Contacts of the helix formed by residues 736 - 750 (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 PRO 736 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482T LYS* 2.4 48.7 - - - +
735T CYS* 1.3 108.8 - - + +
737T GLU* 1.3 65.2 + - - +
738T GLN* 2.8 24.5 - - - +
739T ALA* 3.1 8.1 + - + -
740T VAL* 3.3 0.3 + - - +
765T LEU* 3.8 12.6 - - + -
766T PHE* 4.1 0.9 - - + -
791T GLN* 4.0 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 737 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736T PRO* 1.3 68.4 - - - +
738T GLN* 1.3 63.7 + - + +
739T ALA 2.6 13.0 + - - -
740T VAL* 2.7 24.5 + - + +
741T GLY 4.3 1.0 + - - -
766T PHE* 3.2 43.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 738 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736T PRO* 2.8 27.8 - - - +
737T GLU* 1.3 79.9 + - + +
739T ALA* 1.3 56.1 + - - -
741T GLY* 4.4 5.4 + - - -
742T GLY 5.4 0.2 + - - -
791T GLN* 3.9 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 739 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735T CYS* 3.7 12.3 - - + -
736T PRO* 3.1 12.9 + - + +
737T GLU 2.6 6.3 + - - -
738T GLN* 1.3 75.1 + - - +
740T VAL* 1.3 64.3 + - - +
741T GLY 3.0 2.9 - - - -
742T GLY* 2.9 18.1 + - - -
743T ILE* 3.9 0.3 + - - +
787T ALA 4.8 0.2 - - - +
788T THR* 3.8 26.2 - - - +
791T GLN* 3.9 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 740 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735T CYS* 3.6 14.8 - - - -
736T PRO 3.3 10.5 + - - +
737T GLU* 2.7 29.6 + - + +
739T ALA* 1.3 72.0 - - - +
741T GLY* 1.3 62.2 + - - +
743T ILE* 2.9 21.6 + - + +
744T TYR* 3.2 38.3 + - + +
757T GLU* 4.2 6.7 - - - +
766T PHE* 4.0 22.4 - - + -
768T VAL* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 741 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737T GLU 4.3 1.6 + - - -
738T GLN 4.4 5.4 + - - -
739T ALA 2.9 2.0 + - - -
740T VAL* 1.3 79.2 - - - +
742T GLY* 1.3 60.5 + - - +
744T TYR* 3.6 12.6 + - - +
745T SER* 3.2 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 742 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739T ALA 2.9 9.4 + - - -
741T GLY* 1.3 74.6 - - - +
743T ILE* 1.3 64.8 + - - +
745T SER* 3.1 8.8 + - - -
746T VAL* 2.9 32.0 + - - +
787T ALA* 3.3 27.4 - - - -
788T THR* 4.2 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 743 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733T ILE* 3.5 42.2 - - + +
735T CYS* 3.9 22.0 - - + -
739T ALA 3.9 0.4 + - - -
740T VAL* 2.9 14.0 + - + +
742T GLY* 1.3 77.1 - - - +
744T TYR* 1.3 64.7 + - + +
746T VAL* 3.3 1.7 + - - +
747T LEU* 3.0 47.6 + - + +
768T VAL* 3.9 33.9 - - + -
784T LEU* 4.0 23.1 - - + +
788T THR* 4.2 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 744 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740T VAL* 3.2 39.8 + - + +
741T GLY* 4.0 9.2 - - - +
742T GLY 3.3 0.4 - - - -
743T ILE* 1.3 77.3 - - + +
745T SER* 1.3 63.3 + - - +
747T LEU* 4.5 5.4 - - + -
748T ASN* 2.8 42.1 + - - +
754T VAL* 3.3 45.1 - - + +
757T GLU* 2.4 37.9 + - - +
768T VAL* 4.2 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 745 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741T GLY 3.2 13.1 + - - -
742T GLY* 3.1 13.6 + - - -
744T TYR* 1.3 81.8 - - - +
746T VAL* 1.3 63.0 + - - +
748T ASN* 3.6 7.3 + - - +
749T LYS* 3.1 41.7 + - - +
787T ALA* 5.3 4.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 746 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742T GLY 2.9 21.2 + - - +
743T ILE 3.9 3.1 - - - +
745T SER* 1.3 73.3 - - - +
747T LEU* 1.3 57.8 + - - +
749T LYS* 2.8 34.8 + - + +
750T LYS* 3.2 17.2 + - + +
780T PHE* 3.7 31.9 - - + -
783T GLU* 3.6 31.9 - - + +
784T LEU* 4.2 9.4 - - + +
787T ALA* 3.4 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 747 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731T VAL* 4.8 7.2 - - + -
733T ILE* 5.4 2.0 - - + -
743T ILE* 3.0 40.4 + - + +
744T TYR* 3.9 4.5 - - + +
746T VAL* 1.3 75.8 - - - +
748T ASN* 1.3 60.5 + - - +
750T LYS* 2.8 20.1 + - - +
752T GLY* 2.9 32.9 + - - -
753T GLN 4.8 0.4 - - - +
754T VAL* 4.3 20.0 - - + +
768T VAL* 5.1 1.1 - - + -
770T ALA* 3.6 32.3 - - + -
771T TYR 4.8 0.9 - - - +
772T LEU* 4.4 14.6 - - + -
780T PHE* 4.2 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 748 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744T TYR* 2.8 34.0 + - - +
745T SER* 3.9 7.3 - - - +
747T LEU* 1.3 78.9 - - - +
749T LYS* 1.3 59.5 + - + +
750T LYS 3.2 1.0 + - - -
751T ARG* 4.2 5.4 + - - -
752T GLY 5.0 7.6 - - - +
754T VAL* 5.7 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 749 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745T SER* 3.1 36.0 + - - +
746T VAL* 2.8 13.5 + - + +
748T ASN* 1.3 79.3 - - + +
750T LYS* 1.3 69.7 + - + +
751T ARG* 3.8 1.3 - - - +
776T GLU* 4.5 2.1 - - - +
783T GLU* 5.1 9.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 750 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746T VAL* 3.2 16.4 + - + +
747T LEU* 2.8 7.5 + - - +
749T LYS* 1.3 89.2 + - + +
751T ARG* 1.3 59.2 + - - +
752T GLY* 2.7 19.1 + - - -
772T LEU* 3.8 9.5 - - + +
773T PRO* 3.7 11.1 - - - +
776T GLU* 3.3 48.6 + - + +
778T PHE 5.6 3.5 + - - -
780T PHE* 4.3 21.8 - - + +
783T GLU* 2.9 43.2 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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