Contacts of the strand formed by residues 570 - 576 (chain B) in PDB entry 1JQI
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 570 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B TYR* 3.4 30.3 - - + +
515B TRP* 3.9 14.4 - - + -
519B PHE* 3.5 15.3 - - + -
525B ILE 4.0 0.2 + - - -
526B GLY* 3.4 4.2 - - - -
527B CYS* 3.2 24.9 + - - -
568B ALA* 3.6 1.7 - - - +
569B SER* 1.3 83.7 - - - +
571B THR* 1.3 63.0 + - - +
591B VAL 3.3 11.4 - - - +
593B MET* 3.9 4.9 - - - +
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Residues in contact with THR 571 (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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499B TYR* 4.7 1.6 - - - -
527B CYS* 3.3 32.2 + - - -
529B ALA* 3.8 19.2 - - - +
570B ALA* 1.3 76.3 - - - +
572B VAL* 1.3 66.4 + - - +
573B VAL* 4.7 4.5 - - + +
589B PHE 3.5 0.3 - - - +
590B LEU* 3.5 5.4 - - - +
591B VAL* 2.8 57.9 + - + +
593B MET* 3.8 11.9 - - + -
598B LEU* 6.2 0.7 - - + -
617B LEU* 4.1 11.2 - - + +
619B PHE* 4.7 7.6 - - + -
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Residues in contact with VAL 572 (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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498B LEU 4.5 1.6 - - - +
499B TYR* 3.9 28.9 - - + +
502B PRO* 4.5 12.1 - - + -
503B ILE* 4.6 1.1 - - + -
527B CYS 3.3 8.4 + - - +
528B PHE* 4.0 7.8 - - + -
529B ALA* 3.0 23.4 + - - +
571B THR* 1.3 75.2 + - - +
573B VAL* 1.3 60.5 + - - +
574B PHE* 3.9 28.1 - - + -
588B ALA* 4.6 4.5 - - + -
589B PHE 3.3 9.0 - - - +
590B LEU* 3.6 22.2 - - + -
630B LEU* 4.2 19.5 - - + -
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Residues in contact with VAL 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ALA* 3.6 14.1 - - + +
544B THR* 5.0 4.3 - - + -
555B LEU* 3.7 29.2 - - + -
559B LYS* 3.9 26.7 - - + -
571B THR* 3.8 3.3 - - + -
572B VAL* 1.3 76.0 - - - +
574B PHE* 1.3 70.2 + - - +
575B ALA* 5.1 0.4 - - + -
587B SER 3.8 0.3 - - - +
588B ALA* 3.4 3.3 - - - +
589B PHE* 2.8 47.1 + - + +
591B VAL* 3.7 14.6 - - + -
619B PHE* 4.1 16.2 - - + -
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Residues in contact with PHE 574 (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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502B PRO* 5.9 0.2 - - + -
528B PHE* 3.4 37.9 - + - -
529B ALA 3.3 14.3 + - - +
530B LEU* 3.6 28.7 - - + -
542B ALA* 4.4 6.1 - - + +
544B THR* 4.4 1.0 - - - -
559B LYS* 2.9 28.4 + - - +
572B VAL* 3.9 23.1 - - + -
573B VAL* 1.3 77.3 - - - +
575B ALA* 1.3 60.6 + - - +
586B ILE* 4.1 10.8 - - + -
587B SER 3.5 3.8 - - - -
588B ALA* 3.7 23.1 - - + -
636B GLY 3.3 31.0 - - - -
639B ILE* 4.2 8.3 - - + -
640B ALA* 3.7 20.4 - - + -
643B THR* 5.3 0.2 - - - -
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Residues in contact with ALA 575 (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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542B ALA* 5.2 0.7 - - - -
544B THR* 3.4 28.0 - - + +
545B THR 3.9 2.2 - - - +
546B ALA* 3.9 23.6 - - + -
555B LEU* 4.7 5.2 - - + -
573B VAL* 4.1 3.2 - - + -
574B PHE* 1.3 75.3 - - - +
576B SER* 1.3 61.9 + - - +
577B THR 3.9 0.5 + - - -
586B ILE* 4.3 5.1 - - - +
587B SER* 2.9 34.3 + - - +
589B PHE* 4.2 9.2 - - + -
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Residues in contact with SER 576 (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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542B ALA* 4.2 8.0 - - - +
544B THR 2.8 12.8 + - - -
545B THR* 3.3 8.7 - - - +
546B ALA 3.0 21.9 + - - -
575B ALA* 1.3 73.2 - - - +
577B THR* 1.3 61.8 + - - +
578B ASP 3.2 5.4 + - - -
579B ARG* 3.1 40.1 + - - -
582B GLN 4.7 1.8 + - - -
585B GLY 3.3 9.4 + - - -
586B ILE* 3.8 18.3 - - - +
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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
------------------------------------------------------------
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