Contacts of the helix formed by residues 534 - 539 (chain J) in PDB entry 5LS6
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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523J CYS* 3.7 7.2 - - - -
525J HIS* 3.3 13.7 - - - +
530J CYS* 3.5 17.3 - - + -
531J ASP* 2.7 21.4 + - - +
533J SER* 1.3 71.6 - - - +
535J PRO* 1.4 71.4 - - - +
536J CYS* 3.0 15.7 + - - -
537J VAL* 3.0 8.6 + - + +
538J ILE* 2.9 26.3 + - - +
804J ZN 2.1 38.8 - - - -
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Residues in contact with PRO 535 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521J GLN* 5.8 9.0 - - + +
523J CYS* 4.2 15.9 - - + -
524J ASP 5.9 0.2 - - - +
525J HIS* 4.3 9.9 - - + -
533J SER 3.5 4.7 - - - +
534J CYS* 1.4 89.2 - - - +
536J CYS* 1.3 56.3 + - - +
538J ILE* 3.7 13.6 - - + +
539J ALA* 3.0 29.5 + - - +
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Residues in contact with CYS 536 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520J TYR* 4.6 2.7 - - - -
521J GLN 4.2 12.3 - - - -
523J CYS* 3.5 12.8 - - - -
534J CYS* 3.0 6.6 + - - -
535J PRO* 1.3 76.4 - - - +
537J VAL* 1.3 58.5 + - - +
539J ALA* 3.2 5.3 + - - +
540J GLN 2.9 7.4 + - - -
541J ASN* 2.9 35.1 + - + +
542J PHE 4.5 4.7 - - - +
543J CYS* 3.8 15.9 - - - +
547J CYS* 4.1 2.5 - - - -
555J ASN* 4.0 4.7 - - - +
805J ZN 2.1 40.2 - - - -
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Residues in contact with VAL 537 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530J CYS* 4.4 10.1 - - + +
531J ASP 2.9 32.5 - - - +
532J SER* 3.7 11.9 - - - +
534J CYS* 3.0 15.3 + - + +
536J CYS* 1.3 77.5 - - + +
538J ILE* 1.3 68.4 + - - +
540J GLN* 3.0 17.6 + - - +
541J ASN 4.5 2.5 - - - -
555J ASN* 3.4 38.6 - - + +
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Residues in contact with ILE 538 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532J SER 3.2 23.1 - - - +
533J SER* 3.5 16.8 - - - +
534J CYS 2.9 21.5 + - - +
535J PRO* 3.7 11.0 - - + +
537J VAL* 1.3 78.9 - - - +
539J ALA* 1.3 60.0 + - + +
540J GLN* 3.4 8.3 + - - +
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Residues in contact with ALA 539 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516J HIS 5.3 0.3 - - - +
517J VAL* 5.8 0.2 - - - -
518J TYR* 3.9 46.3 + - + +
519J ASN 5.1 2.7 - - - +
535J PRO 3.0 20.0 + - - +
536J CYS* 3.8 3.4 - - - +
537J VAL 3.1 0.2 - - - -
538J ILE* 1.3 75.9 - - + +
540J GLN* 1.3 68.5 + - - +
541J ASN* 3.0 19.1 + - - +
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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
------------------------------------------------------------
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