Contacts of the helix formed by residues 945 - 962 (chain A) in PDB entry 1HU3
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 ALA 945 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A HIS* 4.0 12.1 - - + +
940A LEU 3.4 25.4 - - - +
942A PHE* 2.5 18.7 + - + +
944A LYS* 1.3 71.8 - - - +
946A LYS* 1.3 63.1 + - - -
947A PRO* 3.1 4.5 - - - -
948A ARG* 3.0 40.1 + - - +
949A MSE 3.0 14.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 946 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941A ASP* 2.8 46.3 + - - +
942A PHE 2.9 6.1 + - - +
943A GLU* 3.2 34.1 - - - +
945A ALA* 1.3 76.7 - - - +
947A PRO* 1.3 57.4 - - + +
949A MSE 3.3 4.8 + - - -
950A ASP* 2.7 46.6 + - - +
980A ARG* 3.5 5.3 + - - +
984A TRP* 5.5 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 947 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
943A GLU 4.2 2.5 - - - +
944A LYS* 3.6 19.1 - - - +
945A ALA 3.2 1.3 - - - -
946A LYS* 1.3 97.2 - - + +
948A ARG* 1.3 65.6 + - + +
950A ASP* 3.3 12.5 + - + +
951A GLN* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 948 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A ALA* 5.6 3.6 - - - +
911A HIS* 3.8 37.7 + - + +
944A LYS* 4.5 5.7 + - - +
945A ALA* 3.0 33.2 + - - +
947A PRO* 1.3 80.1 - - + +
949A MSE 1.3 61.6 + - - +
951A GLN* 3.3 13.1 + - - +
952A TYR* 3.0 51.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 949 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A HIS* 3.4 26.0 - - + -
933A LEU* 4.5 10.8 - - - -
937A GLY 4.9 2.2 - - - +
940A LEU* 2.9 48.9 - - + +
941A ASP* 3.1 30.5 - - + +
945A ALA* 3.0 10.0 + - + +
946A LYS 3.5 7.4 - - - +
948A ARG* 1.3 75.0 - - - +
950A ASP* 1.3 66.4 + - - +
952A TYR* 3.1 20.5 + - - -
953A PHE* 3.0 51.6 + - + -
980A ARG* 3.6 5.6 - - - +
984A TRP* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 950 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946A LYS* 2.7 26.5 + - - +
947A PRO* 3.3 12.0 - - + +
948A ARG 3.2 0.2 - - - -
949A MSE 1.3 77.4 - - - +
951A GLN* 1.3 55.9 + - - +
953A PHE* 3.7 1.6 + - - +
954A ASN* 3.0 41.3 + - - +
980A ARG* 2.4 43.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 951 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
947A PRO 3.1 9.5 + - - +
948A ARG* 3.5 16.8 - - - +
949A MSE 3.1 0.4 - - - -
950A ASP* 1.3 78.1 - - - +
952A TYR* 1.3 70.6 + - + +
954A ASN* 3.2 7.2 + - - +
955A GLN* 2.9 45.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 952 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A HIS* 2.9 49.0 + + - +
914A VAL* 3.7 27.8 - - + -
915A VAL* 3.6 28.8 - - + +
918A LEU* 3.8 19.1 - - + +
933A LEU* 5.5 0.9 - - + -
948A ARG* 3.0 33.6 + - + +
949A MSE 3.5 24.9 - - - +
951A GLN* 1.3 78.1 - - + +
953A PHE* 1.3 61.4 + + + +
955A GLN* 2.9 33.5 + - - +
956A MSE 3.0 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 953 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933A LEU* 3.8 15.5 - - + -
949A MSE 3.0 49.9 + - + +
950A ASP 4.1 1.1 - - - +
952A TYR* 1.3 82.6 - - + +
954A ASN* 1.3 63.3 + - - +
956A MSE 3.2 27.1 + - + +
957A GLU* 3.2 21.8 + - - +
976A VAL* 3.6 31.0 - - + -
