Contacts of the helix formed by residues 771 - 783 (chain A) in PDB entry 3T1N
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 771 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A LEU* 6.6 0.4 - - + -
766A PRO 5.6 0.2 - - - +
768A SER 3.9 5.6 - - - +
769A SER* 5.3 0.7 - - - +
770A PRO* 1.3 96.7 - - + +
772A VAL* 1.3 65.7 + - - +
773A ALA* 3.3 4.7 + - + +
774A LYS* 3.6 19.9 + - + -
775A LEU* 3.3 18.5 + - - +
824C PHE* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 772 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A VAL* 3.6 31.2 - - + +
765A SER 3.8 15.0 - - - +
766A PRO* 3.9 23.8 + - + +
768A SER* 4.0 8.2 + - - -
770A PRO 3.6 0.4 + - - -
771A PRO* 1.3 71.3 - - - +
773A ALA* 1.3 67.0 + - + +
775A LEU* 3.7 3.3 - - - +
776A CYS* 2.8 41.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 773 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A PRO* 3.3 3.5 - - + +
772A VAL* 1.3 86.3 - - + +
774A LYS* 1.3 69.0 + - + +
776A CYS* 3.9 4.3 - - - +
777A GLU* 3.1 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 774 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A ASP* 5.2 11.9 + - - +
679A VAL 5.7 0.8 + - - -
695A LEU* 4.5 24.2 - - + +
699A LEU* 4.0 28.6 - - + +
770A PRO* 5.6 3.6 - - + -
771A PRO* 3.6 25.0 + - + +
772A VAL 3.3 0.4 - - - -
773A ALA* 1.3 87.3 - - + +
775A LEU* 1.3 59.0 + - - +
777A GLU* 3.4 22.8 - - - +
778A LEU* 3.0 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 775 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A VAL* 4.4 15.0 - - + -
768A SER* 4.2 13.0 - - - +
770A PRO* 4.2 17.0 - - + +
771A PRO 3.3 17.0 + - - +
772A VAL* 4.0 3.8 - - - +
774A LYS* 1.3 77.3 - - - +
776A CYS* 1.3 61.8 + - - +
778A LEU* 3.6 17.0 - - + +
779A VAL* 3.1 30.2 + - + +
797A ILE* 4.4 5.8 - - + -
813A GLU* 3.6 34.1 - - + +
816A VAL* 3.8 30.1 - - + -
817A LEU* 4.3 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 776 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
764A VAL* 3.6 31.0 - - - -
772A VAL* 2.8 31.8 + - - +
773A ALA* 3.9 5.4 - - - +
775A LEU* 1.3 75.0 - - - +
777A GLU* 1.3 64.6 + - - +
779A VAL* 3.2 5.3 + - - +
780A HIS* 3.0 23.3 + - - +
786A VAL* 4.0 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 777 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A VAL 5.0 4.0 - - - +
681A GLU* 5.6 0.2 - - - +
699A LEU* 4.3 20.1 - - + +
703A ARG* 3.3 24.8 + - - -
773A ALA 3.1 11.8 + - - +
774A LYS* 3.4 30.1 - - - +
776A CYS* 1.3 78.2 - - - +
778A LEU* 1.3 56.5 + - - +
780A HIS* 3.0 7.0 + - + +
781A LEU* 2.8 52.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 778 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A LEU* 6.5 0.2 - - - -
698A LEU* 3.8 34.1 - - + +
699A LEU* 3.4 25.4 - - + +
702A ALA* 4.4 5.6 - - + -
770A PRO* 5.4 4.5 - - + -
774A LYS* 3.0 24.7 + - + +
775A LEU* 3.6 29.2 - - + +
777A GLU* 1.3 78.1 - - - +
779A VAL* 1.3 62.3 + - + +
781A LEU* 3.4 5.2 + - - +
782A CYS* 3.1 30.2 + - - +
817A LEU* 4.0 18.6 - - + -
820A ILE* 4.1 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 779 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756A PHE* 4.2 11.2 - - + -
762A MET* 3.8 28.7 - - + -
764A VAL* 5.0 8.1 - - + -
775A LEU* 3.1 18.4 + - + +
776A CYS* 3.2 8.6 + - - +
778A LEU* 1.3 75.4 - - - +
780A HIS* 1.3 60.5 + - - +
782A CYS* 3.5 2.6 + - - +
783A GLY 3.3 3.8 + - - -
784A GLY* 2.8 41.7 + - - -
785A ARG 4.5 0.4 - - - +
786A VAL* 4.0 19.3 - - + -
797A ILE* 6.4 0.2 - - + -
816A VAL* 4.0 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 780 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A ARG* 3.0 70.7 + - - -
776A CYS 3.0 12.6 + - - +
777A GLU* 3.5 8.7 - - - +
779A VAL* 1.3 73.2 - - - +
781A LEU* 1.3 79.7 - - + +
782A CYS 3.0 3.2 + - - -
783A GLY 3.1 2.6 + - - -
784A GLY 3.6 9.2 + - - +
785A ARG* 6.0 0.4 - - - -
786A VAL* 5.0 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 781 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699A LEU* 5.6 2.5 - - + -
702A ALA* 3.8 32.8 - - + +
703A ARG* 4.1 33.7 - - + +
751A TYR 6.0 2.0 - - - +
752A ARG* 3.7 12.3 - - + +
753A GLY* 3.1 23.6 + - - -
777A GLU* 2.8 63.4 + - + +
778A LEU* 3.8 1.6 - - - +
780A HIS* 1.3 84.8 - - + +
782A CYS* 1.3 57.9 + - - +
783A GLY 3.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 782 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ALA* 4.1 23.6 - - - -
753A GLY* 3.2 12.0 - - - +
755A LEU* 2.8 38.8 + - + -
756A PHE* 3.2 23.5 + - + -
778A LEU 3.1 19.0 + - - +
779A VAL 4.0 0.2 - - - +
780A HIS 3.0 1.0 - - - -
781A LEU* 1.3 77.2 - - - +
783A GLY* 1.3 56.6 + - - +
784A GLY 3.7 1.3 - - - -
820A ILE* 3.9 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 783 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A ARG* 3.4 16.3 + - - -
753A GLY 3.5 11.2 - - - -
756A PHE 3.8 9.3 - - - +
757A ALA* 3.9 17.7 - - - +
780A HIS 3.1 8.5 + - - -
781A LEU 3.4 0.6 - - - -
782A CYS* 1.3 80.0 - - - +
784A GLY* 1.3 67.0 + - - +
785A ARG* 5.2 0.9 - - - +
----------------------------------------------------------
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