Contacts of the strand formed by residues 549 - 554 (chain A) in PDB entry 1D0N
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 THR 549 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509A MET* 4.1 14.2 + - - +
514A GLY 4.7 4.0 + - - -
515A LYS 4.6 1.4 + - - -
516A PRO* 3.1 29.1 - - - +
517A MET 3.0 16.8 + - - -
541A VAL* 4.4 7.6 - - - -
542A ARG 3.4 7.2 - - - +
543A ALA* 3.8 11.9 - - + -
547A GLY 3.7 9.2 + - - +
548A ALA* 1.3 81.2 - - - +
550A ARG* 1.3 65.0 + - - +
586A ALA 3.3 32.5 - - - +
587A GLU* 4.4 2.2 - - - +
589A THR* 5.5 0.7 - - + -
590A GLY* 4.1 6.3 - - - -
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Residues in contact with ARG 550 (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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502A GLY 3.4 18.8 + - - -
503A LYS* 4.7 5.1 - - - +
504A GLU* 3.3 34.8 + - - +
509A MET* 3.3 38.0 - - + +
516A PRO* 4.1 2.2 - - - -
517A MET* 3.2 24.5 - - + +
540A GLN* 3.3 8.0 + - - +
541A VAL* 3.4 2.8 - - - -
542A ARG* 3.2 64.7 + - + +
549A THR* 1.3 78.0 - - - +
551A ALA* 1.3 60.3 + - - +
552A VAL* 2.9 33.4 + - + +
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Residues in contact with ALA 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A PRO* 4.1 6.3 - - + +
517A MET 2.7 11.3 + - - +
518A ILE* 4.2 8.9 - - + +
519A VAL* 2.8 28.9 + - - +
539A PHE* 4.2 5.7 - - + -
540A GLN 3.5 5.8 - - - -
541A VAL* 4.4 9.9 - - + +
550A ARG* 1.3 71.0 - - - +
552A VAL* 1.3 60.3 + - - +
594A LEU* 3.7 40.4 - - + -
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Residues in contact with VAL 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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501A GLN* 5.5 2.9 - - + +
502A GLY* 5.0 13.0 - - - -
504A GLU* 4.4 6.1 - - - +
519A VAL* 3.8 23.8 - - + -
539A PHE* 3.3 3.2 - - - -
540A GLN* 2.7 45.8 + - + +
550A ARG* 2.9 41.7 - - + +
551A ALA* 1.3 77.7 - - - +
553A GLU* 1.3 71.5 + - - +
554A ILE* 3.9 9.5 + - + +
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Residues in contact with GLU 553 (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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519A VAL 3.1 17.6 + - - +
520A TYR* 3.5 2.4 - - - +
521A LYS* 3.2 52.7 + - + +
522A GLY* 4.1 1.8 + - - -
534A ALA* 5.7 0.7 - - - +
537A ARG* 3.0 55.3 + - - +
538A LEU 3.2 16.2 - - - +
539A PHE* 3.8 14.2 - - + -
552A VAL* 1.3 80.1 - - - +
554A ILE* 1.3 71.1 + - - +
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Residues in contact with ILE 554 (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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521A LYS* 3.6 16.4 - - - +
537A ARG* 5.5 0.2 - - - -
538A LEU* 3.0 31.8 + - + +
540A GLN* 4.0 21.3 - - + +
552A VAL* 4.4 13.7 - - + +
553A GLU* 1.3 83.4 - - - +
555A ILE* 1.3 67.6 + - - +
556A PRO* 3.4 12.1 - - - +
560A ALA* 4.0 30.5 - - + +
567A PHE* 4.1 11.7 - - + -
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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