Contacts of the helix formed by residues 825 - 836 (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 CYS 825 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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765B LEU* 4.3 9.0 - - - -
768B ILE* 3.8 20.9 - - - -
820B PHE* 3.5 39.9 - - - -
821B ILE* 3.1 12.4 + - - +
824B ILE* 1.3 80.7 - - - +
826B LEU* 1.3 68.5 + - - +
827B GLN 3.3 2.0 - - - -
828B LEU* 3.1 5.0 + - - +
829B TYR* 3.0 34.9 + - + -
846B CYS* 3.8 19.7 - - - -
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Residues in contact with LEU 826 (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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821B ILE* 2.9 29.2 + - + +
822B ASP* 3.6 30.0 + - - +
825B CYS* 1.3 74.1 - - - +
827B GLN* 1.3 59.2 + - + +
829B TYR* 3.3 0.7 + - - -
830B GLU* 2.8 45.8 + - - +
843B LEU* 4.0 13.0 - - + +
846B CYS* 3.8 20.4 - - - -
847B ARG* 3.9 29.6 - - + +
850B ARG* 4.4 8.3 - - - +
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Residues in contact with GLN 827 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B TYR* 5.0 0.2 - - - +
732B ARG* 3.6 15.4 - - - +
736B PHE* 3.6 33.3 - - + -
822B ASP 4.1 12.1 + - - +
823B ALA* 3.6 23.6 + - - +
824B ILE* 5.5 0.2 - - - +
825B CYS 3.3 1.4 - - - +
826B LEU* 1.3 77.8 - - + +
828B LEU* 1.3 57.9 + - - +
830B GLU* 3.4 15.1 + - - +
831B ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 828 (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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728B TYR* 3.4 27.5 + - + +
735B PHE* 4.8 7.0 - - + -
736B PHE* 3.9 6.6 - - + -
758B MET* 3.7 33.9 - - + +
761B THR* 3.5 32.5 - - + +
762B ALA* 3.6 26.9 - - + +
765B LEU* 4.7 7.9 - - + -
824B ILE 3.9 1.8 - - - +
825B CYS 3.1 8.5 + - - +
827B GLN* 1.3 79.2 - - - +
829B TYR* 1.3 63.4 + - + +
831B ALA* 3.2 2.4 + - - +
832B LEU* 2.9 29.0 + - + +
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Residues in contact with TYR 829 (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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762B ALA* 2.7 49.0 + - + -
765B LEU* 3.4 25.8 - - + +
766B SER* 3.5 3.1 + - - -
768B ILE* 3.8 13.0 - - + -
769B THR* 3.5 24.2 - - + -
825B CYS* 3.0 35.7 + - + +
828B LEU* 1.3 79.8 - - + +
830B GLU* 1.3 59.3 + - - +
832B LEU* 3.9 5.8 - - + +
833B THR* 2.8 30.3 + - - -
839B CYS 5.4 0.2 - - - +
842B LEU* 3.7 28.9 - - + -
843B LEU* 3.7 28.3 - - + +
846B CYS* 4.2 10.3 - - + -
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Residues in contact with GLU 830 (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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826B LEU* 2.8 34.3 + - - +
827B GLN* 3.6 18.0 - - - +
829B TYR* 1.3 75.9 - - - +
831B ALA* 1.3 57.6 + - - +
833B THR* 3.3 3.6 + - - -
834B HIS* 3.0 26.9 + - - +
843B LEU* 3.8 26.0 - - + +
847B ARG* 3.9 16.6 + - - +
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Residues in contact with ALA 831 (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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735B PHE* 3.4 29.8 - - + -
736B PHE* 3.7 14.8 - - + -
739B ILE* 4.8 10.1 - - + +
827B GLN 2.9 18.0 + - - +
828B LEU 3.6 3.4 - - - +
830B GLU* 1.3 76.2 - - - +
832B LEU* 1.3 62.9 + - - +
834B HIS* 3.1 11.2 + - - +
835B VAL* 3.1 25.6 + - - +
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Residues in contact with LEU 832 (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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628B ALA* 5.4 0.4 - - + -
634B ILE* 3.8 24.2 - - + -
735B PHE* 4.9 2.2 - - + -
755B PHE* 3.9 22.9 - - + -
759B LEU* 4.1 13.9 - - + -
762B ALA* 4.0 22.0 - - + -
828B LEU* 2.9 18.8 + - + +
829B TYR* 3.9 9.6 - - + +
830B GLU 3.3 0.2 - - - -
831B ALA* 1.3 76.4 - - - +
833B THR* 1.3 57.3 + - - +
835B VAL* 3.1 7.9 + - + +
836B SER* 2.9 26.6 + - - +
839B CYS* 3.8 17.4 - - + +
842B LEU* 3.9 28.0 - - + -
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Residues in contact with THR 833 (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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829B TYR 2.8 22.1 + - - -
830B GLU 3.6 5.6 - - - -
831B ALA 3.3 0.2 - - - -
832B LEU* 1.3 73.2 - - - +
834B HIS* 1.3 66.2 + - - +
836B SER 3.0 24.1 - - - -
837B GLU* 3.1 16.2 + - + +
839B CYS* 3.8 5.0 + - - -
840B PHE* 3.5 47.2 + - + -
843B LEU* 3.9 12.7 - - + +
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Residues in contact with HIS 834 (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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739B ILE* 3.3 52.2 + - + +
742B ASN* 5.0 10.0 + - - -
744B PHE* 5.5 3.6 - + + -
830B GLU 3.0 12.8 + - - +
831B ALA* 3.3 12.8 - - - +
833B THR* 1.3 79.0 - - - +
835B VAL* 1.3 63.2 + - - +
836B SER* 4.5 0.3 - - - -
837B GLU 5.0 0.5 + - - -
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Residues in contact with VAL 835 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634B ILE* 5.9 0.7 - - + -
637B LYS* 3.7 29.2 + - + -
735B PHE* 4.2 7.0 - - + -
739B ILE* 4.1 12.6 - - + -
744B PHE* 3.7 30.3 - - + -
746B LEU* 4.4 4.9 - - + -
755B PHE* 3.7 36.6 - - + -
831B ALA 3.1 14.3 + - - +
832B LEU* 3.1 7.4 + - + +
834B HIS* 1.3 77.5 - - - +
836B SER* 1.3 61.2 + - - +
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Residues in contact with SER 836 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632B GLY 2.6 28.2 + - - -
633B LYS* 3.9 10.6 + - - +
634B ILE* 4.5 6.3 - - - -
637B LYS* 4.0 16.5 + - - +
832B LEU 2.9 8.9 + - - -
833B THR* 3.0 15.6 - - - +
835B VAL* 1.3 80.1 - - - +
837B GLU* 1.3 59.9 + - - +
838B ASP* 3.7 6.8 + - - -
839B CYS* 2.9 26.6 + - - +
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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