Contacts of the helix formed by residues 840 - 852 (chain D) in PDB entry 5ZOJ
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 SER 840 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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784D PRO* 3.6 7.9 - - - +
838D CYS* 3.9 0.9 - - - +
839D LEU* 1.3 80.1 - - - +
841D PRO* 1.3 73.8 - - - +
842D GLU* 2.9 28.1 + - - +
843D TYR* 3.1 25.8 + - - +
844D ALA* 3.0 18.0 + - - +
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Residues in contact with PRO 841 (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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781D SER* 2.7 34.7 + - - +
782D LEU 4.7 3.4 - - - +
783D THR* 4.2 11.9 - - - +
784D PRO* 3.8 32.5 - - + -
839D LEU 4.7 0.7 - - - +
840D SER* 1.3 90.3 - - - +
842D GLU* 1.3 61.3 + - - +
844D ALA 3.3 0.7 + - - -
845D GLY 2.8 18.5 + - - -
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Residues in contact with GLU 842 (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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781D SER* 4.2 5.6 - - - +
840D SER* 2.9 16.5 + - - +
841D PRO* 1.3 84.6 - - - +
843D TYR* 1.3 65.9 + - + +
845D GLY* 3.1 2.5 + - - -
846D LYS* 3.0 27.5 + - - +
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Residues in contact with TYR 843 (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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817D ASN* 3.2 25.4 + - - +
818D ASP* 3.8 20.5 - - + +
819D GLY* 3.4 41.3 - - - -
838D CYS* 4.1 6.5 - - + -
839D LEU* 4.9 7.6 - - + -
840D SER* 3.1 32.5 + - - +
842D GLU* 1.3 81.2 - - + +
844D ALA* 1.3 57.4 + - - +
846D LYS* 4.6 4.7 - - + -
847D ALA* 3.1 22.3 + - - +
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Residues in contact with ALA 844 (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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783D THR 3.5 24.7 - - - +
784D PRO* 3.6 23.6 - - + -
786D LEU* 3.6 19.1 - - + +
838D CYS* 3.6 16.5 - - - +
840D SER 3.0 6.8 + - - +
841D PRO 3.6 4.0 - - - +
842D GLU 3.3 0.2 - - - -
843D TYR* 1.3 74.7 - - - +
845D GLY* 1.3 58.2 + - - +
847D ALA* 3.5 1.5 + - - -
848D PHE* 3.0 26.3 + - - +
865D TYR* 4.4 2.0 - - + -
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Residues in contact with GLY 845 (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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780D ASN* 5.9 0.7 - - - -
781D SER* 3.8 7.0 - - - -
841D PRO 2.8 15.6 + - - -
842D GLU 3.1 4.4 + - - -
844D ALA* 1.3 78.9 - - - +
846D LYS* 1.3 60.2 + - - +
848D PHE* 3.2 11.8 + - - +
849D LYS* 3.3 29.5 + - - +
865D TYR* 3.7 15.5 - - - -
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Residues in contact with LYS 846 (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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816D ASP* 3.1 48.3 + - - +
817D ASN* 3.4 24.2 - - + +
818D ASP* 5.3 2.6 + - - +
842D GLU 3.0 13.3 + - - +
843D TYR* 4.6 4.4 - - + -
844D ALA 3.4 0.2 - - - -
845D GLY* 1.3 73.6 - - - +
847D ALA* 1.3 62.4 + - - +
849D LYS* 3.8 13.4 + - + +
850D ALA* 3.7 18.2 + - - +
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Residues in contact with ALA 847 (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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786D LEU* 3.7 20.9 - - + -
814D CYS* 4.1 20.6 - - - -
817D ASN* 4.1 12.3 + - - +
820D ILE* 4.6 4.3 - - + -
836D VAL* 5.4 1.3 - - + -
838D CYS* 4.4 6.1 - - - -
843D TYR 3.1 16.6 + - - +
844D ALA* 3.8 2.2 - - - +
845D GLY 3.3 0.2 - - - -
846D LYS* 1.3 76.6 - - - +
848D PHE* 1.3 63.5 + - - +
850D ALA* 3.5 1.6 + - - +
851D LEU* 3.3 31.0 + - + +
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Residues in contact with PHE 848 (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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772D LEU* 4.7 4.0 - - + -
777D SER* 3.6 17.5 - - - -
778D PRO* 3.8 20.0 - - + -
786D LEU* 4.0 5.1 - - + +
844D ALA 3.0 11.1 + - - +
845D GLY 3.2 10.1 + - - +
847D ALA* 1.3 77.0 - - - +
849D LYS* 1.3 68.0 + - + +
851D LEU* 3.0 1.6 + - - -
852D HIS* 2.8 71.5 + + + +
863D VAL* 3.5 46.2 - - + -
865D TYR* 3.5 40.8 - + - +
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Residues in contact with LYS 849 (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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768D GLN* 3.2 23.4 + - - -
772D LEU* 3.4 25.0 - - + +
780D ASN* 5.7 2.8 + - - -
845D GLY* 3.3 25.3 + - - +
846D LYS* 3.8 11.2 + - - +
847D ALA 3.4 0.2 - - - -
848D PHE* 1.3 81.3 - - + +
850D ALA* 1.3 57.8 + - - +
852D HIS 4.6 0.3 - - - +
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Residues in contact with ALA 850 (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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768D GLN* 4.9 0.9 - - - +
813D LYS* 2.9 62.8 + - - +
814D CYS* 4.2 9.2 - - - -
816D ASP* 5.2 5.8 - - - +
846D LYS 3.7 11.4 + - - +
847D ALA 3.5 7.8 + - - +
848D PHE 3.1 1.2 - - - -
849D LYS* 1.3 77.1 - - - +
851D LEU* 1.3 58.9 + - - +
854D SER* 3.4 6.9 + - - -
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Residues in contact with LEU 851 (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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765D TRP* 3.7 28.4 - - + -
786D LEU* 4.7 3.6 - - + -
788D ILE* 3.6 29.2 - - + -
810D ILE* 4.2 18.8 - - + +
813D LYS* 3.9 19.1 - - + -
814D CYS* 3.7 19.3 - - - -
836D VAL* 5.2 1.6 - - + -
847D ALA* 3.3 23.8 + - + +
848D PHE 3.0 2.0 + - - +
850D ALA* 1.3 78.4 - - - +
852D HIS* 1.3 67.2 + - - +
853D GLY 3.4 0.7 + - - -
854D SER* 3.3 18.8 + - - -
861D VAL* 3.6 14.3 - - + +
863D VAL* 3.9 14.1 - - + -
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Residues in contact with HIS 852 (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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368A TRP* 4.4 11.3 + + - -
768D GLN* 4.7 3.6 + - - +
770D PHE* 4.6 2.0 - + - -
772D LEU* 3.4 34.1 - - + +
776D ASN* 3.0 23.7 + - - +
777D SER* 3.3 23.3 - - - -
848D PHE* 2.8 44.4 + + + +
849D LYS 4.6 1.7 - - - +
851D LEU* 1.3 73.0 - - - +
853D GLY* 1.3 68.1 + - - +
854D SER* 3.4 3.6 + - - -
861D VAL 4.0 0.9 - - - -
862D THR* 3.6 20.3 - - + -
863D VAL* 3.1 38.7 + - + +
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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