Contacts of the helix formed by residues 488 - 497 (chain A) in PDB entry 5QSY
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 LEU 488 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468A LEU* 3.7 39.3 - - + -
484A LEU* 3.1 26.9 + - + +
485A VAL* 3.6 0.9 - - - -
487A SER* 1.3 85.0 + - - +
489A TRP* 1.3 57.0 + - - +
490A GLU 3.5 1.6 - - - -
491A SER* 3.2 10.2 + - - +
492A SER* 2.8 43.5 + - - +
496A LEU* 3.8 17.2 - - + +
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Residues in contact with TRP 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A VAL* 3.1 34.3 + - + +
486A ASP* 3.1 16.3 + - - +
487A SER 3.3 0.2 - - - -
488A LEU* 1.3 77.4 - - - +
490A GLU* 1.3 65.2 - - - +
491A SER 3.3 0.7 + - - -
493A GLN* 3.3 62.7 + - + +
496A LEU* 3.9 26.0 - - + -
497A LYS* 3.7 22.0 - - + -
532A THR* 3.5 26.9 - - - -
535A GLN* 3.3 33.2 + - + +
536A ALA* 3.7 23.3 - - - -
539A ALA* 6.1 2.2 - - - +
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Residues in contact with GLU 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASP 4.4 1.8 + - - -
487A SER 4.8 3.3 + - - +
488A LEU 3.5 0.2 - - - -
489A TRP* 1.3 81.7 - - - +
491A SER* 1.3 60.1 + - - +
493A GLN* 5.0 6.3 + - - +
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Residues in contact with SER 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A SER 5.4 0.9 + - - -
488A LEU* 3.2 17.5 + - - +
489A TRP 3.2 0.6 - - - -
490A GLU* 1.3 79.1 - - - +
492A SER* 1.3 84.6 + - - +
493A GLN 3.8 1.3 - - - -
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Residues in contact with SER 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A LEU* 2.8 27.1 + - - +
491A SER* 1.3 103.1 + - - +
493A GLN* 1.3 58.6 + - - +
494A GLU* 3.4 2.5 - - - -
495A LEU* 3.4 18.2 + - - +
496A LEU* 2.9 39.4 + - - +
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Residues in contact with GLN 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A TRP* 3.3 60.3 + - + +
490A GLU* 4.9 4.8 - - - +
491A SER 3.8 1.0 - - - -
492A SER* 1.3 76.1 - - - +
494A GLU* 1.3 62.2 + - - +
496A LEU* 3.0 6.4 + - - -
497A LYS* 2.8 68.2 + - - +
536A ALA* 5.9 0.2 - - - +
559A THR* 4.2 10.7 - - - +
563A ASP* 4.3 1.8 + - - -
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Residues in contact with GLU 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ASN* 5.0 2.2 + - - -
492A SER 3.4 0.6 - - - -
493A GLN* 1.3 87.5 - - - +
495A LEU* 1.3 62.5 + - - +
497A LYS* 3.4 19.8 + - - +
498A ASP* 3.5 11.6 + - - +
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Residues in contact with LEU 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ASN* 3.5 46.2 - - + +
464A LEU* 3.8 31.0 - - + -
465A ILE* 3.9 19.5 - - + +
468A LEU* 4.6 18.6 - - + -
492A SER* 3.4 19.7 + - - +
493A GLN 3.3 0.6 - - - -
494A GLU* 1.3 77.6 - - - +
496A LEU* 1.3 62.1 + - + +
497A LYS 3.2 0.2 - - - -
498A ASP* 3.1 23.2 + - - +
502A MET* 4.0 6.6 - - - +
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A ILE* 6.3 1.1 - - + -
468A LEU* 3.6 31.0 - - + -
485A VAL* 4.0 22.0 - - + +
488A LEU* 3.8 34.3 - - + +
489A TRP* 3.9 22.4 - - + -
492A SER* 2.9 24.7 + - - +
493A GLN 3.4 3.8 - - - +
495A LEU* 1.3 78.8 - - + +
497A LYS* 1.3 59.4 + - - +
498A ASP 3.5 0.4 - - - -
502A MET* 3.5 12.4 - - + +
528A LEU* 6.5 1.1 - - + -
532A THR* 3.1 39.3 + - + +
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Residues in contact with LYS 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489A TRP* 3.7 26.0 - - + -
493A GLN* 2.8 50.5 + - - +
494A GLU* 3.4 15.8 + - - +
495A LEU 3.2 0.4 - - - -
496A LEU* 1.3 77.9 - - - +
498A ASP* 1.3 59.1 + - - +
499A TRP* 2.9 35.8 + - + -
536A ALA* 3.9 5.6 - - + -
559A THR* 3.4 9.7 - - - +
563A ASP* 2.7 44.3 + - - +
566A LYS* 3.3 18.8 + - + +
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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