Contacts of the strand formed by residues 695 - 702 (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 695 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638J ILE* 3.6 27.8 - - - -
693J PRO* 3.5 15.3 - - - +
694J ASN* 1.3 90.6 - - - +
696J TYR* 1.3 62.0 + - - +
710J ILE* 4.1 16.2 - - + -
711J PHE 3.3 11.4 - - - +
713J LYS* 3.8 7.8 - - - +
716J ILE* 4.2 0.7 - - - -
722J LEU* 3.8 27.4 - - - -
723J PHE 3.0 15.1 + - - +
724J PHE* 3.1 20.5 - - + +
725J ASP 4.5 0.5 + - - -
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Residues in contact with TYR 696 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574J TYR* 5.2 1.7 + - - -
635J ASN* 2.9 40.9 + - - +
695J CYS* 1.3 75.4 - - - +
697J ALA* 1.3 73.9 + - - +
698J LYS* 4.1 28.6 + - + -
710J ILE* 3.4 11.4 - - - +
711J PHE* 2.9 61.8 + + + +
712J ALA 3.4 13.0 - - - -
713J LYS* 3.8 31.4 - - + -
724J PHE* 4.6 4.0 - - - -
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Residues in contact with ALA 697 (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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667J PHE* 6.2 2.0 - - + -
696J TYR* 1.3 83.4 - - - +
698J LYS* 1.3 60.3 + - - +
699J VAL* 5.9 1.3 - - + -
708J ILE* 4.3 11.0 - - + -
709J GLY 3.1 6.3 - - - +
710J ILE* 3.5 20.0 - - + -
724J PHE* 5.1 11.9 - - + +
728J TYR* 5.5 16.1 - - + +
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Residues in contact with LYS 698 (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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574J TYR* 3.3 38.9 + - - -
577J VAL* 4.0 24.9 - - + +
696J TYR* 4.1 28.5 + - + -
697J ALA* 1.3 73.1 - - - +
699J VAL* 1.3 60.7 + - - +
700J MET* 3.6 19.9 + - + +
708J ILE* 3.6 1.9 - - - -
709J GLY* 2.6 39.4 + - - -
711J PHE* 3.9 22.4 - - + -
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Residues in contact with VAL 699 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577J VAL* 3.6 15.8 - - - +
668J ASN 4.3 12.3 - - - +
669J LEU* 3.7 40.2 - - + +
697J ALA* 5.9 1.6 - - + -
698J LYS* 1.3 73.5 - - - +
700J MET* 1.3 59.7 + - - +
706J HIS* 3.9 21.3 - - + -
707J ARG 3.4 11.0 - - - +
708J ILE* 4.8 12.6 - - + -
728J TYR 5.9 3.1 - - - +
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Residues in contact with MET 700 (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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574J TYR* 4.8 10.1 - - + +
577J VAL* 3.6 28.0 - - + +
578J ARG 4.5 2.9 - - - +
579J GLU* 3.9 24.0 - - + +
603J ASN* 4.3 13.2 - - - +
606J ILE* 4.1 19.3 - - + -
698J LYS* 3.9 42.4 - - + +
699J VAL* 1.3 76.9 - - - +
701J MET* 1.3 60.9 + - - +
702J VAL* 3.7 14.5 + - + +
706J HIS* 3.5 3.7 - - - -
707J ARG* 2.8 34.4 + - - +
711J PHE* 4.3 13.9 - - + -
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Residues in contact with MET 701 (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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520J TYR* 4.0 12.1 - - + -
541J ASN* 5.3 4.7 - - - +
544J GLU* 4.3 5.4 - - - +
577J VAL 3.3 13.6 + - - +
578J ARG* 3.5 35.0 + - + +
579J GLU 3.3 22.0 + - - +
699J VAL 4.2 0.2 + - - -
700J MET* 1.3 69.5 - - - +
702J VAL* 1.3 62.8 + - - +
703J ASN 4.1 1.1 + - - +
704J GLY* 3.2 46.9 - - - +
705J ASP 3.4 2.7 - - - +
706J HIS* 3.4 43.1 - - + +
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Residues in contact with VAL 702 (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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579J GLU* 3.7 31.0 - - + +
606J ILE* 4.3 13.7 - - + -
607J GLN* 3.7 37.9 - - + +
700J MET* 3.8 16.4 - - + +
701J MET* 1.3 80.0 - - - +
703J ASN* 1.3 78.0 + - - +
704J GLY 3.3 0.4 - - - -
705J ASP* 2.7 28.2 + - - +
707J ARG* 4.1 20.4 + - + +
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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