Contacts of the strand formed by residues 798 - 803 (chain A) in PDB entry 5J9H
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 798 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733A MET* 3.2 6.3 - - - -
734A ASP* 2.8 47.6 + - + +
796A LYS* 3.3 8.9 + - + +
797A LEU* 1.3 77.2 - - - +
799A SER* 1.3 75.2 + - - +
800A VAL* 3.4 5.4 + - + +
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Residues in contact with SER 799 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A HIS* 3.2 32.5 + - - +
732A TRP 3.6 1.1 - - - -
733A MET* 3.5 22.9 - - - -
797A LEU 4.5 0.2 + - - -
798A LYS* 1.3 83.7 - - - +
800A VAL* 1.3 61.3 + - - +
801A GLY* 4.2 2.9 + - - -
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Residues in contact with VAL 800 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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732A TRP* 2.8 45.3 + - + +
733A MET 4.5 0.2 - - - +
734A ASP* 3.8 27.4 - - + +
798A LYS* 3.8 5.4 - - + +
799A SER* 1.3 76.9 - - - +
801A GLY* 1.3 56.6 + - - +
859A LEU* 3.3 31.4 - - + +
923A TYR* 3.5 47.3 - - + -
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Residues in contact with GLY 801 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A HIS* 3.2 12.9 - - - +
732A TRP 2.9 25.3 + - - -
799A SER* 3.8 3.0 + - - -
800A VAL* 1.3 84.1 - - - +
802A LYS* 1.3 62.4 + - - -
857A LEU* 4.3 9.2 - - - -
858A PHE 3.0 15.3 - - - -
859A LEU* 4.2 2.2 - - - -
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Residues in contact with LYS 802 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728A HIS* 4.5 17.9 + - - +
730A GLY* 3.9 7.2 - - - +
731A HIS* 3.6 35.7 - - + +
801A GLY* 1.3 73.5 - - - -
803A VAL* 1.3 61.4 + - - +
804A PHE* 4.2 30.7 - - + -
856A LEU 3.6 1.0 - - - +
857A LEU* 3.5 3.8 - - - -
858A PHE* 2.9 42.8 + - + +
862A LEU* 5.6 2.9 - - + -
943A ILE* 5.8 1.6 - - - +
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Residues in contact with VAL 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729A LEU* 3.1 31.6 + - + -
730A GLY 3.0 20.3 + - - +
732A TRP* 4.0 9.6 - - + +
802A LYS* 1.3 81.0 - - - +
804A PHE* 1.3 69.2 + - - +
855A THR* 3.3 33.2 - - + -
856A LEU 3.4 3.8 - - - +
857A LEU* 3.7 20.0 - - + -
872A TRP* 3.8 23.6 - - + +
886A MET* 3.8 16.2 - - + -
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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