Contacts of the helix formed by residues 498 - 508 (chain B) 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 ASP 498 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460B PRO* 4.7 7.6 - - - +
461B ASN* 2.9 32.7 + - + +
465B ILE* 5.6 1.2 - - + +
494B GLU 3.7 8.1 + - - +
495B LEU* 3.2 16.6 + - + +
496B LEU 3.5 0.8 - - - -
497B LYS* 1.3 70.7 - - - +
499B TRP* 1.3 60.7 + - - +
500B GLU* 3.8 8.5 + - - +
501B CYS* 2.8 47.4 + - + +
502B MET* 3.2 18.3 + - - +
566B LYS* 5.2 2.0 - - - +
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Residues in contact with TRP 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B LEU 3.7 4.2 + - - -
497B LYS* 2.7 48.4 + - + -
498B ASP* 1.3 71.2 - - - +
500B GLU* 1.3 53.7 + - - +
502B MET* 3.0 20.7 + - + +
503B THR* 2.7 38.6 + - - +
529B MET* 4.3 0.9 - - + -
532B THR* 3.1 27.5 + - - -
533B ILE* 3.9 18.8 - - + +
536B ALA* 3.7 32.8 - - + -
563B ASP* 4.0 8.5 - - + -
566B LYS* 3.8 30.1 - - + +
567B LEU* 3.5 33.0 - - + -
570B HIS* 4.0 9.0 - - + -
571B PHE* 3.5 33.9 - + + -
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Residues in contact with GLU 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B ASP* 3.8 7.4 - - - +
499B TRP* 1.3 76.6 - - - +
501B CYS* 1.3 63.2 + - - +
503B THR* 3.1 8.6 + - - +
504B GLU* 2.9 52.6 + - + +
566B LYS* 4.9 16.9 + - - +
570B HIS* 3.8 24.1 + - + +
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Residues in contact with CYS 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B PRO* 5.6 5.2 - - + -
461B ASN* 4.0 7.9 - - + +
462B GLY* 3.7 34.3 - - - -
465B ILE* 4.0 15.0 - - + -
498B ASP* 2.8 39.3 + - + +
500B GLU* 1.3 74.6 - - - +
502B MET* 1.4 51.8 + - - +
504B GLU* 3.2 14.8 + - - +
505B LEU* 2.8 41.0 + - - +
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Residues in contact with MET 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ILE* 4.3 18.6 - - + -
495B LEU 3.8 8.3 - - - +
496B LEU* 3.0 37.0 - - + +
498B ASP 3.2 18.2 + - - +
499B TRP* 3.0 17.8 + - + +
501B CYS* 1.4 69.5 - - - +
503B THR* 1.3 65.0 + - - +
505B LEU* 3.4 9.6 + - - +
506B LEU* 3.1 29.2 + - - +
525B LEU* 4.0 22.2 - - + +
528B LEU* 5.3 0.7 - - - -
529B MET* 3.7 44.0 - - - -
532B THR* 4.2 5.6 - - + +
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Residues in contact with THR 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499B TRP 2.7 15.1 + - - +
500B GLU 3.1 12.5 + - - -
502B MET* 1.3 66.6 - - - +
504B GLU* 1.3 53.1 + - - +
506B LEU* 2.7 28.0 + - - +
507B LEU* 2.8 37.0 + - - +
529B MET* 4.2 3.8 - - - -
570B HIS* 2.6 37.4 + - + +
571B PHE* 3.6 26.0 - - + -
574B THR* 4.2 6.1 - - - +
578B LEU* 4.1 15.9 - - + -
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Residues in contact with GLU 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B PRO* 5.4 7.4 - - - +
500B GLU* 2.9 43.1 + - + +
501B CYS* 3.2 15.4 - - - +
503B THR* 1.3 77.1 + - - +
505B LEU* 1.3 67.4 + - + +
506B LEU 3.1 1.0 + - - -
507B LEU* 5.1 1.5 - - - +
508B GLU* 3.3 49.7 + - - +
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Residues in contact with LEU 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462B GLY* 3.7 29.2 - - - +
465B ILE* 3.8 27.6 - - + -
466B ARG* 4.0 34.3 - - + +
501B CYS* 2.8 27.5 + - - +
502B MET* 3.7 7.0 - - - +
503B THR 3.3 0.4 - - - -
504B GLU* 1.3 76.2 - - + +
506B LEU* 1.3 59.2 + - - +
508B GLU 4.6 7.0 + - - +
517B MET* 3.9 23.1 - - - +
525B LEU* 3.9 13.7 - - + -
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Residues in contact with LEU 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B MET 3.1 18.7 + - - +
503B THR* 2.7 13.4 + - - +
505B LEU* 1.3 73.3 - - - +
507B LEU* 1.3 59.3 + - - +
508B GLU 3.6 1.5 + - - +
517B MET* 5.4 0.4 - - - -
522B GLU* 4.1 14.7 - - + +
525B LEU* 3.6 27.6 - - + -
526B ILE* 3.8 24.9 - - + -
529B MET* 3.4 36.6 - - + -
578B LEU* 3.9 18.8 - - + -
581B LYS* 3.4 14.4 + - - +
582B TYR* 2.6 36.2 + - + +
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Residues in contact with LEU 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756A SER* 4.8 19.4 - - - +
503B THR* 2.8 35.6 + - - +
504B GLU* 5.1 0.9 - - - +
506B LEU* 1.3 74.2 - - - +
508B GLU* 1.3 66.0 + - + +
509B GLU* 5.2 1.2 - - - +
574B THR* 4.6 12.3 - - + +
577B MET* 3.7 56.5 - - + +
578B LEU* 3.8 15.3 - - + +
581B LYS* 4.1 24.6 - - + +
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Residues in contact with GLU 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A SER* 5.9 5.8 - - - -
504B GLU* 3.3 40.3 + - - +
505B LEU 4.6 6.6 - - - +
506B LEU 3.6 2.4 - - - +
507B LEU* 1.3 86.7 - - + +
509B GLU* 1.3 79.8 + - - +
581B LYS* 5.5 3.9 + - - -
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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