.1 20.9 - - + +
589D TYR* 4.6 21.8 - - + -
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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