Contacts of the strand formed by residues 538 - 545 (chain A) in PDB entry 1PDR
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 538 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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468A VAL* 4.7 6.3 - - + -
469A LEU 3.6 4.9 - - - -
470A HIS* 4.0 21.1 - - + +
516A ASN* 3.8 6.6 + - - +
535A ALA 3.3 13.7 - - - +
537A GLN* 1.3 76.7 - - - +
539A VAL* 1.3 62.3 + - - +
540A THR* 3.9 4.9 + - - +
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Residues in contact with VAL 539 (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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467A VAL 3.4 2.8 - - - +
468A VAL* 3.4 4.1 - - - +
469A LEU* 2.8 42.4 + - + +
471A ARG* 4.0 4.7 - - - +
476A LEU* 3.8 33.4 - - + -
515A VAL* 3.6 18.4 - - + -
516A ASN* 3.7 1.8 - - - -
535A ALA* 3.5 31.4 - - + -
536A GLY 3.8 14.1 - - - +
537A GLN 4.2 2.2 - - - +
538A ALA* 1.3 76.1 - - - +
540A THR* 1.3 62.4 + - - +
541A ILE* 3.6 17.2 + - + +
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Residues in contact with THR 540 (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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466A LYS* 3.6 38.8 - - + +
467A VAL 3.6 4.5 - - - +
468A VAL* 4.2 15.9 - - + +
514A SER* 3.8 1.9 + - - +
515A VAL* 3.4 3.3 - - - -
516A ASN* 2.8 46.9 + - - +
538A ALA* 3.9 4.4 + - - +
539A VAL* 1.3 69.9 - - - +
541A ILE* 1.3 62.0 + - - +
542A VAL* 4.1 2.9 + - + +
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Residues in contact with ILE 541 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465A ARG 3.4 0.9 - - - +
466A LYS* 3.3 2.9 - - - -
467A VAL* 2.7 45.5 + - + +
469A LEU* 3.9 29.8 - - + -
476A LEU* 4.8 1.3 - - + -
478A PHE* 4.0 21.8 - - + -
506A LEU* 4.2 12.8 - - + -
512A ILE* 4.3 17.0 - - + -
514A SER 3.5 4.9 - - - +
515A VAL* 4.3 14.1 - - + -
532A LEU* 5.0 0.7 - - + -
539A VAL* 4.0 22.9 - - + +
540A THR* 1.3 76.9 - - - +
542A VAL* 1.3 73.2 + - - +
543A ALA* 4.1 13.2 - - + +
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Residues in contact with VAL 542 (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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464A PRO* 3.9 22.9 - - + -
465A ARG 3.0 10.5 - - - +
466A LYS* 4.1 25.1 - - + +
512A ILE* 3.7 2.9 - - - -
513A ILE* 2.8 42.7 + - + -
514A SER* 3.1 30.7 + - - +
540A THR* 5.0 4.5 - - + +
541A ILE* 1.3 75.9 - - - +
543A ALA* 1.3 60.1 - - - +
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Residues in contact with ALA 543 (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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464A PRO* 3.3 2.4 - - - +
465A ARG* 2.8 53.2 + - - +
467A VAL* 5.3 0.9 - - + -
506A LEU* 3.7 26.7 - - + -
510A ASP* 4.0 7.9 - - + +
511A ARG 3.1 11.9 - - - +
512A ILE* 4.9 2.0 - - + -
513A ILE* 4.4 1.1 - - - -
541A ILE* 3.8 7.3 + - + -
542A VAL* 1.3 76.1 - - - +
544A GLN* 1.3 61.4 + - - +
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Residues in contact with GLN 544 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A ARG 3.2 28.5 - - - +
463A GLU 4.8 1.6 - - - -
464A PRO* 3.9 23.4 - - + +
465A ARG* 3.8 2.0 - - - +
511A ARG* 2.8 27.9 + - + +
513A ILE* 3.3 25.6 - - + +
543A ALA* 1.3 75.4 - - - +
545A TYR* 1.3 61.9 + - - +
546A ARG* 3.2 48.1 + - - +
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Residues in contact with TYR 545 (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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460A ILE* 4.2 23.1 - - + +
461A THR 3.6 18.0 + - - +
462A ARG* 3.1 44.7 + - - +
465A ARG* 3.4 10.2 - - - +
507A ARG* 3.3 29.7 - - + -
508A LYS 3.4 18.3 + - - -
509A GLY* 4.1 6.7 - - - -
510A ASP* 3.1 24.5 - - - +
544A GLN* 1.3 71.3 - - - +
546A ARG* 1.3 61.0 + - - +
547A PRO* 3.7 28.7 - - + +
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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