Contacts of the strand formed by residues 819 - 829 (chain D) in PDB entry 1JZ3
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 GLU 819 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781D ARG* 6.0 0.9 - - - +
817D GLN 3.8 12.6 - - - +
818D ALA* 1.3 75.1 - - - +
820D ALA* 1.4 58.4 + - - +
821D ALA* 3.3 8.1 + - - +
841D ALA 3.6 0.7 - - - +
842D TRP* 3.6 3.3 - - - -
843D GLN* 3.5 26.4 + - - +
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Residues in contact with ALA 820 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762D SER* 4.9 3.3 - - - +
764D PHE* 4.2 13.5 - - + -
781D ARG* 4.4 13.5 - - - +
819D GLU* 1.4 67.2 - - - +
821D ALA* 1.3 66.8 + - - +
822D LEU* 3.2 3.5 + - - +
840D HIS* 4.0 17.0 - - + -
841D ALA 3.8 5.4 - - - -
842D TRP* 3.7 33.8 - - + +
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Residues in contact with ALA 821 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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819D GLU 3.3 4.8 + - - +
820D ALA* 1.3 70.9 - - - +
822D LEU* 1.3 63.7 + - - +
823D LEU* 3.5 5.8 + - + +
840D HIS* 3.2 3.7 - - - -
841D ALA* 2.9 42.6 + - + +
843D GLN* 3.7 20.6 - - - +
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Residues in contact with LEU 822 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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760D ARG 3.2 27.8 - - - +
761D GLN 3.5 21.1 - - - +
762D SER 4.6 1.6 - - - +
763D GLY* 3.8 12.8 - - - +
820D ALA 3.2 3.6 + - - +
821D ALA* 1.3 73.8 - - - +
823D LEU* 1.3 62.4 + - - +
824D GLN 3.4 28.7 - - - +
825D CYS* 4.0 11.0 - - + -
838D THR* 5.0 0.4 - - - -
839D ALA 3.6 9.0 - - - +
840D HIS* 3.7 25.6 - - + +
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Residues in contact with LEU 823 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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727C SER 5.3 0.4 - - - +
728C VAL* 3.7 38.1 - - + +
730C LEU* 4.3 31.5 - - + +
821D ALA* 3.5 6.5 + - + +
822D LEU* 1.3 79.5 - - - +
824D GLN* 1.3 61.9 + - + +
839D ALA* 2.7 29.1 + - + +
840D HIS 4.2 8.3 - - - +
841D ALA* 4.0 33.0 - - + +
851D ILE* 4.7 10.1 - - + -
853D ARG* 5.8 2.9 - - - +
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Residues in contact with GLN 824 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822D LEU* 3.4 11.4 - - - +
823D LEU* 1.3 83.4 - - + +
825D CYS* 1.3 64.8 + - - +
826D THR* 4.1 19.8 - - + +
837D THR* 3.5 29.8 - - - +
838D THR* 3.1 5.8 + - - -
839D ALA* 2.9 44.2 + - + +
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Residues in contact with CYS 825 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747D PHE* 3.8 28.7 - - - -
758D PHE* 5.5 3.1 - - - -
759D ASN 4.5 1.8 - - - -
760D ARG* 4.4 28.1 + - + +
763D GLY* 4.4 9.2 - - - -
822D LEU* 4.0 20.0 - - + -
824D GLN* 1.3 77.4 - - - +
826D THR* 1.3 68.3 + - - +
836D ILE* 4.7 4.0 - - - -
837D THR 3.2 4.9 - - - -
838D THR* 4.2 15.3 - - - -
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Residues in contact with THR 826 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747D PHE* 3.7 7.9 - - - -
824D GLN* 4.1 20.4 - - + +
825D CYS* 1.3 80.2 - - - +
827D ALA* 1.3 63.7 + - - +
828D ASP* 4.3 8.4 + - - -
835D LEU 4.4 0.2 - - - -
836D ILE* 3.2 9.7 - - - +
837D THR* 2.7 52.8 + - - +
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Residues in contact with ALA 827 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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831C ALA* 5.6 1.7 - - - +
740D LEU* 3.7 25.6 - - + +
747D PHE* 3.8 22.4 - - + -
826D THR* 1.3 79.1 - - - +
828D ASP* 1.3 69.6 + - - +
834D VAL* 5.0 0.4 - - + -
835D LEU 3.2 4.5 - - - -
836D ILE* 3.4 22.0 - - + -
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Residues in contact with ASP 828 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830C LEU* 3.7 22.4 - - + +
831C ALA* 2.9 35.1 + - - +
832C ASP* 5.3 2.2 - - - +
857C ARG* 6.0 0.2 + - - -
740D LEU* 5.2 1.1 - - - -
826D THR* 4.3 10.9 + - - -
827D ALA* 1.3 82.5 - - - +
829D THR* 1.3 63.4 + - - +
830D LEU* 3.8 16.7 + - + -
834D VAL* 3.5 5.0 - - - +
835D LEU* 2.8 45.9 + - + +
837D THR* 5.0 2.1 + - - -
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Residues in contact with THR 829 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829C THR 4.1 8.5 - - - +
737D ILE* 4.6 9.6 - - + -
738D PRO 4.9 2.7 - - - +
740D LEU* 4.0 25.4 - - + +
828D ASP* 1.3 76.9 - - - +
830D LEU* 1.3 82.0 + - - +
833D ALA 3.5 7.6 - - - +
834D VAL* 4.2 11.8 - - + +
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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