Contacts of the helix formed by residues 813 - 826 (chain T) in PDB entry 2P8Z
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 813 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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806T SER* 3.5 17.3 - - - -
807T ASP* 2.6 34.2 + - - -
810T ASP* 3.0 17.6 + - - -
812T THR* 1.3 81.1 + - - +
814T LYS* 1.3 59.4 + - - +
816T GLY 3.2 4.0 + - - -
817T GLU* 2.8 31.8 + - - +
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Residues in contact with LYS 814 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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751T ARG* 3.2 39.7 - - - +
804T LEU* 4.8 12.3 - - + -
806T SER* 3.7 12.7 + - - +
813T SER* 1.3 74.7 - - - +
815T ALA* 1.3 62.6 + - - +
817T GLU* 3.5 14.2 + - - +
818T ILE* 3.4 26.9 + - + +
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Residues in contact with ALA 815 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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724T ILE* 4.0 22.7 - - + +
804T LEU* 4.0 17.0 - - + +
806T SER* 3.1 35.4 + - - +
808T PRO* 4.1 11.7 - - + -
813T SER 3.3 0.2 - - - -
814T LYS* 1.3 74.4 - - - +
816T GLY* 1.3 59.4 + - - +
818T ILE* 3.1 9.7 + - - +
819T VAL* 3.0 28.1 + - - +
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Residues in contact with GLY 816 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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807T ASP 3.5 1.4 + - - -
808T PRO 3.5 18.7 - - - +
810T ASP 3.2 25.8 - - - -
811T PRO* 3.9 5.4 - - - +
813T SER* 3.2 9.0 + - - -
815T ALA* 1.3 79.1 - - - +
817T GLU* 1.3 56.2 + - - +
819T VAL* 3.2 2.3 + - - +
820T LEU* 2.8 30.5 + - - +
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Residues in contact with GLU 817 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811T PRO 3.8 14.9 - - - +
812T THR* 3.9 13.1 - - - +
813T SER 2.8 32.4 + - - +
814T LYS* 3.8 13.5 - - - +
816T GLY* 1.3 72.0 - - - +
818T ILE* 1.3 59.8 + - + +
820T LEU* 3.3 4.9 + - - +
821T ALA* 2.9 31.2 + - - +
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Residues in contact with ILE 818 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563T TYR* 3.5 58.3 - - + +
677T PHE* 4.8 6.1 - - + -
724T ILE* 4.9 2.7 - - + -
775T ASN* 4.4 13.5 - - - +
804T LEU* 4.0 18.6 - - + -
814T LYS* 3.4 17.5 - - + +
815T ALA* 3.1 6.7 + - - +
817T GLU* 1.3 78.7 - - + +
819T VAL* 1.3 62.7 + - + +
821T ALA* 3.5 5.9 + - - +
822T ALA* 3.1 23.4 + - + +
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Residues in contact with VAL 819 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676T ILE* 3.6 31.9 - - + +
677T PHE* 3.9 22.8 - - + +
724T ILE* 4.2 10.5 - - + -
808T PRO* 3.7 22.2 - - + +
815T ALA 3.0 16.1 + - - +
816T GLY 3.6 6.7 - - - +
817T GLU 3.2 0.2 - - - -
818T ILE* 1.3 75.9 - - + +
820T LEU* 1.3 60.1 + - - +
822T ALA* 3.5 1.7 + - - +
823T ARG* 3.1 32.1 + - - +
832T VAL* 3.9 23.1 - - + -
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Residues in contact with LEU 820 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811T PRO* 4.0 35.0 - - + +
816T GLY 2.8 21.0 + - - +
817T GLU* 3.8 4.9 - - - +
819T VAL* 1.3 72.5 - - - +
821T ALA* 1.3 64.4 + - - +
823T ARG* 3.8 3.3 - - - +
824T LYS* 3.1 45.6 + - + +
830T GLU* 3.7 50.5 - - + +
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Residues in contact with ALA 821 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817T GLU 2.9 18.2 + - - +
818T ILE* 3.8 6.1 - - - +
819T VAL 3.3 0.2 - - - -
820T LEU* 1.3 79.0 - - - +
822T ALA* 1.3 56.9 + - - +
824T LYS* 4.0 8.5 - - - +
825T ARG* 3.0 37.9 + - - +
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Residues in contact with ALA 822 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677T PHE* 3.3 38.1 - - + -
818T ILE* 3.1 13.4 + - + +
819T VAL 4.0 0.2 - - - +
821T ALA* 1.3 75.1 - - - +
823T ARG* 1.3 65.9 + - - +
825T ARG* 3.3 27.4 + - - +
826T HIS* 3.0 36.6 + - + +
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Residues in contact with ARG 823 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675T PRO 4.2 5.5 + - - -
676T ILE 3.3 15.6 + - - -
677T PHE* 4.0 11.9 - - + -
819T VAL* 3.1 24.4 + - - +
820T LEU* 3.8 5.8 - - - +
822T ALA* 1.3 74.1 - - - +
824T LYS* 1.3 66.3 + - - +
826T HIS 3.2 1.9 + - - -
827T GLY 3.1 3.8 + - - -
828T MET* 3.0 73.1 + - - +
829T LYS* 2.5 35.1 + - - +
830T GLU* 3.3 23.8 - - - +
831T GLU 3.9 8.2 + - - -
832T VAL* 3.3 20.8 - - - +
833T PRO* 3.4 24.9 - - - +
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Residues in contact with LYS 824 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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820T LEU* 3.1 36.7 + - + +
821T ALA* 4.0 7.2 - - - +
823T ARG* 1.3 76.1 - - - +
825T ARG* 1.3 63.1 + - - +
827T GLY* 3.0 14.5 + - - -
828T MET 4.9 4.0 - - - -
830T GLU* 3.1 40.3 + - + +
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Residues in contact with ARG 825 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560T VAL* 3.5 42.8 - - - +
561T VAL 5.4 1.0 + - - -
821T ALA* 3.0 28.0 + - - +
822T ALA* 3.6 34.6 - - - +
824T LYS* 1.3 76.5 - - - +
826T HIS* 1.3 82.6 + - + +
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Residues in contact with HIS 826 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677T PHE* 4.9 8.7 - + - -
679T GLU* 5.6 3.8 + - - -
822T ALA* 3.0 33.0 + - + +
823T ARG 3.2 2.9 + - - +
824T LYS 3.1 0.4 - - - -
825T ARG* 1.3 102.2 + - + +
827T GLY* 1.3 62.8 + - - +
828T MET* 3.4 23.4 + - + +
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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