Contacts of the strand formed by residues 784 - 787 (chain G) in PDB entry 5JLH
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 784 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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517G GLU* 3.4 15.7 + - - -
521G GLU* 3.0 31.8 + - - +
735G ARG* 3.8 36.3 - - + +
736G ILE 3.2 12.3 - - - +
737G LEU* 3.5 24.0 - - + +
738G PHE* 3.9 2.7 - - - -
781G GLY* 2.9 30.9 + - - +
782G GLN 3.5 0.2 - - - -
783G SER* 1.3 82.7 - - - +
785G ILE* 1.3 68.3 + - - +
786G PHE* 3.9 21.3 - - + -
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Residues in contact with ILE 785 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735G ARG* 3.7 0.5 - - - -
736G ILE 2.8 34.8 + - - +
737G LEU 5.6 0.2 - - - -
738G PHE* 3.4 42.4 - - + -
741G PHE* 5.8 2.0 - - + -
764G CYS* 4.4 17.7 - - + -
768G ILE* 5.3 5.6 - - + -
778G TYR* 4.1 9.4 - - + -
779G ARG 3.2 19.1 - - - +
780G VAL* 3.9 10.8 - - + -
784G LYS* 1.3 75.1 - - - +
786G PHE* 1.3 70.0 + - - +
787G PHE* 3.2 43.1 - - + -
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Residues in contact with PHE 786 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517G GLU* 4.4 6.1 - - + -
518G TYR* 3.4 38.8 - + - -
521G GLU* 3.4 30.1 - - + -
523G ILE* 3.3 27.8 - - + -
732G PHE* 3.6 26.0 - + + +
734G ASN 3.6 2.2 - - - -
735G ARG* 3.4 40.4 - - + -
778G TYR* 3.2 29.1 - - - +
779G ARG* 3.3 9.2 + - + -
784G LYS* 3.9 20.2 - - + -
785G ILE* 1.3 78.7 - - - +
787G PHE* 1.3 60.8 + - - +
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Residues in contact with PHE 787 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732G PHE* 3.2 21.7 - - - -
734G ASN* 2.7 37.1 + - + +
736G ILE* 4.6 9.4 - - + -
741G PHE* 4.1 21.5 - + + -
768G ILE* 3.9 26.7 - - + -
773G LEU* 4.4 5.8 - - + -
777G LEU 3.8 9.2 - - - -
778G TYR* 4.0 6.1 - - + -
785G ILE* 3.2 46.7 - - + -
786G PHE* 1.3 75.6 - - - +
788G ARG* 1.3 62.5 + - - +
791G VAL* 3.3 27.6 - - + -
792G LEU* 4.3 24.0 - - + -
795G LEU* 5.0 2.2 - - + -
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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