Contacts of the helix formed by residues 780 - 789 (chain A) in PDB entry 3F2B
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 THR 780 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ARG* 5.2 2.0 - - - -
333A GLN 3.5 6.6 + - - +
334A ASP* 3.2 31.2 + - - +
342A ARG* 4.4 0.7 - - - -
370A TRP* 3.8 20.5 - - - -
778A PHE 3.8 1.2 + - - -
779A ARG* 1.3 78.2 - - - +
781A THR* 1.3 56.0 + - - +
782A ASN* 2.9 32.8 - - - +
783A GLU* 2.8 43.7 + - + +
784A MET* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASP* 2.6 43.0 + - - +
336A ALA* 3.8 17.3 - - + +
340A GLU 4.1 4.0 + - - -
341A LYS* 3.8 6.2 - - + -
342A ARG* 3.0 45.8 + - + +
372A HIS* 4.4 1.1 + - - +
780A THR* 1.3 70.1 - - - +
782A ASN* 1.3 65.6 + - - +
784A MET* 3.1 4.0 + - - +
785A LEU* 3.0 31.8 + - - +
800A VAL* 4.4 6.2 - - - +
801A VAL* 4.5 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN 3.9 2.6 + - - +
334A ASP* 3.4 4.8 + - - +
335A THR* 2.5 54.8 + - - +
336A ALA* 3.7 9.4 - - + +
780A THR* 2.9 27.5 - - - +
781A THR* 1.3 79.9 + - - +
783A GLU* 1.3 60.5 + - - +
785A LEU* 3.6 14.9 + - + +
786A ASP* 3.0 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ARG* 2.8 35.7 + - - +
777A TYR* 3.8 13.0 + - - -
779A ARG* 3.4 11.3 - - + -
780A THR* 2.8 52.0 + - + +
782A ASN* 1.3 77.6 - - - +
784A MET* 1.3 56.9 + - - +
786A ASP* 3.5 14.7 + - + +
787A CYS* 2.7 37.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 784 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 3.4 33.4 - - - +
701A PRO* 3.6 35.4 - - + -
740A ALA* 3.8 13.0 - - + +
741A THR 3.7 18.6 - - - -
742A GLY* 3.8 3.4 - - - +
779A ARG* 3.8 17.7 - - + -
780A THR 3.0 18.8 + - - +
781A THR* 3.1 7.1 + - - +
783A GLU* 1.3 75.4 - - - +
785A LEU* 1.3 62.9 + - - +
787A CYS* 3.4 3.5 + - - +
788A PHE* 3.2 36.2 + - + +
800A VAL* 3.8 26.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 785 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ALA* 5.4 5.8 - - + -
781A THR* 3.0 20.7 + - - +
782A ASN* 3.6 16.8 - - + +
784A MET* 1.3 75.4 - - - +
786A ASP* 1.3 53.9 + - - +
788A PHE 2.8 6.2 + - - -
789A SER* 2.7 35.0 + - - -
796A ALA* 4.0 24.5 - - + +
797A LYS* 4.1 10.3 - - + +
800A VAL* 3.7 30.5 - - + -
801A VAL* 4.6 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 786 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A ASN* 3.0 19.7 + - - +
783A GLU* 3.6 16.3 - - + +
784A MET 3.4 0.4 - - - -
785A LEU* 1.3 75.9 - - - +
787A CYS* 1.3 58.7 + - - +
789A SER* 3.0 28.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 787 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A PRO* 4.3 15.5 - - + -
702A PRO* 3.7 24.8 - - + +
779A ARG* 3.9 27.6 - - - -
783A GLU* 2.7 30.7 - - - -
784A MET* 3.6 11.0 - - - +
785A LEU 3.2 0.4 - - - -
786A ASP* 1.3 76.4 - - - +
788A PHE* 1.3 67.1 + - + +
789A SER* 3.5 0.4 + - - -
790A PHE* 3.9 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 788 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A VAL* 3.4 29.6 - - + -
700A HIS 3.5 26.5 - - - -
701A PRO* 3.6 24.7 - - + -
702A PRO* 4.5 2.2 - - + -
724A ILE* 4.2 11.2 - - + -
740A ALA* 3.7 24.5 - - + -
784A MET* 3.2 26.0 + - + +
785A LEU 2.8 5.9 + - - +
787A CYS* 1.3 78.5 - - + +
789A SER* 1.3 64.0 + - - +
790A PHE* 3.0 14.8 + + - -
791A LEU* 3.2 39.9 + - + +
796A ALA* 3.9 15.7 - - - +
799A ILE* 3.9 7.2 - - + -
800A VAL* 4.2 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 789 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A LEU 2.7 14.0 + - - -
786A ASP* 3.0 22.5 + - - -
787A CYS 3.5 0.9 - - - -
788A PHE* 1.3 72.7 - - - +
790A PHE* 1.3 61.9 + - - +
792A GLY* 2.8 25.6 + - - -
793A PRO* 5.0 0.7 - - - +
796A ALA* 4.8 5.4 - - - -
----------------------------------------------------------
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