977A ILE* 4.2 27.2 - - + +
980A ARG* 3.6 34.1 - - + +
984A TRP* 3.4 24.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 954 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950A ASP* 3.0 29.3 + - - +
951A GLN* 3.2 7.1 + - - +
953A PHE* 1.3 79.1 - - - +
955A GLN* 1.3 63.5 + - - +
957A GLU* 3.4 9.4 + - - +
958A LYS* 3.2 21.8 + - - +
980A ARG* 5.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 955 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A VAL* 6.2 0.2 - - - +
918A LEU* 3.5 39.7 - - + +
951A GLN* 2.9 40.0 + - + +
952A TYR* 2.9 19.9 + - - +
954A ASN* 1.3 79.1 - - + +
956A MSE 1.3 59.9 + - - +
958A LYS* 3.5 8.1 + - - +
959A ILE* 3.2 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 956 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A LEU* 4.1 16.4 - - + -
929A LEU* 4.3 13.5 - - + -
930A CYS* 6.1 0.2 - - - -
933A LEU* 3.5 23.1 - - + -
952A TYR* 3.0 18.5 + - + +
953A PHE* 3.2 70.0 - - + +
954A ASN 3.1 0.2 - - - -
955A GLN* 1.3 74.9 - - - +
957A GLU* 1.3 65.9 + - - +
958A LYS 3.1 2.0 - - - -
959A ILE* 3.1 12.4 + - + +
960A VAL* 3.0 25.8 + - - +
973A LEU* 4.2 21.3 - - + +
976A VAL* 5.1 8.5 - - - -
977A ILE* 4.4 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 957 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A PHE 3.2 16.0 + - - +
954A ASN* 3.7 9.5 - - - +
956A MSE 1.3 76.1 - - - +
958A LYS* 1.3 62.8 + - - +
960A VAL* 3.0 10.6 + - + +
961A LYS* 2.8 49.3 + - - +
977A ILE* 4.0 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 958 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954A ASN 3.2 11.3 + - - +
955A GLN* 3.6 12.6 - - - +
956A MSE 3.1 0.2 - - - -
957A GLU* 1.3 84.9 + - - +
959A ILE* 1.3 60.6 + - + +
961A LYS* 3.4 7.5 + - - +
962A GLU* 3.2 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 959 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A LEU* 4.0 27.4 - - + +
921A HIS* 4.9 14.1 - - + -
926A LEU* 4.0 20.4 - - + -
955A GLN* 3.2 16.6 + - + +
956A MSE 3.1 11.8 + - + +
958A LYS* 1.3 76.9 - - + +
960A VAL* 1.3 57.3 + - - +
962A GLU* 2.8 23.9 - - - +
965A THR* 3.7 27.7 + - + +
973A LEU* 3.6 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 960 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A MSE 3.0 18.7 + - - +
957A GLU* 3.0 17.9 + - + +
959A ILE* 1.3 79.1 - - - +
961A LYS* 1.3 69.9 + - - +
962A GLU 3.1 5.7 + - - -
963A ARG* 4.0 2.6 + - - +
970A ARG* 3.4 47.3 + - + +
973A LEU* 3.8 26.0 - - + -
974A GLN* 4.1 25.1 - - + +
977A ILE* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 961 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957A GLU* 2.8 38.2 + - - +
958A LYS* 3.8 8.5 - - - +
960A VAL* 1.3 76.3 - - - +
962A GLU* 1.3 66.3 + - + +
963A ARG* 3.5 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 962 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A LYS 3.2 14.4 + - - +
959A ILE* 2.8 22.4 - - - +
960A VAL 3.1 1.7 - - - +
961A LYS* 1.3 82.0 - - + +
963A ARG* 1.3 59.5 + - - +
964A LYS* 2.8 18.3 + - + +
965A THR* 4.2 1.4 + - - +
----------------------------------------------------------
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