Contacts of the helix formed by residues 533 - 543 (chain E) in PDB entry 2HDX
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 533 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605C ARG* 6.0 0.4 - - - +
531E MET 3.9 1.8 + - - -
532E LEU* 1.3 78.2 - - - +
534E ARG* 1.3 64.6 + - - +
535E LEU* 3.7 6.5 + - - +
536E LYS* 2.9 47.7 + - - +
537E ALA* 3.0 26.7 + - - +
555E ARG* 4.3 0.4 - - - -
558E GLU* 3.9 21.3 + - - -
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Residues in contact with ARG 534 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532E LEU 3.9 0.4 + - - -
533E SER* 1.3 73.0 - - - +
535E LEU* 1.3 59.1 + - - +
537E ALA* 3.4 1.7 + - - +
538E ALA* 2.8 31.1 + - + +
555E ARG* 3.7 14.9 - - - +
558E GLU* 4.9 5.6 + - - +
576E HIS* 3.4 38.7 + - + +
812K ASP* 2.7 49.4 + - - +
813K PTR 2.6 64.1 + - - +
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Residues in contact with LEU 535 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533E SER* 3.3 6.1 + - - +
534E ARG* 1.3 78.1 - - - +
536E LYS* 1.3 66.4 + - + +
538E ALA* 3.1 8.7 + - + +
539E GLN* 2.9 58.5 + - + +
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Residues in contact with LYS 536 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602C GLU 5.8 0.2 + - - -
605C ARG* 5.4 11.5 - - - +
606C VAL* 4.1 23.0 - - - +
532E LEU* 3.7 24.2 - - + -
533E SER* 2.9 28.2 + - - +
535E LEU* 1.3 81.7 - - + +
537E ALA* 1.3 56.9 + - - +
539E GLN* 3.3 18.9 + - - +
540E LEU* 2.9 37.2 + - + +
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Residues in contact with ALA 537 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532E LEU* 3.8 17.4 - - + +
533E SER 3.0 20.2 + - - +
534E ARG 3.6 4.0 - - - +
536E LYS* 1.3 73.9 - - - +
538E ALA* 1.3 66.1 + - - +
540E LEU* 3.3 2.3 + - - +
541E VAL* 3.2 29.3 + - - +
553E LEU* 4.2 12.8 - - + -
555E ARG* 3.7 25.1 - - - +
567E THR* 4.2 7.4 - - - +
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Residues in contact with ALA 538 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534E ARG* 2.8 19.0 + - + +
535E LEU* 3.3 10.1 - - + +
537E ALA* 1.3 79.3 - - - +
539E GLN* 1.3 63.2 + - + +
541E VAL* 3.4 3.3 - - - +
542E LEU* 3.0 34.3 + - + +
567E THR* 4.5 2.9 - - - -
574E ALA* 3.8 25.1 - - + -
576E HIS* 4.2 7.9 - - + +
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Residues in contact with GLN 539 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535E LEU* 2.9 42.7 + - + +
536E LYS* 3.5 22.6 - - - +
537E ALA 3.3 0.2 - - - -
538E ALA* 1.3 77.0 - - + +
540E LEU* 1.3 64.3 + - + +
542E LEU* 3.2 8.2 + - - +
543E GLU* 3.2 22.2 + - - +
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Residues in contact with LEU 540 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529E HIS* 4.4 7.2 - - + +
532E LEU* 3.9 28.7 - - + -
536E LYS* 2.9 22.4 + - + +
537E ALA 3.7 4.9 - - - +
538E ALA 3.3 0.4 - - - -
539E GLN* 1.3 81.0 - - + +
541E VAL* 1.3 60.0 + - - +
542E LEU 3.4 0.7 + - - -
543E GLU* 3.5 17.8 + - - +
551E VAL* 5.1 0.5 - - - +
553E LEU* 4.2 5.2 - - + -
625E VAL* 3.6 40.6 - - + +
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Residues in contact with VAL 541 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537E ALA 3.2 12.3 + - - +
538E ALA* 3.4 12.6 - - - +
540E LEU* 1.3 75.5 - - - +
542E LEU* 1.3 56.4 + - + +
543E GLU 3.3 1.1 - - - -
548E SER* 3.8 7.8 - - - -
551E VAL* 4.1 20.4 - - + +
552E PHE 4.2 2.5 - - - -
553E LEU* 3.9 17.5 - - + -
567E THR* 3.6 36.8 - - + +
568E PHE 4.1 12.3 - - - +
569E ASN* 2.7 31.4 + - - +
574E ALA* 4.2 8.3 - - + -
625E VAL* 4.0 12.6 - - + -
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Residues in contact with LEU 542 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538E ALA* 3.0 30.1 + - + +
539E GLN* 3.7 7.9 - - - +
540E LEU 3.2 0.6 - - - -
541E VAL* 1.3 76.0 - - - +
543E GLU* 1.3 66.5 + - - +
544E GLY 3.0 0.2 + - - -
545E GLY* 2.9 21.9 + - - -
569E ASN* 3.7 8.3 - - - +
572E GLY* 3.2 31.4 - - - +
573E LYS* 3.8 1.3 - - - -
574E ALA* 3.5 34.5 - - + +
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Residues in contact with GLU 543 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521B PRO* 4.4 22.9 - - + +
539E GLN 3.2 10.6 + - - +
540E LEU* 3.5 18.1 - - + +
541E VAL 3.3 1.6 - - - +
542E LEU* 1.3 76.5 - - - +
544E GLY* 1.3 57.0 + - - +
548E SER* 2.8 15.8 + - - -
551E VAL* 6.0 0.7 - - - +
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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