Contacts of the helix formed by residues 974 - 987 (chain A) in PDB entry 3H2U
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 ASP 974 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A CYS* 3.5 5.4 - - - -
973A THR* 1.3 76.9 + - - +
975A LYS* 1.3 61.8 + - - +
976A ARG* 3.2 19.0 + - - +
977A ILE* 2.8 44.3 + - + +
978A ARG* 2.8 33.8 + - - +
1047A LYS* 3.6 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 975 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
973A THR 3.9 2.2 + - - -
974A ASP* 1.3 70.3 + - - +
976A ARG* 1.3 67.1 + - - +
978A ARG* 3.0 37.9 - - - +
979A THR* 2.8 48.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 976 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974A ASP* 3.2 17.8 + - - +
975A LYS* 1.3 81.0 - - - +
977A ILE* 1.4 93.3 + - - +
979A THR* 3.6 2.7 - - - -
980A ASN* 2.9 52.0 + - - +
1040A GLU* 5.0 4.4 + - - -
1043A ALA* 5.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 977 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972A CYS* 4.3 2.0 - - - -
974A ASP* 2.8 37.9 + - + +
976A ARG* 1.4 96.9 - - - +
978A ARG* 1.3 58.2 + - - +
979A THR 3.1 1.3 - - - -
980A ASN* 3.9 5.5 - - - +
981A LEU* 2.7 34.6 + - + +
1040A GLU* 3.6 33.2 - - + +
1043A ALA* 4.3 17.9 - - + +
1044A ALA* 3.9 18.4 - - + +
1047A LYS* 4.3 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 978 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A ALA* 3.0 34.9 - - + +
970A LYS* 5.3 1.8 - - - +
972A CYS* 3.2 31.1 + - - +
973A THR* 3.7 8.5 + - - +
974A ASP 2.8 35.0 + - - +
975A LYS* 3.0 45.9 - - - +
977A ILE* 1.3 73.8 - - - +
979A THR* 1.3 58.8 + - - +
981A LEU* 3.8 5.5 - - - +
982A LEU* 2.9 45.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 979 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975A LYS* 2.8 43.3 + - - +
976A ARG* 3.6 4.0 - - - +
978A ARG* 1.3 75.9 + - - +
980A ASN* 1.3 69.7 - - - +
981A LEU 3.1 0.9 - - - -
982A LEU* 3.2 5.8 + - - +
983A GLN* 2.8 49.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 980 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976A ARG* 2.9 46.5 + - - +
977A ILE* 4.2 0.3 - - - -
979A THR* 1.3 76.7 - - - +
981A LEU* 1.3 64.7 + - - +
983A GLN* 4.3 14.0 - - - +
984A VAL* 2.8 36.9 + - + +
1040A GLU* 3.6 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 981 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965A ALA* 3.8 14.6 - - + +
968A VAL* 3.6 31.4 - - + -
969A ALA* 3.8 18.4 - - + +
977A ILE* 2.7 22.9 + - + +
978A ARG* 3.8 5.6 - - - +
980A ASN* 1.3 76.0 - - - +
982A LEU* 1.3 61.5 + - - +
984A VAL* 3.5 6.1 - - + +
985A CYS* 3.4 22.7 - - - +
1037A THR* 3.8 23.6 - - + +
1040A GLU* 3.4 26.0 - - + +
1041A ALA* 3.6 16.6 - - + +
1044A ALA* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 982 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A LYS* 4.2 21.1 - - + +
969A ALA* 3.7 24.5 - - + -
978A ARG* 2.9 32.3 + - + +
979A THR* 3.2 4.9 + - - +
981A LEU* 1.3 72.1 - - - +
983A GLN* 1.3 70.8 + - + +
985A CYS* 3.3 4.3 + - - -
986A GLU* 2.6 51.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 983 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A THR* 2.8 39.6 + - + +
980A ASN* 3.7 14.6 + - - +
982A LEU* 1.3 79.7 - - + +
984A VAL* 1.3 54.7 - - - +
985A CYS 2.5 15.6 + - - -
986A GLU* 2.9 14.2 + - - +
987A ARG* 3.5 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 984 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980A ASN* 2.8 41.3 + - + +
981A LEU* 3.5 14.1 - - + +
983A GLN* 1.3 75.0 - - + +
985A CYS* 1.3 55.2 + - + +
987A ARG* 3.1 33.3 + - - +
988A ILE* 3.9 6.6 - - - +
1033A SER* 3.7 8.0 - - - +
1036A GLU* 4.1 24.9 - - + +
1037A THR* 3.4 36.8 + - - +
1040A GLU* 4.4 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 985 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A THR* 3.2 28.1 - - + +
965A ALA* 4.0 22.2 - - + -
966A LYS* 4.1 24.0 - - - -
981A LEU 3.4 19.0 + - - +
982A LEU* 3.3 8.5 + - - -
983A GLN 2.5 13.9 + - - -
984A VAL* 1.3 77.5 - - + +
986A GLU* 1.3 58.0 + - - +
987A ARG 3.1 5.3 + - - -
988A ILE* 3.7 25.4 + - + +
989A PRO* 3.7 0.5 - - - +
1037A THR* 4.1 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 986 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A LYS* 3.8 27.6 + - - +
982A LEU* 2.6 57.8 + - - +
983A GLN* 2.9 7.5 + - - +
985A CYS* 1.3 77.9 - - - +
987A ARG* 1.3 58.4 + - - +
988A ILE 3.5 0.2 - - - -
989A PRO* 3.8 10.5 - - - +
990A THR* 4.5 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 987 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983A GLN* 3.5 23.8 + - - +
984A VAL* 3.1 48.8 + - - +
986A GLU* 1.3 77.8 - - - +
988A ILE* 1.3 65.3 + - - +
989A PRO* 3.3 3.4 - - - -
990A THR* 3.1 13.0 + - - -
991A ILE* 3.0 34.3 + - + +
1033A SER* 4.0 17.6 + - - +
1036A GLU* 4.4 9.3 + - - -
----------------------------------------------------------
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