Contacts of the helix formed by residues 683 - 687 (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 LYS 683 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J TRP* 4.7 6.8 - - + -
611J LYS* 6.2 1.7 - - - +
613J HIS* 4.2 19.0 + - - -
614J LEU* 3.4 36.7 + - + +
616J LEU* 5.5 5.2 - - + +
626J ILE* 3.1 26.7 - - + +
682J ASN* 1.3 74.9 - - - +
684J ILE* 1.3 59.1 + - - +
685J ARG 2.7 7.8 + - - -
686J PHE* 3.0 22.3 + - + -
568L SER* 3.8 36.7 + - - +
586L GLU* 3.6 27.3 + - - -
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Residues in contact with ILE 684 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614J LEU* 3.8 23.2 - - + +
626J ILE* 4.0 4.9 - - + -
638J ILE* 4.9 3.1 - - + -
639J SER* 4.1 10.0 + - - +
640J GLU 3.4 26.7 - - - +
641J TYR* 3.9 24.0 - - + -
682J ASN* 3.1 8.0 + - - +
683J LYS* 1.3 74.8 - - - +
685J ARG* 1.3 63.9 + - - +
686J PHE 3.1 1.5 + - - -
687J ALA* 3.2 31.8 + - + +
710J ILE* 4.3 27.8 - - + -
722J LEU* 3.8 26.5 - - + -
724J PHE* 4.7 1.7 - - + -
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Residues in contact with ARG 685 (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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111J TYR 4.1 7.9 + - - -
113J TRP* 3.2 52.3 - - - +
641J TYR* 3.8 21.1 + - + +
665J PHE* 4.3 8.1 - - + +
677J ALA* 2.6 57.8 + - + +
678J THR* 3.1 14.1 + - - +
682J ASN* 2.9 34.1 + - - +
683J LYS 2.7 4.9 + - - -
684J ILE* 1.3 76.2 - - - +
686J PHE* 1.3 74.6 + - + +
687J ALA 3.3 5.9 + - - +
726J TYR* 4.4 0.7 + - - -
809J 74D 3.1 55.4 + - - +
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Residues in contact with PHE 686 (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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110J MET* 3.4 41.5 - - + -
113J TRP* 3.7 27.6 - + - -
616J LEU* 4.0 19.5 - - + -
624J TRP* 3.9 11.2 - - + -
625J GLY* 3.3 25.4 - - - +
626J ILE* 3.6 20.2 - - + -
683J LYS* 3.0 26.2 + - + +
685J ARG* 1.3 92.4 - - + +
687J ALA* 1.3 59.8 + - - +
688J ASN* 3.4 0.3 - - - +
809J 74D 3.2 53.7 - + - +
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Residues in contact with ALA 687 (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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626J ILE* 3.3 10.4 - - + +
684J ILE* 3.2 32.3 + - + +
685J ARG 3.9 2.4 - - - +
686J PHE* 1.3 76.7 - - - +
688J ASN* 1.3 61.0 + - - +
722J LEU* 3.5 25.1 - - + +
723J PHE* 4.5 0.2 - - - -
724J PHE* 4.2 19.1 - - + -
726J TYR* 2.9 21.0 + - - -
809J 74D 3.9 1.3 - - - +
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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