Contacts of the strand formed by residues 529 - 535 (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 529 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474J ALA* 5.6 1.2 - - - +
485J GLU* 3.9 19.7 + - - +
486J GLY 3.2 21.1 + - - +
487J LYS* 3.5 33.3 - - + +
514J TYR 4.3 0.5 - - - +
515J ASP* 4.4 2.1 - - - -
516J GLU* 2.8 53.4 + - + +
527J GLY 3.7 2.3 + - - +
528J ASP* 1.3 70.9 - - - +
530J VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 530 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471J MET* 3.8 25.6 - - - -
485J GLU* 3.5 5.4 - - - +
486J GLY 3.0 33.0 + - - +
488J ILE* 4.2 13.9 - - + -
513J ILE* 3.7 16.4 - - + -
514J TYR 3.8 5.6 - - - +
515J ASP* 5.4 1.1 - - - -
521J ILE* 4.9 1.1 - - + -
524J SER* 3.1 36.1 - - - +
528J ASP* 3.8 8.9 + - + -
529J GLN* 1.3 79.1 - - - +
531J ARG* 1.3 62.4 + - - +
532J LEU* 4.1 14.5 + - + -
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Residues in contact with ARG 531 (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* 3.8 33.8 - - + +
477J TYR* 4.1 13.7 + - - +
483J ILE* 4.0 12.6 - - + -
484J LEU 3.7 2.7 - - - -
485J GLU* 3.5 26.2 - - + +
513J ILE* 3.7 2.4 - - - -
514J TYR* 3.0 39.4 + - + +
515J ASP 3.1 23.2 + - - -
516J GLU* 3.9 12.5 + - - +
518J ASP* 2.6 32.9 + - - +
530J VAL* 1.3 72.5 - - - +
532J LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 532 (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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469J PHE* 4.8 9.4 - - + -
471J MET* 3.8 18.4 - - + -
482J THR 3.6 0.3 - - - +
483J ILE* 3.2 8.6 - - - -
484J LEU* 2.7 41.4 + - + +
493J ILE* 4.5 6.7 - - + -
510J VAL* 3.9 20.6 - - + -
512J ALA 3.5 1.3 - - - +
513J ILE* 3.2 41.5 - - + -
530J VAL* 4.1 12.8 - - + -
531J ARG* 1.3 75.8 - - - +
533J ARG* 1.3 59.8 + - - +
534J VAL* 3.9 8.6 + - + -
547J LEU* 3.5 30.5 - - + -
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Residues in contact with ARG 533 (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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479D ASP* 4.2 1.8 + - - -
480D LEU* 3.0 25.2 + - - +
514D TYR* 4.8 5.4 - - - -
533D ARG* 3.5 48.1 - - - +
479J ASP 5.4 2.4 + - - -
480J LEU 4.3 6.9 + - - -
481J GLY* 4.8 3.6 - - - -
482J THR 3.4 10.3 - - - +
483J ILE* 3.6 26.9 - - + +
510J VAL* 3.6 3.1 - - - -
511J THR* 2.8 46.6 + - - +
512J ALA* 3.0 19.7 + - + +
514J TYR* 2.8 37.9 + - + -
531J ARG 4.2 0.2 + - - -
532J LEU* 1.3 72.5 - - - +
534J VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 534 (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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481J GLY* 5.3 1.0 - - - -
482J THR* 3.1 42.6 + - + +
484J LEU* 3.6 33.0 - - + -
499J VAL* 5.2 0.4 - - + -
508J LEU* 3.8 30.1 - - + -
509J GLU 3.0 9.9 - - - +
510J VAL* 4.8 9.2 - - + -
511J THR* 4.9 0.7 - - - -
532J LEU* 4.5 13.7 - - + +
533J ARG* 1.3 82.2 - - - +
535J ARG* 1.3 61.9 + - - +
536J GLY 4.5 0.2 + - - -
538J ASP* 4.7 4.9 - - + +
547J LEU* 5.0 3.6 - - + -
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Residues in contact with ARG 535 (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* 3.3 36.9 - - - +
496D ASN* 5.4 0.6 + - - -
511D THR 3.4 22.4 + - - -
512D ALA* 4.9 1.0 - - - +
520D GLU* 2.9 39.0 + - - +
508J LEU* 3.7 5.4 - - - -
509J GLU* 2.8 57.9 + - + +
511J THR* 3.8 22.2 + - + +
534J VAL* 1.3 77.0 - - - +
536J GLY* 1.3 62.5 + - - +
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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