Contacts of the strand formed by residues 523 - 530 (chain B) in PDB entry 1JXO
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 TYR 523 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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433B ILE* 3.7 31.2 - - + -
434B ARG 3.3 8.5 - - - +
435B ALA* 3.8 13.7 - - + -
436B LEU* 4.0 6.9 - - - +
437B PHE* 3.5 20.0 - + - -
454B PHE* 3.7 13.5 - + - -
460B LEU* 4.1 11.0 - - + -
471B TRP* 4.4 7.2 - + + -
488B ILE* 3.7 10.4 - - + +
489B PRO* 2.5 50.0 + - - +
490B SER 4.0 1.1 - - - -
491B LYS* 3.9 39.6 - - + +
494B VAL* 4.0 8.3 - - + -
522B SER* 1.3 94.6 + - - +
524B GLU* 1.3 63.2 + - - +
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Residues in contact with GLU 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B ILE* 3.3 4.3 - - - -
434B ARG* 2.6 81.9 + - + +
436B LEU* 4.2 14.3 - - + +
523B TYR* 1.3 75.7 - - - +
525B THR* 1.3 62.9 + - - +
526B VAL* 3.4 9.9 + - + +
686B GLU* 4.8 8.5 - - - +
719B PRO* 4.2 24.3 - - + +
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Residues in contact with THR 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B PHE* 4.9 10.5 - - + -
432B TYR 3.7 10.3 - - - +
433B ILE* 4.5 10.3 - - + -
524B GLU* 1.3 75.1 - - - +
526B VAL* 1.3 63.7 + - - +
719B PRO* 3.5 4.0 - - - +
720B ALA* 2.8 38.5 + - - +
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Residues in contact with VAL 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B TYR* 3.2 37.7 + - + +
433B ILE 3.9 11.4 - - - +
434B ARG* 3.8 22.4 - - + -
459B VAL* 4.4 4.5 - - + -
524B GLU* 3.6 20.2 - - + +
525B THR* 1.3 79.4 - - - +
527B THR* 1.3 60.8 + - - +
717B TRP* 3.5 27.0 - - + -
718B VAL 3.1 23.8 - - - +
719B PRO 4.3 0.2 - - - -
720B ALA* 3.9 5.6 - - - +
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Residues in contact with THR 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526B VAL* 1.3 74.7 - - - +
528B GLN* 1.3 66.6 + - - +
717B TRP* 3.4 10.3 - - - -
718B VAL* 2.9 39.0 + - - +
720B ALA* 4.6 14.1 - - - -
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Residues in contact with GLN 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476B VAL* 5.8 0.7 - - - +
527B THR* 1.3 78.0 - - - +
529B MET* 1.3 62.0 + - - +
715B TYR* 4.2 29.8 - - + +
716B ILE 3.2 13.2 - - - +
717B TRP* 3.5 49.6 + - + +
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Residues in contact with MET 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527B THR 3.8 0.2 + - - -
528B GLN* 1.3 75.4 - - - +
530B GLU* 1.3 69.5 + - - +
531B VAL* 3.4 27.1 - - + -
533B TYR* 4.3 4.9 - - + +
642B HIS* 5.3 4.3 - - + +
644B HIS* 3.6 34.1 - - + +
715B TYR* 3.4 6.8 - - - -
716B ILE* 2.8 38.2 + - + +
718B VAL* 4.0 23.8 - - + -
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Residues in contact with GLU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B MET* 1.3 89.5 - - - +
531B VAL* 1.3 67.7 + - - +
532B HIS* 3.7 37.9 + - + +
714B PRO* 3.2 17.5 - - - +
715B TYR* 3.8 37.4 + - + -
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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