Contacts of the helix formed by residues 533 - 543 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602B GLU* 3.9 23.5 + - - -
605B ARG* 6.0 1.6 - - - +
531F MET 3.9 1.8 + - - -
532F LEU* 1.3 81.1 - - - +
534F ARG* 1.3 63.5 + - - +
535F LEU* 3.9 6.9 + - - +
536F LYS* 3.3 33.3 + - - +
537F ALA* 3.0 22.7 + - - +
555F ARG* 4.5 0.2 - - - -
558F GLU* 4.1 15.7 - - - -
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Residues in contact with ARG 534 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532F LEU 3.8 1.0 + - - -
533F SER* 1.3 72.2 - - - +
535F LEU* 1.3 71.1 + - + +
537F ALA* 3.2 4.7 + - - +
538F ALA* 2.8 28.3 + - + +
555F ARG* 3.7 20.3 - - - +
558F GLU* 4.6 4.6 + - - +
576F HIS* 3.2 33.9 + - - +
812L ASP* 2.9 46.7 + - - +
813L PTR 2.7 62.6 + - - +
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Residues in contact with LEU 535 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533F SER* 3.3 6.1 + - - +
534F ARG* 1.3 91.9 - - + +
536F LYS* 1.3 58.3 + - + +
538F ALA* 3.2 10.4 + - + +
539F GLN* 3.0 36.1 + - + +
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Residues in contact with LYS 536 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602B GLU* 5.0 7.4 + - - -
605B ARG* 4.4 11.8 - - + +
606B VAL* 3.0 34.2 - - - +
532F LEU* 4.0 23.3 - - + -
533F SER* 3.3 23.1 + - - +
535F LEU* 1.3 75.2 - - + +
537F ALA* 1.3 66.2 + - - +
539F GLN* 3.1 18.6 + - - +
540F LEU* 2.9 31.6 + - + +
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Residues in contact with ALA 537 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532F LEU* 3.7 16.5 - - + +
533F SER 3.0 13.9 + - - +
534F ARG 3.3 9.0 - - - +
536F LYS* 1.3 76.2 - - - +
538F ALA* 1.3 62.8 + - - +
540F LEU* 3.4 2.5 + - - +
541F VAL* 3.2 29.1 + - - +
553F LEU* 4.1 9.0 - - + -
555F ARG* 3.5 27.6 - - - +
567F THR* 3.9 12.3 - - + +
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Residues in contact with ALA 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534F ARG* 2.8 13.8 + - + +
535F LEU* 3.4 15.0 - - + +
536F LYS 3.1 0.2 - - - -
537F ALA* 1.3 77.5 - - - +
539F GLN* 1.3 63.1 + - + +
541F VAL* 3.4 3.4 + - - +
542F LEU* 3.1 33.5 + - + +
567F THR* 4.2 2.6 - - - +
574F ALA* 3.7 25.8 - - + -
576F HIS* 4.3 8.3 - - + +
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Residues in contact with GLN 539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535F LEU* 3.0 23.8 + - + +
536F LYS* 3.5 20.0 - - - +
538F ALA* 1.3 75.0 - - + +
540F LEU* 1.3 64.4 + - + +
542F LEU* 3.2 16.5 + - - +
543F GLU* 3.2 13.3 + - - +
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Residues in contact with LEU 540 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529F HIS* 4.3 7.6 - - + +
532F LEU* 3.7 33.2 - - + -
536F LYS* 2.9 17.7 + - + +
537F ALA 3.7 5.2 - - - +
538F ALA 3.3 0.2 - - - -
539F GLN* 1.3 79.4 - - + +
541F VAL* 1.3 61.2 + - - +
542F LEU 3.4 0.5 + - - -
543F GLU* 3.6 16.4 + - - +
551F VAL* 4.9 0.7 - - - +
553F LEU* 4.1 10.1 - - + -
625F VAL* 3.7 34.1 - - + +
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Residues in contact with VAL 541 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537F ALA 3.2 12.5 + - - +
538F ALA* 3.5 11.7 - - - +
540F LEU* 1.3 75.7 - - - +
542F LEU* 1.3 62.0 + - + +
543F GLU 3.3 1.3 - - - -
548F SER* 3.9 8.0 - - - -
551F VAL* 3.9 18.4 - - + +
552F PHE* 4.0 9.6 - - - -
553F LEU* 4.1 8.5 - - + -
567F THR* 3.7 29.8 - - + +
568F PHE 3.8 20.9 - - - +
569F ASN* 2.9 25.5 + - - +
574F ALA* 4.4 6.7 - - + -
625F VAL* 3.9 16.2 - - + -
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Residues in contact with LEU 542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538F ALA* 3.1 26.8 + - + +
539F GLN* 3.7 7.6 - - - +
540F LEU 3.2 0.4 - - - -
541F VAL* 1.3 77.9 - - + +
543F GLU* 1.3 65.5 + - - +
544F GLY 3.1 0.3 + - - -
545F GLY* 2.9 21.2 + - - -
569F ASN* 3.7 11.9 - - - +
572F GLY 3.1 36.1 - - - +
573F LYS* 3.6 3.1 - - - -
574F ALA* 3.6 29.6 - - + +
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Residues in contact with GLU 543 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521D PRO* 4.8 10.7 - - + +
523D SER* 5.5 0.5 - - - -
539F GLN 3.2 9.7 + - - +
540F LEU* 3.6 15.9 - - - +
541F VAL 3.3 2.7 - - - +
542F LEU* 1.3 76.7 - - - +
544F GLY* 1.3 50.8 + - - +
548F SER* 2.7 24.1 + - - -
551F VAL* 5.5 0.9 - - - +
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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