Contacts of the strand formed by residues 527 - 532 (chain A) in PDB entry 5JPM
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 527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492A ASN* 3.5 6.1 - - - +
493A LEU* 2.9 45.1 + - + +
505A TYR* 3.4 28.9 + - + -
521A GLU* 3.6 23.3 - - + -
522A PRO 3.3 17.0 + - - +
524A ARG* 2.9 36.3 + - - +
525A THR 4.2 0.2 - - - -
526A LEU* 1.3 70.6 - - - +
528A SER* 1.3 62.7 + - - +
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Residues in contact with SER 528 (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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490A ASN* 4.1 19.8 + - - +
491A LEU 3.4 4.9 + - - -
492A ASN* 3.5 18.1 + - - -
521A GLU* 4.0 15.2 - - - +
524A ARG* 5.7 1.0 - - - +
526A LEU 4.0 3.2 + - - -
527A THR* 1.3 76.0 - - - +
529A VAL* 1.3 65.3 + - - +
530A SER* 4.1 4.2 + - - -
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Residues in contact with VAL 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489A LEU 3.6 1.7 - - - +
490A ASN* 3.4 1.6 - - - -
491A LEU* 2.7 43.3 + - + +
493A LEU* 3.7 31.6 - - + -
507A TYR* 3.6 43.5 - - + +
521A GLU* 3.9 24.7 - - + +
527A THR* 4.8 0.2 - - + -
528A SER* 1.3 75.3 + - - +
530A SER* 1.3 64.1 + - - +
531A VAL* 3.9 7.6 + - + +
543A PHE* 4.0 17.9 - - + -
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Residues in contact with SER 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A THR* 4.1 12.7 - - - +
489A LEU 3.5 4.7 - - - -
490A ASN* 2.7 21.1 + - - -
507A TYR* 4.9 5.2 + - - -
517A PHE* 6.2 0.2 - - - -
521A GLU* 5.1 1.6 + - - -
528A SER* 4.1 4.4 + - - -
529A VAL* 1.3 75.1 - - - +
531A VAL* 1.3 63.1 + - - +
532A PHE 4.1 1.2 + - - -
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Residues in contact with VAL 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A THR* 3.5 4.4 - - - -
489A LEU* 2.7 49.3 + - + +
491A LEU* 4.8 6.7 - - + -
507A TYR* 5.1 2.9 - - + -
509A ILE* 4.2 20.6 - - + -
517A PHE* 6.3 1.6 - - + -
529A VAL* 4.1 10.1 - - + +
530A SER* 1.3 76.6 - - - +
532A PHE* 1.3 64.7 + - - +
533A VAL* 3.7 7.9 + - + +
537A LEU* 4.3 20.9 - - + -
541A PHE* 4.5 7.2 - - + -
543A PHE* 3.8 32.1 - - + -
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Residues in contact with PHE 532 (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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486A GLY* 3.2 34.5 - - - -
487A ASP 4.0 2.7 - - - -
488A THR* 3.7 19.5 - - + +
530A SER 4.1 1.6 + - - -
531A VAL* 1.3 73.2 - - - +
533A VAL* 1.3 61.0 + - - +
534A ASP* 3.5 31.5 + - + +
537A LEU* 4.2 8.1 - - - +
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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