Contacts of the strand formed by residues 556 - 566 (chain J) in PDB entry 3E20
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 556 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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502J MET* 4.2 12.8 - - + +
503J PRO* 3.6 30.7 - - + -
554J VAL 3.9 0.4 + - - -
555J HIS* 1.3 76.6 - - - +
557J THR* 1.3 69.3 + - - +
628J PRO* 4.6 2.7 - - + -
629J VAL 3.6 15.5 - - - +
630J CYS* 3.8 6.5 - - - -
631J MET 4.5 0.4 - - - +
660J ILE* 4.4 2.0 - - - +
662J ASP* 3.1 14.4 - - - +
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Residues in contact with THR 557 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556J ALA* 1.3 82.6 - - - +
558J THR* 1.3 70.3 + - - +
559J ARG 2.8 30.6 + - - +
560J PHE* 4.4 0.8 - - + -
625J THR* 3.7 3.6 + - - -
628J PRO* 3.3 6.5 - - - +
629J VAL* 3.0 26.4 + - - +
631J MET* 4.0 30.5 - - + +
660J ILE* 3.7 15.3 - - + -
661J LEU 3.2 13.3 + - - -
662J ASP* 3.7 11.6 + - - -
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Residues in contact with THR 558 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557J THR* 1.3 74.4 + - - +
559J ARG* 1.3 72.4 + - - +
560J PHE* 4.9 2.7 - - - -
623J LEU 3.5 0.8 - - - +
624J GLU* 3.0 11.7 - - - +
625J THR* 2.9 52.8 + - - +
626J GLN 4.6 1.3 - - - +
627J THR* 3.4 27.8 - - - -
628J PRO* 3.4 11.2 - - + -
662J ASP* 5.4 0.2 + - - -
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Residues in contact with ARG 559 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557J THR* 2.8 18.8 + - - +
558J THR* 1.3 93.2 + - - +
560J PHE* 1.3 64.8 + - - +
594J LYS* 5.4 1.2 - - - +
622J GLU* 2.9 26.6 + - - +
623J LEU 3.4 2.7 - - - +
624J GLU* 3.5 37.1 + - + +
661J LEU* 2.9 44.3 + - + +
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Residues in contact with PHE 560 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557J THR* 4.4 3.8 - - + -
558J THR 4.9 0.9 - - - -
559J ARG* 1.3 80.1 - - - +
561J ILE* 1.3 63.6 - - - +
562J ALA* 4.1 5.8 + - + -
581J MET* 3.0 36.8 - - + -
590J VAL* 4.7 0.4 - - + -
622J GLU* 3.4 3.5 - - - +
623J LEU* 2.8 66.8 + - + -
625J THR* 4.4 17.5 - - + -
631J MET* 3.6 43.3 - - + -
643J PHE* 3.8 14.6 - + - -
657J VAL* 4.1 11.2 - - + -
659J LYS 3.3 14.1 - - - +
660J ILE* 4.4 3.1 - - - -
661J LEU* 4.1 4.0 - - - +
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Residues in contact with ILE 561 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560J PHE* 1.3 78.3 - - - +
562J ALA* 1.3 56.5 + - - +
596J LEU* 3.8 24.2 - - + -
620J ILE* 4.1 18.2 - - + -
621J ALA 3.2 16.8 - - - +
622J GLU* 4.2 8.7 - - + +
657J VAL* 3.7 1.7 - - - +
658J VAL* 2.7 48.6 + - + +
659J LYS* 2.8 24.2 + - + +
661J LEU* 4.2 29.4 - - + -
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Residues in contact with ALA 562 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560J PHE* 4.1 8.2 - - + -
561J ILE* 1.3 75.6 - - - +
563J GLN* 1.3 64.7 + - - +
564J ILE* 3.6 7.4 + - + +
620J ILE* 3.5 3.2 - - - -
621J ALA 3.1 29.8 + - - +
623J LEU* 4.9 3.5 - - + +
643J PHE* 3.7 24.5 - - + -
656J LYS 3.1 19.1 - - - +
657J VAL* 3.7 8.5 - - - -
658J VAL* 3.9 4.7 - - - -
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Residues in contact with GLN 563 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562J ALA* 1.3 75.3 - - - +
564J ILE* 1.3 63.7 + - - +
599J LEU* 3.7 28.1 - - + +
603J ASN* 4.2 17.5 + - - +
618J LYS* 6.1 5.3 - - + +
619J ILE 3.7 3.6 - - - -
620J ILE* 4.3 17.0 - - + +
655J GLY* 3.2 19.1 - - - -
656J LYS* 3.1 42.7 + - + +
658J VAL* 4.4 9.9 - - + +
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Residues in contact with ILE 564 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562J ALA 3.7 10.5 - - - +
563J GLN* 1.3 83.3 - - - +
565J ALA* 1.3 62.6 + - - +
566J ILE* 3.6 12.7 + - + -
592J PHE* 3.4 34.3 - - + -
618J LYS* 3.6 3.6 - - - -
619J ILE* 2.8 45.7 + - + +
621J ALA* 5.1 3.8 - - + +
623J LEU* 3.9 23.8 - - + -
643J PHE* 4.3 8.7 - - + -
645J LEU* 4.0 7.6 - - + -
653J ALA* 3.6 22.7 - - + -
654J VAL 3.4 11.9 - - - +
655J GLY* 4.2 0.4 - - - -
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Residues in contact with ALA 565 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564J ILE* 1.3 72.6 - - - +
566J ILE* 1.3 66.4 + - - +
567J LEU* 3.1 8.2 - - + +
617J MET 4.3 3.8 - - - -
618J LYS* 4.6 16.6 - - + +
653J ALA* 3.2 1.2 - - - -
654J VAL* 2.9 46.5 + - + -
655J GLY* 4.7 0.8 - - - -
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Residues in contact with ILE 566 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564J ILE* 3.8 12.8 - - + +
565J ALA* 1.3 74.4 - - - +
567J LEU* 1.3 66.1 + - - +
569J LEU* 3.8 29.2 - - + -
573J LEU* 4.8 9.6 - - + -
592J PHE* 6.0 1.8 - - + -
613J ALA* 4.4 13.2 - - + -
614J THR 3.4 15.9 - - - +
615J LYS* 3.4 26.5 - - - +
616J GLY* 2.9 23.2 + - - -
617J MET 3.4 11.4 + - - +
619J ILE* 3.1 36.1 - - + -
652J VAL 3.7 3.4 - - - -
653J ALA* 4.0 6.7 - - + -
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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