Contacts of the helix formed by residues 802 - 811 (chain B) in PDB entry 5JO3
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 THR 802 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793B GLU* 4.7 1.8 + - - -
800B GLU 3.7 1.2 + - - +
801B PRO* 1.3 79.1 - - - +
803B ASP* 1.3 66.4 + - - +
804B LEU* 3.9 13.1 + - - +
805B MET* 2.9 26.0 + - - +
806B ASN* 3.1 7.0 + - - +
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Residues in contact with ASP 803 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787B PHE* 4.2 2.4 - - - -
801B PRO 5.1 0.7 - - - +
802B THR* 1.3 74.9 - - - +
804B LEU* 1.3 64.2 + - - +
805B MET 3.0 1.0 + - - -
806B ASN* 3.0 24.1 + - - +
809B LYS* 2.8 47.7 + - + +
812B LYS* 3.8 24.1 - - + +
816B MET* 4.0 21.6 - - - +
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Residues in contact with LEU 804 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783B ALA* 5.7 0.3 - - - -
786B PHE* 3.4 51.8 - - + +
787B PHE* 3.5 12.2 - - - -
802B THR* 3.1 10.8 + - - +
803B ASP* 1.3 77.0 - - - +
805B MET* 1.3 69.6 + - + +
816B MET* 3.7 21.0 - - + +
903B 6LK 3.6 65.7 + - + +
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Residues in contact with MET 805 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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661B SER* 4.5 9.6 - - - +
786B PHE* 3.4 44.9 - - + +
787B PHE* 3.6 10.8 - - - +
789B GLN* 3.2 48.0 - - - +
790B GLY* 3.2 23.8 - - - -
793B GLU* 3.9 9.4 - - - +
801B PRO* 3.6 12.1 - - + +
802B THR* 2.9 16.7 + - - +
804B LEU* 1.3 93.1 - - + +
806B ASN* 1.3 59.0 + - - +
807B ARG 3.8 0.9 + - - -
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Residues in contact with ASN 806 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787B PHE* 3.5 9.4 - - - -
794B ARG* 3.1 30.4 + - - +
800B GLU* 3.8 14.5 + - - -
801B PRO* 4.0 16.7 + - + +
802B THR 3.3 13.9 - - - +
803B ASP* 3.0 14.4 + - - +
804B LEU 3.5 0.4 - - - -
805B MET* 1.3 75.6 - - - +
807B ARG* 1.3 64.7 + - - +
808B GLU* 3.0 18.3 + - - +
809B LYS* 2.9 42.7 + - + +
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Residues in contact with ARG 807 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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784B THR* 4.9 1.8 + - - +
787B PHE* 3.4 56.6 + - + +
788B ASP* 3.8 4.9 + - - +
791B ASP* 2.8 41.9 + - - +
805B MET 3.8 1.8 + - - -
806B ASN* 1.3 71.8 + - - +
808B GLU* 1.3 64.0 + - + +
809B LYS 3.1 1.1 + - - -
810B LYS* 3.2 27.3 + - + +
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Residues in contact with GLU 808 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B ARG* 3.8 26.0 + - - +
800B GLU* 5.3 2.8 - - - +
806B ASN* 3.0 15.5 + - - +
807B ARG* 1.3 78.4 - - + +
809B LYS* 1.3 60.9 + - + +
810B LYS* 3.5 3.0 + - - +
811B ASN* 3.9 5.7 - - - +
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Residues in contact with LYS 809 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800B GLU* 5.5 2.9 - - - +
803B ASP* 2.8 44.8 + - - +
806B ASN* 2.9 33.0 + - + +
808B GLU* 1.3 83.4 - - + +
810B LYS* 1.3 59.7 + - - +
811B ASN* 3.0 17.3 - - - +
812B LYS* 3.0 36.9 + - + +
813B ILE 4.5 0.3 + - - -
816B MET* 5.1 1.0 - - - +
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Residues in contact with LYS 810 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787B PHE* 3.8 30.5 - - + -
806B ASN 3.7 0.4 + - - -
807B ARG* 3.2 22.3 + - + +
808B GLU 3.5 1.7 - - - +
809B LYS* 1.3 76.5 - - - +
811B ASN* 1.3 62.6 + - - +
812B LYS 3.0 2.6 + - - -
813B ILE* 3.1 27.0 + - + +
814B PRO* 4.5 1.2 - - - +
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Residues in contact with ASN 811 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808B GLU 3.9 5.2 - - - +
809B LYS* 3.4 21.8 - - - +
810B LYS* 1.3 81.8 + - - +
812B LYS* 1.3 79.0 + - - +
813B ILE 3.2 1.2 + - - -
814B PRO* 3.7 11.0 - - - +
815B SER* 5.2 0.7 + - - -
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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