Contacts of the helix formed by residues 534 - 539 (chain A) in PDB entry 5IJ7
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 534 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A CYS* 3.8 0.2 - - - -
525A HIS* 3.3 6.7 - - + +
529A PRO 4.7 0.8 + - - +
530A CYS* 3.6 20.0 - - - -
531A ASP* 2.8 17.0 + - - +
533A SER* 1.4 77.3 + - - +
535A PRO* 1.4 69.1 - - - +
536A CYS* 3.6 22.7 - - - -
537A VAL* 3.2 6.1 + - + -
538A ILE* 2.8 29.9 + - - +
9004A ZN 2.1 38.1 - - - -
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Residues in contact with PRO 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A GLN* 5.6 4.3 - - + +
523A CYS* 4.2 12.1 - - + -
525A HIS* 4.2 13.5 - - + -
533A SER 3.6 6.0 - - - +
534A CYS* 1.4 89.0 - - - +
536A CYS* 1.4 51.2 + - - +
538A ILE* 3.4 11.2 + - + +
539A ALA* 2.8 37.7 + - - +
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Residues in contact with CYS 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A TYR* 4.1 11.4 - - - -
521A GLN 3.8 15.7 - - - -
523A CYS* 3.6 10.8 - - - -
534A CYS* 3.3 6.4 - - - -
535A PRO* 1.4 74.0 - - - +
537A VAL* 1.3 59.2 + - - +
539A ALA* 3.5 2.8 + - - -
540A GLN 3.2 3.6 + - - -
541A ASN* 2.8 48.8 + - + +
542A PHE 4.4 2.7 - - - +
543A CYS* 3.8 0.9 - - - -
547A CYS* 3.7 6.5 - - - -
555A ASN* 3.8 7.4 - - - +
9003A ZN 2.3 37.5 - - - -
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Residues in contact with VAL 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A CYS 3.6 18.2 - - - +
531A ASP* 3.2 33.2 - - - +
532A ASN* 4.2 10.5 - - - +
534A CYS* 3.2 11.2 + - + +
536A CYS* 1.3 74.7 - - - +
538A ILE* 1.4 62.1 + - - +
540A GLN* 3.1 16.5 + - - +
541A ASN 4.5 1.1 - - - -
555A ASN* 3.6 28.3 - - + +
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Residues in contact with ILE 538 (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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518A TYR* 5.3 3.1 - - - -
532A ASN 3.3 19.1 - - - +
533A SER* 3.4 23.8 - - - +
534A CYS 2.8 24.9 + - - +
535A PRO* 3.6 9.0 - - + +
537A VAL* 1.4 68.2 - - - +
539A ALA* 1.4 55.6 + - + +
540A GLN* 2.9 17.2 + - - +
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Residues in contact with ALA 539 (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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517A VAL* 5.7 0.2 - - - -
518A TYR* 3.5 40.3 + - + +
519A ASN 5.0 2.5 - - - +
535A PRO 2.8 21.2 + - - +
536A CYS* 3.5 3.8 + - - +
538A ILE* 1.4 70.8 - - - +
540A GLN* 1.4 67.0 + - - +
541A ASN* 3.4 27.3 + - + +
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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
------------------------------------------------------------
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