Contacts of the strand formed by residues 502 - 507 (chain J) in PDB entry 4DHJ
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 502 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501J MET* 1.3 74.8 - - - +
503J ILE* 1.3 58.8 + - - +
504J PHE* 4.6 17.6 - - + -
514J THR* 3.2 28.0 - - + +
515J LEU 3.2 6.3 - - - +
516J GLU* 3.8 16.4 - - - +
563J LYS* 3.8 4.4 - - - +
564J GLU* 2.8 42.7 + - + +
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Residues in contact with ILE 503 (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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501J MET* 3.7 5.4 + - + -
502J GLN* 1.3 80.0 - - - +
504J PHE* 1.3 68.0 + - - +
505J VAL* 5.0 0.4 - - + -
514J THR* 3.7 4.9 - - - +
515J LEU* 3.0 51.9 + - + +
517J VAL* 3.7 33.2 - - + -
526J VAL* 4.6 1.6 - - + -
556J LEU* 4.2 14.4 - - + -
561J ILE* 4.2 11.7 - - + -
562J GLN 3.6 20.2 - - - +
564J GLU* 4.4 2.5 - - - +
565J SER 3.6 10.5 - - - +
567J LEU* 3.8 31.6 - - + -
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Residues in contact with PHE 504 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502J GLN* 4.6 15.5 - - + -
503J ILE* 1.3 77.0 - - - +
505J VAL* 1.3 62.3 + - - +
506J LYS 4.1 0.4 - - - -
512J THR* 4.2 20.9 - - + -
513J ILE 3.4 2.0 - - - +
514J THR* 3.8 28.0 - - + -
564J GLU* 3.6 55.0 - - + -
565J SER 2.9 7.3 + - - +
566J THR* 3.3 21.9 - - + +
567J LEU* 2.7 33.8 + - - +
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Residues in contact with VAL 505 (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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503J ILE* 5.0 1.3 - - + -
504J PHE* 1.3 79.6 - - - +
506J LYS* 1.3 61.7 + - - +
507J THR 3.8 0.3 + - - -
511J LYS 3.7 1.4 - - - +
512J THR* 3.5 3.5 - - - -
513J ILE* 2.7 53.8 + - + +
515J LEU* 3.8 30.1 - - + -
530J ILE* 4.1 14.6 - - + -
543J LEU* 4.0 12.1 - - + -
567J LEU* 3.5 20.6 - - + +
569J LEU* 3.7 32.1 - - + -
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Residues in contact with LYS 506 (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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187I GLU* 5.8 1.6 + - - -
191I PHE* 3.6 19.4 - - + -
504J PHE 4.1 0.8 - - - -
505J VAL* 1.3 71.3 - - - +
507J THR* 1.3 68.5 + - - +
508J LEU 5.4 0.4 + - - -
510J GLY* 2.9 26.7 + - - -
511J LYS 3.7 4.3 - - - +
512J THR* 3.7 20.2 - - - +
566J THR* 4.2 10.2 - - + +
567J LEU 3.0 7.5 + - - +
568J HIS* 3.5 24.0 - - + +
569J LEU* 2.9 25.6 + - - -
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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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191I PHE* 3.8 3.9 - - - -
505J VAL 5.0 0.2 - - - -
506J LYS* 1.3 88.5 + - - +
508J LEU* 1.3 63.4 + - - +
509J THR* 2.9 24.4 + - - +
510J GLY* 3.2 9.4 + - - -
511J LYS* 2.8 38.1 + - + +
513J ILE* 3.4 33.9 - - + -
536J ILE* 5.8 2.7 - - + -
569J LEU* 3.8 24.2 - - + -
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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