Contacts of the strand formed by residues 511 - 516 (chain H) in PDB entry 1P8J
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 THR 511 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412H ALA* 6.5 0.7 - - + -
413H THR 4.6 5.0 + - - +
414H ASN* 3.7 10.1 + - - +
415H GLY* 3.4 11.4 + - - -
420H VAL* 6.0 0.2 - - + -
505H LEU 3.4 3.1 - - - +
506H ILE* 3.3 2.7 - - - -
507H SER* 3.0 35.3 + - - -
509H MET 3.4 0.4 + - - -
510H GLY* 1.3 73.5 - - - +
512H ARG* 1.3 62.7 - - - +
513H SER* 3.6 5.3 + - - +
537H HIS* 3.7 34.8 - - + +
538H SER* 3.7 7.7 + - - +
541H GLU* 2.4 24.5 + - - -
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Residues in contact with ARG 512 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422H HIS* 4.1 11.6 - - - -
504H HIS* 3.2 45.2 + - + -
505H LEU 3.5 2.9 - - - -
506H ILE* 3.8 27.6 - - + +
510H GLY 3.3 6.6 + - - +
511H THR* 1.3 74.5 - - - +
513H SER* 1.3 60.6 + - - +
514H THR* 4.0 1.6 + - - -
537H HIS* 5.0 1.4 + - - -
550H GLU* 2.7 30.7 + - - -
552H GLU* 5.1 5.7 + - - -
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Residues in contact with SER 513 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H SER* 4.2 6.3 - - - -
422H HIS* 3.9 4.5 - - - -
504H HIS* 3.2 5.8 - - - +
505H LEU* 2.7 45.3 + - - -
511H THR* 3.6 5.6 + - - +
512H ARG* 1.3 73.3 - - - +
514H THR* 1.3 61.0 + - - +
515H LEU* 3.3 7.1 + - - +
535H THR* 2.8 41.2 + - - +
537H HIS* 3.5 14.4 - - - +
538H SER* 4.8 2.6 + - - -
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Residues in contact with THR 514 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333H CYS* 4.6 3.1 - - - -
334H SER* 3.6 19.1 + - - -
422H HIS* 2.9 33.2 + - - -
503H ILE 3.7 3.1 - - - +
504H HIS* 3.3 29.4 + - + +
512H ARG* 5.1 0.7 + - - -
513H SER* 1.3 69.8 - - - +
515H LEU* 1.3 61.3 + - - +
516H LEU* 3.8 25.1 - - - +
517H ALA* 4.0 13.5 - - + +
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Residues in contact with LEU 515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302H SER* 4.4 0.7 + - - -
304H ASN* 3.3 31.0 + - - +
334H SER* 3.9 16.4 - - - +
489H ALA* 3.4 29.6 - - + -
491H LEU* 4.8 0.4 - - + -
503H ILE* 2.8 31.6 + - + +
505H LEU* 3.8 35.0 - - + +
513H SER* 4.4 2.7 - - - +
514H THR* 1.3 73.6 - - - +
516H LEU* 1.3 61.0 + - - +
533H PHE* 3.4 33.2 - - + +
535H THR* 4.4 14.8 - - + -
549H LEU* 4.2 5.4 - - + -
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Residues in contact with LEU 516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302H SER* 4.1 11.2 - - - +
305H CYS* 3.6 29.2 - - - -
498H ARG* 4.9 4.5 - - + +
501H LEU* 4.2 16.2 - - + +
502H ALA* 3.0 5.2 - - - +
503H ILE* 2.7 52.1 + - + +
514H THR* 3.3 7.9 - - - +
515H LEU* 1.3 81.4 - - - +
517H ALA* 1.3 76.5 + - - +
519H ARG* 4.1 10.5 - - - -
528H PHE* 3.5 34.8 - - + -
533H PHE* 4.0 9.4 - - + -
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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