Contacts of the strand formed by residues 506 - 514 (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 GLN 506 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500J LEU* 3.4 3.9 - - - -
501J VAL* 2.5 39.6 + - + +
504J ILE* 3.2 27.0 - - + +
505J ASN* 1.3 78.3 - - - +
507J THR* 1.3 69.9 + - - +
508J LEU* 4.4 5.8 - - + -
537J ASP* 2.9 55.0 + - - +
538J ASP* 4.7 1.4 - - - +
540J ASP* 4.0 19.4 + - - +
541J VAL* 4.9 1.8 - - + -
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Residues in contact with THR 507 (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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498J ASN* 4.4 21.3 - - + +
499J VAL 3.5 13.2 - - - +
500J LEU* 3.8 12.0 - - - +
505J ASN 4.3 2.4 + - - -
506J GLN* 1.3 83.0 + - - +
508J LEU* 1.3 80.8 + - - +
536J GLY* 4.8 3.8 - - - -
537J ASP 5.0 0.5 + - - -
550J THR* 4.7 8.8 - - + +
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Residues in contact with LEU 508 (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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484J LEU* 4.0 10.3 - - + -
498J ASN* 3.4 8.8 - - - +
499J VAL* 3.0 39.9 + - + +
501J VAL* 3.6 26.7 - - + -
506J GLN* 4.2 1.5 + - + -
507J THR* 1.3 84.4 - - - +
509J GLU* 1.3 61.3 + - - +
534J VAL* 3.8 30.3 - - + -
535J ARG 3.7 4.5 - - - +
536J GLY* 3.6 24.2 - - - +
537J ASP 3.3 24.2 - - - +
538J ASP* 4.2 2.9 - - + -
541J VAL* 4.0 13.7 - - + -
547J LEU* 5.1 0.9 - - + -
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Residues in contact with GLU 509 (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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495D LYS* 4.8 4.0 + - - -
496J ASN* 3.7 25.3 - - - +
497J SER 3.6 10.5 - - - +
498J ASN* 3.7 11.2 - - - +
508J LEU* 1.3 73.9 - - - +
510J VAL* 1.3 70.5 + - - +
511J THR* 3.5 11.6 + - + +
534J VAL* 3.0 8.1 - - - -
535J ARG* 2.8 67.2 + - + +
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Residues in contact with VAL 510 (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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493J ILE* 4.0 11.2 - - + -
494J LYS 4.4 2.2 - - - +
496J ASN* 2.6 37.8 + - - +
497J SER 2.9 16.6 + - - +
499J VAL* 3.6 39.0 - - + -
509J GLU* 1.3 72.0 - - - +
511J THR* 1.3 56.5 + - - +
512J ALA 3.9 6.1 - - - +
513J ILE* 3.9 27.8 - - + -
532J LEU* 3.9 25.4 - - + -
533J ARG 3.6 4.7 - - - +
534J VAL* 4.6 6.1 - - + +
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Residues in contact with THR 511 (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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511D THR* 6.0 3.6 - - - -
535D ARG* 3.5 20.4 + - - -
495J LYS* 4.5 1.9 - - - +
496J ASN* 3.7 15.5 - - - +
509J GLU* 4.0 22.9 - - - +
510J VAL* 1.3 76.9 - - - +
512J ALA* 1.3 64.0 + - - +
533J ARG* 2.8 37.4 + - - +
534J VAL* 4.9 0.7 - - - -
535J ARG* 3.8 38.2 + - + +
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Residues in contact with ALA 512 (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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535D ARG* 5.1 0.7 - - - +
495J LYS* 5.1 3.6 - - - -
496J ASN 5.0 0.4 - - - +
510J VAL* 3.5 5.0 - - - +
511J THR* 1.3 84.9 + - - +
513J ILE* 1.3 69.5 + - - +
514J TYR* 3.6 32.5 - - + +
520J GLU* 4.2 12.6 - - - +
531J ARG 3.9 0.3 - - - +
532J LEU* 3.5 4.0 - - - -
533J ARG* 3.0 36.9 + - + +
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Residues in contact with ILE 513 (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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493J ILE* 4.3 14.8 - - + +
494J LYS 3.8 5.4 - - - -
495J LYS* 3.5 37.4 - - + +
510J VAL* 3.9 8.3 - - + -
512J ALA* 1.3 76.7 - - - +
514J TYR* 1.3 66.3 + - - +
520J GLU* 3.4 7.5 - - - +
521J ILE* 2.9 54.8 + - + +
522J SER 4.5 1.3 - - - +
523J SER* 4.7 0.4 - - - -
524J SER* 3.7 18.4 - - - +
530J VAL* 3.7 21.1 - - + -
531J ARG 3.7 2.9 - - - -
532J LEU* 3.2 20.4 - - + -
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Residues in contact with TYR 514 (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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480D LEU* 2.9 57.0 + - + -
481D GLY* 3.6 8.8 + - - -
533D ARG* 5.0 2.3 + - - -
483J ILE* 5.4 0.4 - - + -
512J ALA* 3.6 24.3 - - + +
513J ILE* 1.3 78.4 - - - +
515J ASP* 1.3 67.9 + - - +
518J ASP* 4.0 9.9 - - - -
519J GLU 3.5 4.9 - - - +
520J GLU* 3.5 44.0 + - + -
530J VAL* 3.8 5.2 - - - -
531J ARG* 3.0 39.5 + - + +
533J ARG* 2.8 36.0 + - + -
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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