Contacts of the strand formed by residues 705 - 712 (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 ASP 705 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288J ARG* 3.0 20.5 + - - +
296J LEU* 3.6 25.0 - - + +
297J HIS* 3.1 21.6 + - - -
519J ASN* 4.9 4.0 - - - +
701J MET* 3.4 3.0 - - - +
702J VAL* 2.7 42.1 + - - +
703J ASN* 3.3 8.6 - - - +
704J GLY* 1.3 75.5 - - - +
706J HIS* 1.3 66.0 + - - +
707J ARG* 4.5 14.5 + - + +
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Residues in contact with HIS 706 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J ASN* 4.6 3.5 + - - -
517J VAL* 3.3 24.4 - - + +
518J TYR 3.5 24.7 - - - -
519J ASN* 3.6 12.5 + - - +
541J ASN* 4.9 1.5 + - - -
645J ILE* 5.4 2.6 - - - +
669J LEU* 3.9 30.6 - - + +
670J ASN* 3.1 20.6 + - - +
699J VAL* 3.9 26.7 - - + -
700J MET 3.5 2.9 - - - -
701J MET* 3.4 37.2 - - + +
704J GLY 3.8 0.2 + - - -
705J ASP* 1.3 76.8 - - - +
707J ARG* 1.3 66.1 + - - +
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Residues in contact with ARG 707 (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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117J GLN 4.5 6.3 + - - -
118J GLN* 4.3 25.6 - - - +
119J ASN* 4.7 5.5 - - - +
296J LEU* 6.5 2.0 - - - -
606J ILE* 3.1 44.3 + - + +
607J GLN* 3.8 19.4 + - - +
609J GLY* 5.5 1.2 - - - +
640J GLU* 2.8 37.2 + - - +
669J LEU* 4.4 2.2 - - - -
699J VAL* 3.4 4.1 - - - -
700J MET* 2.8 36.5 + - - +
702J VAL* 4.1 24.2 + - + +
705J ASP* 3.8 15.2 + - + +
706J HIS* 1.3 79.9 - - - +
708J ILE* 1.3 63.4 + - - +
709J GLY 3.6 0.3 + - - -
627L ILE* 5.9 2.2 - - - +
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Residues in contact with ILE 708 (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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119J ASN* 5.1 1.1 - - - +
606J ILE* 4.6 2.5 - - - +
640J GLU* 3.1 27.2 + - - +
641J TYR* 3.1 42.3 + - + +
667J PHE* 4.0 29.2 - - + +
668J ASN 4.3 10.8 - - - +
669J LEU* 3.7 23.6 - - + -
675J VAL* 4.0 13.2 - - + -
697J ALA* 4.3 14.8 - - + -
698J LYS 3.7 7.4 - - - +
699J VAL* 4.4 8.5 - - + +
707J ARG* 1.3 72.6 - - - +
709J GLY* 1.3 68.1 + - - +
710J ILE* 4.4 1.8 - - + -
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Residues in contact with GLY 709 (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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606J ILE* 4.2 14.8 - - - +
637J PHE* 4.2 4.7 - - - -
697J ALA* 3.1 7.6 - - - +
698J LYS 2.6 39.5 + - - -
700J MET* 5.5 0.2 - - - -
707J ARG 3.6 1.6 + - - -
708J ILE* 1.3 73.7 - - - +
710J ILE* 1.3 64.7 + - - +
711J PHE* 3.5 17.2 - - - -
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Residues in contact with ILE 710 (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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637J PHE* 3.9 2.5 - - - -
638J ILE* 2.8 40.0 + - + +
639J SER 2.9 22.1 + - - +
641J TYR* 4.2 18.6 - - + +
684J ILE* 4.3 26.7 - - + -
695J CYS* 4.1 19.5 - - + -
696J TYR 3.4 8.5 - - - +
697J ALA* 3.5 22.2 - - + -
708J ILE* 4.4 7.9 - - + -
709J GLY* 1.3 81.5 - - - +
711J PHE* 1.3 57.3 - - - +
724J PHE* 4.2 26.2 - - + -
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Residues in contact with PHE 711 (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* 5.9 1.1 - - - -
606J ILE* 4.7 1.1 - - + -
635J ASN 3.8 11.4 - - - -
636J GLU 3.5 5.6 - - - +
637J PHE* 3.5 47.3 - + + -
638J ILE* 3.8 5.6 - - - -
695J CYS* 3.3 3.1 - - - -
696J TYR* 2.9 68.2 + + + +
698J LYS* 3.9 21.3 - - + -
700J MET* 4.3 23.6 - - + -
709J GLY* 3.5 28.9 - - - -
710J ILE* 1.3 73.5 - - - +
712J ALA* 1.3 62.9 + - - +
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Residues in contact with ALA 712 (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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632J VAL* 4.1 9.0 - - + -
633J GLN 3.9 17.0 - - - +
635J ASN* 2.8 26.2 + - - +
636J GLU 3.3 9.1 + - - +
638J ILE* 3.5 14.9 - - + +
694J ASN 3.9 4.9 - - - -
696J TYR* 3.4 4.6 - - - -
711J PHE* 1.3 75.0 - - - +
713J LYS* 1.3 57.9 + - - +
714J ARG 3.3 19.7 - - - +
716J ILE* 3.7 15.0 - - + -
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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