Contacts of the helix formed by residues 531 - 544 (chain C) in PDB entry 2XYN
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 SER 531 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401C GLU* 3.4 16.6 - - - -
468C VAL* 5.9 0.4 - - - -
529C ARG 3.9 0.8 + - - -
530C PRO* 1.3 77.1 - - - +
532C PHE* 1.3 60.4 + - - +
533C ALA* 3.9 11.0 - - - -
534C GLU* 3.3 19.1 + - - +
535C THR* 3.0 28.1 + - - -
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Residues in contact with PHE 532 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C SER* 4.2 2.8 - - - +
397C MET* 3.5 39.7 - - + +
398C GLU* 3.7 5.8 - - - +
401C GLU* 2.8 22.4 + - + +
530C PRO 4.0 0.2 + - - -
531C SER* 1.3 72.5 - - - +
533C ALA* 1.3 55.6 + - - +
535C THR* 3.8 7.1 - - - -
536C HIS* 3.1 30.0 + - - +
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Residues in contact with ALA 533 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C GLU* 4.5 10.5 - - + -
401C GLU* 3.1 15.2 + - - +
531C SER* 3.1 5.8 - - - -
532C PHE* 1.3 73.5 - - - +
534C GLU* 1.3 65.0 + - + +
536C HIS* 3.4 3.7 + - - +
537C GLN* 3.0 23.6 + - - +
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Residues in contact with GLU 534 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C LEU* 5.7 1.1 - - + -
530C PRO* 4.3 9.6 - - + -
531C SER* 3.3 28.6 + - - +
533C ALA* 1.3 77.8 - - + +
535C THR* 1.3 64.1 + - - +
537C GLN* 3.2 8.6 + - - +
538C ALA* 3.0 22.2 + - - +
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Residues in contact with THR 535 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394C SER* 4.5 9.9 - - - -
517C LEU* 4.4 22.4 - - - +
521C CYS* 5.9 5.6 - - - -
530C PRO* 4.9 4.8 - - - +
531C SER 3.0 17.0 + - - -
532C PHE* 3.8 8.7 - - - -
534C GLU* 1.3 76.0 - - - +
536C HIS* 1.3 60.8 + - - +
538C ALA* 3.1 9.5 + - - +
539C PHE* 3.1 22.3 + - - +
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Residues in contact with HIS 536 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C THR* 3.5 13.8 + - - -
394C SER* 3.7 18.5 + - - +
395C SER* 3.4 40.9 + - - -
398C GLU* 4.5 7.9 - - + -
532C PHE 3.1 18.4 + - - +
533C ALA* 3.8 4.3 - - - +
535C THR* 1.3 72.0 - - - +
537C GLN* 1.3 63.6 + - - +
539C PHE* 3.3 1.6 + - - +
540C GLU* 2.9 58.3 + - + +
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Residues in contact with GLN 537 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533C ALA 3.0 14.4 + - - +
534C GLU* 3.2 11.9 + - - +
536C HIS* 1.3 80.9 - - - +
538C ALA* 1.3 62.9 + - - +
540C GLU* 4.0 4.4 - - - +
541C THR* 3.0 29.3 + - - +
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Residues in contact with ALA 538 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C LEU* 4.3 26.0 - - + -
534C GLU 3.0 11.9 + - - +
535C THR 3.1 9.2 + - - +
537C GLN* 1.3 78.9 - - - +
539C PHE* 1.3 56.9 + - - +
541C THR* 3.5 6.2 + - - +
542C MET* 3.0 27.7 + - - +
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Residues in contact with PHE 539 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C LEU* 5.0 3.9 - - - +
390C ALA* 4.9 5.2 - - + -
391C THR* 4.0 30.2 - - - +
394C SER* 4.2 5.6 - - - +
517C LEU* 5.3 4.9 - - + +
535C THR 3.1 14.5 + - - +
536C HIS 4.0 2.7 - - - +
538C ALA* 1.3 75.6 - - - +
540C GLU* 1.3 59.3 + - - +
542C MET* 3.7 6.5 - - - +
543C PHE* 2.8 32.4 + - - +
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Residues in contact with GLU 540 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391C THR* 4.9 7.3 - - - -
536C HIS* 2.9 46.4 + - + +
537C GLN* 4.1 4.5 - - - +
539C PHE* 1.3 76.0 - - - +
541C THR* 1.3 63.8 + - - +
543C PHE* 3.5 8.8 + - + +
544C HIS* 3.5 14.7 + - - +
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Residues in contact with THR 541 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537C GLN 3.0 19.1 + - - -
538C ALA* 3.6 6.3 - - - +
540C GLU* 1.3 73.4 - - - +
542C MET* 1.3 68.1 + - - +
544C HIS* 3.1 23.9 + - - +
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Residues in contact with MET 542 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C LEU* 6.0 5.2 - - + -
513C LYS* 6.3 3.8 - - + -
514C VAL* 5.7 8.5 - - + -
538C ALA 3.0 18.1 + - - +
539C PHE* 3.7 7.4 - - - +
541C THR* 1.3 77.9 - - - +
543C PHE* 1.3 63.4 - - - +
544C HIS 2.8 9.4 + - - +
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Residues in contact with PHE 543 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387C LEU* 5.2 17.5 - - + +
388C TYR* 5.8 2.2 - - - +
391C THR* 5.1 9.9 - - - -
539C PHE 2.8 21.7 + - - +
540C GLU* 3.7 11.0 - - + +
541C THR 3.3 0.2 - - - -
542C MET* 1.3 72.4 - - - +
544C HIS* 1.3 60.2 + - - +
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Residues in contact with HIS 544 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540C GLU 3.5 7.0 + - - +
541C THR* 3.1 19.4 + - + +
542C MET 2.8 9.8 + - - +
543C PHE* 1.3 82.2 - - - +
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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