Contacts of the helix formed by residues 353 - 365 (chain A) in PDB entry 5XJY
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 PRO 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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352A THR* 1.3 94.8 - - - +
354A TYR* 1.3 62.3 + - + +
356A ASN* 3.3 8.1 + - + +
357A ASP* 2.9 28.6 + - - +
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Residues in contact with TYR 354 (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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352A THR 3.4 1.7 - - - +
353A PRO* 1.3 80.1 - - + +
355A CYS* 1.3 60.7 + - - +
357A ASP* 4.3 12.1 - - + -
358A LEU* 2.9 63.2 + - + +
497A THR* 5.9 2.9 - - + +
500A ARG* 3.3 56.5 - - + +
501A PHE* 5.9 1.3 - - + -
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Residues in contact with CYS 355 (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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352A THR* 3.3 26.0 - - + +
353A PRO 3.1 0.4 - - - -
354A TYR* 1.3 82.0 - - - +
356A ASN* 1.3 62.1 + - - +
358A LEU* 3.2 9.9 + - - +
359A MET* 2.9 33.2 + - - +
504A CYS* 2.0 54.1 - - - -
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Residues in contact with ASN 356 (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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352A THR* 3.0 25.9 + - - +
353A PRO* 3.3 7.6 + - + +
355A CYS* 1.3 76.9 - - - +
357A ASP* 1.3 64.8 + - - +
359A MET* 3.2 23.0 - - + +
360A LYS* 3.1 23.2 + - - +
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Residues in contact with ASP 357 (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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353A PRO 2.9 18.6 + - - +
354A TYR* 3.9 13.6 - - + +
356A ASN* 1.3 77.7 - - - +
358A LEU* 1.3 56.0 - - - +
360A LYS* 3.3 19.6 + - - +
361A ASN* 2.8 48.7 + - - +
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Residues in contact with LEU 358 (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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354A TYR* 2.9 56.7 + - + +
355A CYS* 3.5 10.3 - - - +
356A ASN 3.2 0.4 - - - -
357A ASP* 1.3 77.9 - - - +
359A MET* 1.3 60.7 + - + +
361A ASN* 3.1 8.7 + - + +
362A LEU* 2.8 56.6 + - + +
372A TRP* 5.7 0.9 - - + -
501A PHE* 4.1 31.2 - - + -
504A CYS* 6.0 2.7 - - + -
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Residues in contact with MET 359 (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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355A CYS* 2.9 18.9 + - - +
356A ASN* 3.2 35.0 - - - +
358A LEU* 1.3 76.7 - - + +
360A LYS* 1.3 65.2 + - + +
362A LEU* 4.3 0.7 - - - +
363A GLU* 3.0 23.9 + - - +
372A TRP* 3.5 32.3 + - + +
376A LYS* 3.4 29.6 - - - +
380A VAL* 5.4 5.8 - - + -
530A ARG* 5.1 13.9 - - + -
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Residues in contact with LYS 360 (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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356A ASN 3.1 14.0 + - - +
357A ASP* 3.5 21.6 + - - +
359A MET* 1.3 79.3 - - + +
361A ASN* 1.3 69.1 + - - +
363A GLU* 3.4 7.6 + - - +
364A SER* 2.9 31.2 + - - -
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Residues in contact with ASN 361 (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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357A ASP* 2.8 41.4 + - - +
358A LEU* 3.6 8.3 - - + +
360A LYS* 1.3 86.8 - - - +
362A LEU* 1.3 60.7 + - + +
364A SER* 3.4 10.6 + - - -
365A SER* 2.9 31.0 + - - -
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Residues in contact with LEU 362 (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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301A TYR* 4.3 18.2 - - - +
358A LEU* 2.8 42.8 + - + +
359A MET 4.0 1.1 - - - +
360A LYS 3.3 0.4 - - - -
361A ASN* 1.3 76.1 - - + +
363A GLU* 1.3 64.3 + - - +
365A SER* 4.5 3.1 - - - +
368A SER* 3.0 35.3 + - - +
372A TRP* 3.5 39.5 - - + +
501A PHE* 4.9 9.6 - - + -
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Residues in contact with GLU 363 (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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359A MET 3.0 17.3 + - - +
360A LYS* 3.9 6.0 - - - +
362A LEU* 1.3 78.0 - - - +
364A SER* 1.3 64.6 + - - +
365A SER 4.4 2.8 - - - +
368A SER 5.5 0.2 - - - -
369A ARG* 5.2 13.7 + - - +
372A TRP* 3.9 28.2 - - + +
373A LYS* 5.1 10.5 + - - +
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Residues in contact with SER 364 (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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360A LYS* 2.9 22.3 + - - -
361A ASN* 3.1 16.0 + - - -
363A GLU* 1.3 81.6 + - - +
365A SER* 1.3 63.6 + - - +
366A PRO* 3.3 10.6 - - - +
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Residues in contact with SER 365 (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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301A TYR* 4.5 12.7 + - - -
361A ASN 2.9 14.9 + - - -
362A LEU* 3.8 6.8 + - - +
363A GLU 3.5 3.4 - - - +
364A SER* 1.3 75.7 - - - +
366A PRO* 1.3 73.5 + - - +
368A SER* 2.3 39.3 + - - -
369A ARG* 4.3 2.4 + - - +
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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