Contacts of the helix formed by residues 496 - 505 (chain A) in PDB entry 3SXS
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 CYS 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PP2 3.7 18.9 - - + +
494A ASN 3.8 0.9 + - - +
495A GLY* 1.3 72.4 - - - -
497A LEU* 1.3 69.8 + - - +
498A LEU* 3.6 11.7 - - - -
499A ASN* 3.4 30.2 + - - +
500A TYR* 3.0 21.4 + - - +
539A ALA 3.7 0.9 - - - -
540A ARG* 3.5 35.7 - - - -
542A CYS 3.5 6.1 - - - -
543A LEU* 3.9 4.0 - - + -
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Residues in contact with LEU 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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495A GLY 3.6 1.8 + - - -
496A CYS* 1.3 72.7 - - - +
498A LEU* 1.3 57.1 + - - +
500A TYR* 3.2 1.2 + - + -
501A LEU* 2.8 46.2 + - + +
516A MET* 3.9 28.0 - - + -
520A VAL* 5.0 4.3 - - + -
539A ALA* 3.5 22.2 - - + +
542A CYS* 2.8 37.4 + - + +
544A VAL* 3.6 27.1 - - + -
550A VAL* 4.1 14.8 - - + -
601A LEU* 5.0 2.0 - - + -
605A VAL* 4.1 17.5 - - + -
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Residues in contact with LEU 498 (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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496A CYS* 3.3 8.0 - - - -
497A LEU* 1.3 79.6 - - - +
499A ASN* 1.3 66.8 + - - +
501A LEU* 3.3 4.7 + - - +
502A ARG* 3.1 55.6 + - - +
539A ALA* 3.4 23.3 + - + -
540A ARG* 4.4 18.4 - - + +
604A GLU* 3.8 21.3 - - - +
609A GLY* 3.7 33.7 - - - +
610A LYS 5.3 0.4 - - - +
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Residues in contact with ASN 499 (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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496A CYS* 3.4 32.3 + - + +
497A LEU 3.3 0.4 - - - -
498A LEU* 1.3 78.7 - - - +
500A TYR* 1.4 58.2 + - - +
502A ARG* 3.3 8.6 + - - +
503A SER* 2.9 35.8 + - - +
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Residues in contact with TYR 500 (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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494A ASN* 3.8 44.6 + - + +
496A CYS 3.0 14.3 + - - +
497A LEU* 3.2 8.9 + - + +
499A ASN* 1.4 77.6 - - - +
501A LEU* 1.4 59.9 + - - +
504A HIS* 2.8 71.1 + + + +
505A GLY 3.5 0.2 + - - -
508A LEU* 4.3 21.7 - - + +
516A MET* 4.2 18.6 - - + -
544A VAL* 4.1 15.0 - - + -
548A LEU* 3.2 32.4 - - + +
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 2.8 43.6 + - + +
498A LEU* 3.3 7.8 + - - +
500A TYR* 1.4 73.5 - - - +
502A ARG* 1.3 57.9 + - - +
505A GLY* 2.9 28.8 + - - +
508A LEU* 4.3 6.7 - - + -
513A LEU* 4.2 9.4 - - + -
516A MET* 4.2 24.2 - - + -
539A ALA* 4.4 5.4 - - + -
604A GLU 4.1 7.4 - - - +
605A VAL* 3.8 40.2 - - + +
608A LEU* 3.5 26.2 - - + +
609A GLY* 3.9 6.3 - - - +
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Residues in contact with ARG 502 (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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498A LEU* 3.1 47.2 + - - +
499A ASN* 3.7 7.6 - - - +
501A LEU* 1.3 78.6 - - - +
503A SER* 1.3 59.4 + - - +
505A GLY 5.1 0.2 + - - -
608A LEU 3.9 14.4 - - - +
609A GLY* 2.8 25.9 + - - +
610A LYS* 4.5 0.4 - - - +
611A MET* 4.4 22.2 - - - +
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Residues in contact with SER 503 (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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499A ASN* 2.9 19.4 + - - +
502A ARG* 1.3 77.1 - - - +
504A HIS* 1.3 86.8 + - - +
505A GLY 3.8 0.4 - - - -
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Residues in contact with HIS 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ASN* 5.9 0.2 + - - -
500A TYR* 2.8 60.4 + + + +
503A SER* 1.3 91.9 + - - +
505A GLY* 1.3 66.0 + - - +
506A LYS 3.3 3.1 - - - -
507A GLY* 3.2 16.0 + - - -
508A LEU* 3.8 10.6 - - - +
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Residues in contact with GLY 505 (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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500A TYR 3.5 1.6 + - - -
501A LEU* 2.9 24.6 + - - -
502A ARG 4.8 0.2 - - - -
503A SER 3.8 0.6 - - - -
504A HIS* 1.3 76.9 - - - +
506A LYS* 1.4 62.2 + - - +
508A LEU* 3.0 30.1 + - - +
608A LEU* 3.6 30.9 - - - +
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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