Contacts of the strand formed by residues 584 - 591 (chain F) in PDB entry 2JJD
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 VAL 584 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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515F TRP* 4.1 1.1 - - - -
570F LEU* 3.4 31.6 - - + -
571F VAL 3.4 5.4 - - - +
572F THR* 3.4 23.6 - - + -
581F GLY 5.1 6.3 - - - +
582F GLU 3.4 4.1 - - - +
583F GLN* 1.3 83.2 + - + +
585F ARG* 1.3 69.0 + - - +
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Residues in contact with ARG 585 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514F ILE* 5.5 0.7 - - - -
515F TRP* 3.3 65.6 + - + +
518F LYS* 3.4 41.0 - - - +
519F SER 4.5 8.7 - - - -
520F HIS* 3.6 33.8 + - + +
570F LEU* 3.5 6.1 - - - +
571F VAL* 2.7 36.2 + - + +
582F GLU* 4.4 13.9 + - - +
584F VAL* 1.3 79.4 + - - +
586F VAL* 1.3 62.0 + - - +
587F VAL* 4.0 11.2 - - + -
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Residues in contact with VAL 586 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520F HIS* 4.0 18.3 - - - +
556F LYS* 6.5 0.7 - - + -
568F ASP* 5.0 9.4 - - + -
569F PHE 3.2 14.8 - - - +
570F LEU* 4.2 18.4 - - + -
585F ARG* 1.3 74.8 - - - +
587F VAL* 1.3 69.3 + - - +
588F ARG* 5.7 0.6 - - + +
617F GLN* 5.8 2.3 + - - -
621F THR* 6.0 1.2 - - - -
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Residues in contact with VAL 587 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511F TRP* 4.8 3.8 - - + -
514F ILE* 4.6 7.2 - - + -
519F SER 4.1 18.4 - - - +
520F HIS* 3.3 15.7 - - - +
522F ILE* 3.8 28.9 - - + -
568F ASP* 3.5 1.6 - - - -
569F PHE* 2.7 48.5 + - + +
571F VAL* 3.6 30.5 - - + -
585F ARG* 4.0 10.3 - - + -
586F VAL* 1.3 80.0 - - - +
588F ARG* 1.3 67.1 + - - +
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Residues in contact with ARG 588 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520F HIS 2.9 9.2 + - - +
521F THR* 3.4 4.2 - - - +
522F ILE* 2.9 25.3 + - - +
566F ILE* 3.3 36.7 - - + +
567F ARG 3.3 4.0 - - - -
568F ASP* 2.8 44.0 + - - +
586F VAL* 4.4 1.1 + - + +
587F VAL* 1.3 75.7 - - - +
589F GLN* 1.3 61.0 + - - +
590F PHE* 3.8 28.3 - - + -
617F GLN* 3.1 42.1 + - + +
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Residues in contact with GLN 589 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522F ILE* 3.4 19.3 - - + +
524F MET* 2.9 27.1 - - + +
539F TYR* 2.8 38.2 + - - +
540F TRP* 3.5 8.5 - - - -
565F SER 3.7 1.4 - - - +
566F ILE* 3.4 7.6 - - - +
567F ARG* 2.7 73.1 + - + +
569F PHE* 3.7 22.1 - - + -
587F VAL 4.2 0.6 + - - -
588F ARG* 1.3 74.0 - - - +
590F PHE* 1.3 68.8 + - - +
591F HIS 4.4 0.4 - - - +
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Residues in contact with PHE 590 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521F THR* 3.9 21.3 - - + -
522F ILE 2.8 12.0 + - - +
523F VAL* 3.5 5.5 - - + +
524F MET 3.0 23.7 + - - -
564F ILE* 4.1 11.2 - - + -
565F SER 4.0 2.5 - - - -
566F ILE* 3.5 32.3 - - + -
588F ARG* 3.8 27.8 - - + -
589F GLN* 1.3 74.5 - - - +
591F HIS* 1.3 60.9 + - - +
592F PHE 3.5 2.7 + - - -
610F LEU* 4.0 17.1 - - + +
613F ALA* 3.7 38.8 - - + -
614F VAL* 3.6 23.3 - - + -
617F GLN* 3.9 14.6 - - + -
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Residues in contact with HIS 591 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524F MET* 3.1 39.7 - - + +
526F THR 3.1 24.8 + - - -
527F GLU* 4.2 7.5 - - + +
528F VAL* 5.3 3.8 - - + -
540F TRP* 4.0 10.5 - + - -
564F ILE* 3.6 2.1 - - - +
565F SER* 3.0 45.1 + - - +
567F ARG* 3.1 26.5 + - - +
589F GLN* 3.8 2.5 - - - +
590F PHE* 1.3 69.5 - - - +
592F PHE* 1.3 71.7 + - - +
593F HIS* 3.4 29.8 + + - -
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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