Contacts of the strand formed by residues 548 - 552 (chain A) in PDB entry 3K57
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 SER 548 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A VAL* 4.7 4.5 - - - -
418A LEU 3.2 10.3 - - - -
419A ASP* 3.7 18.2 - - - -
527A MET* 3.3 12.5 - - - +
544A GLY* 2.9 21.3 - - - -
545A ASP* 3.0 27.4 + - - +
547A ASP* 1.3 81.0 - - - +
549A THR* 1.3 65.3 + - - +
550A PHE* 3.5 20.7 - - - -
1002A MG 4.5 1.3 - - - -
913P DOC 5.6 1.6 + - - -
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Residues in contact with THR 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A MET* 5.3 3.4 - - - -
416A LEU 3.4 2.4 - - - +
417A VAL* 3.7 0.7 - - - -
418A LEU* 2.9 41.6 + - - +
420A TYR* 6.3 0.4 - - + -
527A MET* 4.7 9.6 - - + +
530A THR* 3.8 29.5 - - + +
531A LYS* 4.5 8.5 - - + +
534A ILE* 3.6 24.3 - - + +
541A VAL* 4.4 14.1 - - + -
543A TYR 3.6 4.3 - - - +
548A SER* 1.3 79.4 - - - +
550A PHE* 1.3 64.2 + - - +
551A VAL* 3.7 2.5 + - - +
592A LEU* 4.8 1.1 - - + +
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Residues in contact with PHE 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 4.0 10.1 - - + -
416A LEU 3.2 4.7 - - - -
417A VAL* 3.9 31.6 - - + -
541A VAL* 3.4 5.1 - - - -
542A ILE* 2.9 33.5 + - + +
543A TYR* 2.8 51.8 + + + +
545A ASP* 5.6 0.2 - - + -
548A SER* 3.5 21.8 - - - -
549A THR* 1.3 75.8 - - - +
551A VAL* 1.3 61.9 + - - +
601A PHE* 3.4 38.6 - + - -
617A TYR* 3.5 38.4 - + - -
913P DOC 4.6 1.6 - - - -
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Residues in contact with VAL 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A VAL* 3.2 6.2 - - - -
416A LEU* 2.8 47.6 + - + +
418A LEU* 4.0 28.0 - - + -
534A ILE* 3.8 22.9 - - + -
539A TYR* 3.5 31.6 - - + -
540A ASP 3.5 6.3 - - - +
541A VAL* 4.5 2.0 - - + -
549A THR 4.1 7.2 - - - +
550A PHE* 1.3 74.8 - - - +
552A TRP* 1.3 64.7 + - - +
553A LEU* 3.5 14.3 + - + +
569A LEU* 4.4 7.0 - - + -
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Residues in contact with TRP 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ARG* 4.0 33.4 - - - -
412A TYR* 3.6 35.9 - + + +
413A ASP* 5.1 4.0 - - - +
414A SER 3.6 14.4 - - - -
415A VAL* 4.6 2.5 - - + +
539A TYR* 4.1 5.7 - - - -
540A ASP* 2.8 54.2 + - + +
542A ILE* 4.0 22.9 - - + +
550A PHE 3.9 1.6 + - - -
551A VAL* 1.3 71.2 - - - +
553A LEU* 1.3 71.3 + - - +
554A LYS* 3.4 48.2 + - + +
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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