Contacts of the helix formed by residues 802 - 811 (chain A) in PDB entry 3JWR
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 ILE 802 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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793A GLU* 4.2 2.0 + - - -
800A GLN 3.9 0.8 + - - -
801A PRO* 1.3 76.9 - - - +
803A PRO* 1.3 74.8 - - + +
804A MET* 3.6 35.0 - - + -
805A MET* 2.9 41.3 + - + +
806A ASP* 2.9 8.1 + - - +
82C ALA* 3.5 25.4 - - + +
83C GLN* 3.6 19.3 - - - +
85C GLY* 4.2 7.4 - - - +
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Residues in contact with PRO 803 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A TRP* 5.0 1.2 + - - -
801A PRO 3.6 1.5 - - - +
802A ILE* 1.3 89.8 - - + +
804A MET* 1.3 63.1 + - - +
806A ASP* 3.1 30.8 + - + +
809A LYS* 3.9 21.1 - - + +
812A GLU* 4.9 7.2 - - - +
816A LEU* 4.0 25.4 - - + +
83C GLN* 4.9 11.2 - - + +
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Residues in contact with MET 804 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
783A ALA* 6.0 0.3 - - - -
786A PHE* 3.4 53.8 - - + +
787A TRP* 4.1 9.6 + - - -
802A ILE* 3.1 19.9 - - + -
803A PRO* 1.3 80.1 - - - +
805A MET* 1.3 63.7 + - + +
816A LEU* 3.6 30.3 - - + +
820A PHE* 5.4 0.9 - - - -
901A IBM 4.1 15.0 - - + -
83C GLN 4.1 6.5 - - - +
84C TYR* 4.4 16.8 - - - -
85C GLY* 3.5 31.4 - - - +
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Residues in contact with MET 805 (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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661A ASN* 4.3 13.7 - - - +
667A ARG* 5.5 1.8 - - - +
786A PHE* 3.5 40.6 - - + +
787A TRP* 3.6 7.8 - - - -
789A GLN* 3.6 28.5 - - - +
790A GLY* 3.0 26.5 + - - +
793A GLU* 3.2 30.1 - - - +
801A PRO* 4.1 2.7 - - + -
802A ILE* 2.9 37.8 + - + +
804A MET* 1.3 86.7 - - + +
806A ASP* 1.3 59.9 + - - +
807A ARG 3.4 5.8 + - - -
85C GLY* 5.4 0.2 - - - -
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Residues in contact with ASP 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
787A TRP* 3.7 5.6 + - - -
794A ARG* 2.9 32.6 + - - +
800A GLN* 3.5 22.0 + - - +
801A PRO* 4.3 6.4 - - + +
802A ILE 2.9 13.3 + - - +
803A PRO* 3.1 19.0 + - + +
805A MET* 1.3 74.4 - - - +
807A ARG* 1.3 65.2 + - - +
808A ASN* 3.3 11.7 + - - +
809A LYS* 2.8 40.4 + - + +
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Residues in contact with ARG 807 (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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784A THR* 4.9 0.8 + - - +
787A TRP* 3.2 57.1 + - + +
788A GLU* 3.8 15.2 + - - +
791A ASP* 2.7 41.3 + - - +
794A ARG* 3.7 7.7 - - - +
805A MET 3.4 3.4 + - - -
806A ASP* 1.3 73.0 + - - +
808A ASN* 1.3 69.1 + - - +
809A LYS 3.2 1.4 + - - -
810A ARG* 3.3 22.7 + - - +
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Residues in contact with ASN 808 (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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794A ARG* 3.6 17.2 + - - +
806A ASP* 2.9 12.4 + - - +
807A ARG* 1.3 83.7 - - - +
809A LYS* 1.3 87.6 + - + +
810A ARG* 3.2 9.9 + - - +
811A ASP* 3.7 6.9 - - - +
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Residues in contact with LYS 809 (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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787A TRP* 5.4 0.4 - - - -
803A PRO* 3.9 21.7 - - + +
806A ASP* 2.8 37.2 + - + +
808A ASN* 1.3 108.2 + - + +
810A ARG* 1.3 50.6 + - - +
811A ASP* 2.7 27.5 + - - -
812A GLU* 2.7 49.2 + - + +
813A LEU* 3.9 1.7 + - - -
816A LEU* 5.7 0.9 - - + +
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Residues in contact with ARG 810 (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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780A GLU* 5.6 3.8 + - - -
787A TRP* 3.5 45.6 - - + +
806A ASP 4.1 0.6 + - - -
807A ARG 3.3 15.3 + - - +
808A ASN* 4.0 7.9 - - - +
809A LYS* 1.3 74.9 - - - +
811A ASP* 1.3 68.8 + - - +
812A GLU 3.2 1.3 - - - -
813A LEU* 3.3 29.4 - - - +
814A PRO* 4.7 0.9 - - - +
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Residues in contact with ASP 811 (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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808A ASN 3.7 9.2 - - - +
809A LYS* 2.7 24.5 + - - +
810A ARG* 1.3 88.4 - - - +
812A GLU* 1.3 55.2 + - + +
813A LEU 3.3 4.0 - - - -
814A PRO* 4.0 3.5 - - - +
815A LYS* 2.7 26.7 + - - -
859A GLN* 4.3 8.8 + - - +
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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