Contacts of the helix formed by residues 955 - 964 (chain A) in PDB entry 6DBV
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 955 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A ILE* 5.8 1.7 - - - +
821A GLY* 6.1 0.9 - - - -
825A GLU* 4.8 22.4 - - + +
950A TYR* 5.7 2.9 - - + +
954A ILE* 1.3 78.6 - - - +
956A ASN* 1.3 66.8 + - - +
957A TYR* 4.0 6.1 + - - +
958A LEU* 3.4 34.4 + - + +
959A HIS* 3.1 22.4 + - - +
14E T 4.6 11.6 + - - -
15E T 2.6 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 956 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A GLU* 5.3 9.4 - - - +
735A ARG* 5.6 1.4 + - - -
743A SER* 4.2 14.5 + - - +
748A ILE* 3.3 44.9 - - - +
756A ARG* 5.1 2.4 - - - +
954A ILE 5.4 0.4 + - - -
955A THR* 1.3 71.0 + - - +
957A TYR* 1.3 62.1 + - + +
959A HIS* 2.6 31.8 + - - +
960A LYS* 2.9 25.9 + - - +
14E T 3.2 12.3 + - - -
15E T 2.5 47.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 957 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A ASP* 4.8 0.5 - - - -
731A GLU* 4.0 23.4 + - + +
813A LEU* 4.6 17.4 - - + +
814A ASP* 5.3 5.4 - - - +
817A HIS* 3.1 41.4 - - + +
818A CYS* 3.8 23.9 - - + +
821A GLY* 4.4 12.3 - - - -
822A ASN* 4.3 7.2 - - - +
955A THR* 3.8 3.6 + - - +
956A ASN* 1.3 81.4 - - + +
958A LEU* 1.3 56.7 + - - +
960A LYS* 3.2 16.3 + - + +
961A THR* 2.9 33.2 + - - +
15E T 3.8 15.7 + - - -
16E A 2.8 42.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 958 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A MET* 6.6 0.2 - - + -
822A ASN* 4.4 15.4 + - - +
825A GLU* 5.5 7.0 - - + -
826A PHE* 5.9 6.1 - - + -
908A TYR* 6.3 1.6 - - + -
938A PHE* 4.5 14.8 - - + -
942A LEU* 5.6 5.8 - - + -
950A TYR* 4.7 20.9 - - + +
954A ILE* 4.1 17.0 - - + -
955A THR* 3.4 32.5 - - + +
957A TYR* 1.3 77.8 - - - +
959A HIS* 1.3 61.9 + - - +
961A THR* 3.1 10.8 - - + +
962A LEU* 2.9 53.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 959 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A ILE* 5.4 10.1 - - + -
749A CYS* 2.8 29.4 - - + +
754A SER* 5.6 2.0 - - - -
759A ALA* 4.7 17.6 - - + +
763A MET* 5.2 1.4 + - - -
766A HIS* 4.5 9.4 + + - -
954A ILE* 5.1 8.7 - - + +
955A THR 3.1 11.8 + - - +
956A ASN* 2.6 18.6 + - - +
958A LEU* 1.3 76.1 - - - +
960A LYS* 1.3 71.3 + - + +
962A LEU* 5.0 2.5 - - - -
963A ALA* 2.9 42.0 + - + +
964A HIS* 2.9 13.8 + + - -
1101A ZN 2.2 37.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 960 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A GLU* 3.5 18.4 + - - -
748A ILE 4.4 2.4 + - - -
749A CYS 4.1 0.2 - - - -
750A THR* 2.6 51.9 + - - +
751A LEU* 4.4 17.9 - - + +
813A LEU* 4.3 31.4 - - + +
956A ASN* 2.9 24.4 + - - +
957A TYR* 3.4 21.1 - - + +
959A HIS* 1.3 89.4 - - + +
961A THR* 1.3 56.7 + - - +
964A HIS* 2.6 34.7 + - + +
965A VAL* 3.1 9.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 961 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A LEU* 5.9 2.7 - - - -
818A CYS* 5.8 6.1 - - + -
822A ASN* 4.6 13.5 - - - +
908A TYR* 6.3 0.2 - - + -
911A MET* 5.6 2.3 - - - +
915A TRP* 3.2 28.7 + - - -
931A TYR* 2.7 34.1 + - - -
957A TYR 2.9 17.0 + - - +
958A LEU* 3.1 26.0 - - + +
960A LYS* 1.3 77.4 - - - +
962A LEU* 1.3 71.8 + - + +
963A ALA 3.4 0.2 - - - -
965A VAL* 3.5 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 962 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A MET* 3.3 34.2 - - + +
764A VAL* 4.0 15.6 - - - +
911A MET* 4.3 15.5 - - + -
935A SER* 4.5 17.5 - - - +
938A PHE* 3.4 49.4 - - + -
939A ALA* 5.3 2.7 - - + -
942A LEU* 5.8 1.6 - - + -
954A ILE* 6.4 0.2 - - + -
958A LEU* 2.9 36.7 + - + +
959A HIS* 4.4 2.7 - - - +
961A THR* 1.3 90.4 - - + +
963A ALA* 1.3 59.1 + - - +
966A PRO* 5.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 963 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
763A MET 3.2 19.3 - - - +
764A VAL 3.5 13.0 - - - +
766A HIS* 3.4 26.8 + - + +
959A HIS* 2.9 22.4 + - + +
962A LEU* 1.3 78.6 - - - +
964A HIS* 1.3 72.5 + - + +
965A VAL 3.9 0.9 - - - -
966A PRO* 4.3 9.1 - - - +
967A GLU* 5.6 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 964 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A CYS* 2.8 12.4 - - - -
751A LEU* 3.4 33.6 - - + +
752A CYS* 3.5 11.7 - - + -
766A HIS* 3.8 20.0 + - + +
767A SER 4.6 0.2 - - - -
768A ILE* 3.6 15.2 - - + +
813A LEU* 6.0 0.7 - - + -
959A HIS* 3.0 27.8 - + - -
960A LYS* 2.6 21.3 + - + +
963A ALA* 1.3 75.6 - - + +
965A VAL* 1.3 65.9 + - - +
966A PRO* 3.4 3.3 - - - -
967A GLU* 3.5 11.8 + - - +
968A ILE* 3.1 20.4 + - + +
1101A ZN 2.2 32.1 - - - -
----------------------------------------------------------
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