Contacts of the helix formed by residues 758 - 769 (chain B) in PDB entry 6XRA
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 758 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145A LEU* 5.6 0.7 - - - -
1146A ASP* 6.0 1.3 - - - -
1151A GLU* 2.8 20.8 + - - +
1154A LYS* 5.8 4.3 - - - +
757B GLY* 1.3 68.4 - - - -
759B PHE* 1.3 62.5 + - - +
760B CYS* 3.1 4.7 - - - -
761B THR* 3.0 32.5 + - - +
762B GLN* 3.3 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 759 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1145A LEU* 5.9 0.4 - - - -
1151A GLU* 4.6 0.4 + - - -
738B CYS* 4.6 4.3 - - + -
742B ILE* 3.7 13.5 - - + -
753B LEU* 3.5 24.7 - - + -
756B TYR* 3.7 26.0 + - + +
757B GLY 3.0 9.3 + - - -
758B SER* 1.3 76.7 - - - +
760B CYS* 1.3 71.7 + - + +
762B GLN* 3.2 3.3 - - - +
763B LEU* 3.1 34.9 + - + +
1001B LEU* 3.2 33.7 - - + -
1004B LEU* 4.2 17.7 - - + -
999C GLY* 3.1 30.3 - - - +
1002C GLN* 4.0 20.0 - - + -
1003C SER* 4.0 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 760 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B VAL 3.8 1.1 - - - -
737B ASP* 4.3 3.1 - - - -
738B CYS* 2.0 61.2 - - + -
739B THR 5.1 0.2 - - - -
758B SER* 4.8 2.5 - - - -
759B PHE* 1.3 85.6 - - + +
761B THR* 1.3 62.4 + - - +
763B LEU* 3.4 5.6 + - - +
764B ASN* 2.8 38.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 761 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758B SER* 3.0 22.7 + - - -
760B CYS* 1.3 81.0 - - - +
762B GLN* 1.3 63.4 + - - +
764B ASN* 2.7 12.5 + - + +
765B ARG* 2.7 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 762 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A LEU 5.5 0.2 - - - +
1143A PRO* 3.1 39.4 + - + +
1144A GLU 2.9 29.3 + - - +
1145A LEU* 3.7 13.6 - - + +
758B SER* 3.4 15.6 - - - +
759B PHE* 3.2 8.5 - - - +
761B THR* 1.3 90.4 - - - +
763B LEU* 1.3 63.2 + - + +
765B ARG* 3.5 24.2 + - - +
766B ALA 3.6 4.2 + - - -
1003C SER* 3.3 26.2 - - - +
1006C THR* 3.9 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 763 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
736B VAL* 5.3 4.5 - - + -
738B CYS* 5.3 1.1 - - - -
759B PHE* 3.1 35.0 + - + +
760B CYS* 3.6 10.1 - - - +
762B GLN* 1.3 77.4 - - + +
764B ASN* 1.3 59.4 + - - +
766B ALA* 3.3 8.7 + - - +
767B LEU* 3.2 29.7 + - - +
1001B LEU 6.0 0.4 - - - +
1004B LEU* 3.7 37.7 - - + +
1005B GLN* 4.1 11.7 - - - +
1008B VAL* 3.9 21.8 - - + -
1002C GLN* 4.1 15.7 - - + +
1006C THR* 3.4 25.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 764 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B SER* 3.3 17.2 - - - -
736B VAL* 2.8 51.8 + - - +
738B CYS* 3.7 2.4 - - - -
760B CYS* 2.8 32.1 + - - +
761B THR* 2.7 19.8 + - + +
763B LEU* 1.3 69.2 - - - +
765B ARG* 1.3 56.4 + - - -
766B ALA 3.2 0.4 - - - -
767B LEU* 4.4 3.3 - - - +
768B THR* 2.9 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 765 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A LEU* 3.7 58.3 + - + +
1142A GLN 2.8 31.1 + - - +
1143A PRO* 4.0 7.5 - - + +
1144A GLU* 4.2 11.2 - - - +
761B THR* 2.7 22.4 + - + +
762B GLN* 3.6 26.7 - - - +
763B LEU 3.4 0.2 - - - -
764B ASN* 1.3 70.8 - - - +
766B ALA* 1.3 64.0 + - - +
768B THR* 3.8 8.6 - - + +
769B GLY* 3.3 14.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 766 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A LEU 4.4 0.8 + - - -
762B GLN 3.6 1.2 + - - -
763B LEU* 3.3 11.2 + - - +
764B ASN 3.2 0.4 - - - -
765B ARG* 1.3 77.9 - - - +
767B LEU* 1.3 63.6 + - + +
769B GLY* 3.2 15.9 + - - -
770B ILE* 3.6 13.5 + - - +
1008B VAL* 4.8 0.9 - - + -
1012B LEU* 4.0 18.4 - - + -
1006C THR* 3.8 19.5 - - + -
1010C GLN* 3.3 32.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 767 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B LYS* 3.7 22.7 - - - +
734B THR* 3.7 26.8 + - - +
735B SER* 4.7 6.7 - - - -
736B VAL* 4.3 9.6 - - + -
763B LEU 3.2 12.9 + - - +
764B ASN* 4.5 4.5 - - - +
766B ALA* 1.3 78.2 - - - +
768B THR* 1.3 60.4 + - - +
769B GLY 3.6 2.4 + - - +
770B ILE* 3.9 10.1 - - + +
1007B TYR* 3.8 23.6 - - + -
1008B VAL* 3.8 43.5 - - + +
1011B GLN* 4.2 20.2 - - + +
1012B LEU* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 768 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A LEU* 4.9 9.2 - - + -
733B LYS* 3.1 33.6 + - - +
735B SER* 5.4 10.2 - - - -
764B ASN* 2.9 31.3 + - - +
765B ARG* 3.8 9.6 - - + +
767B LEU* 1.3 67.7 - - - +
769B GLY* 1.3 63.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 769 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1138A TYR* 3.4 13.5 - - - -
1141A LEU* 4.5 8.5 - - - -
733B LYS* 3.1 26.9 - - - +
765B ARG 3.3 11.4 + - - -
766B ALA 3.2 8.6 + - - -
768B THR* 1.3 75.3 - - - +
770B ILE* 1.3 71.3 + - - +
----------------------------------------------------------
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