Contacts of the helix formed by residues 965 - 980 (chain D) in PDB entry 6PUO
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 TRP 965 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962D ARG* 3.8 16.2 - - + +
963D VAL 3.7 1.0 - - - -
964D ASP* 1.3 78.5 - - - +
966D LEU* 1.3 62.6 + - + +
968D ARG* 4.3 0.2 - - - +
969D GLY* 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 966 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953D GLN* 4.6 20.1 - - - +
960D GLU* 5.2 11.9 - - + +
962D ARG* 3.7 19.7 - - + +
965D TRP* 1.3 76.3 - - - +
967D PHE* 1.3 60.1 + - - +
969D GLY* 3.8 1.3 - - - -
970D ALA* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 967 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A MET* 6.5 1.6 - - + -
953D GLN* 5.9 1.8 - - - +
962D ARG 4.4 7.4 + - - +
963D VAL 3.4 21.8 - - - +
965D TRP 3.4 0.4 - - - -
966D LEU* 1.3 77.8 - - - +
968D ARG* 1.3 57.0 + - - +
970D ALA* 3.4 5.7 + - - +
971D VAL* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 968 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022C GLU* 6.0 7.4 - - + -
964D ASP* 3.2 28.8 + - + +
965D TRP 3.7 1.4 + - - +
966D LEU 3.4 0.2 - - - -
967D PHE* 1.3 76.5 - - - +
969D GLY* 1.3 58.9 + - - +
971D VAL* 3.6 8.2 - - - +
972D TYR* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 969 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965D TRP 2.9 18.5 + - - -
966D LEU* 3.8 2.0 - - - -
967D PHE 3.3 0.2 - - - -
968D ARG* 1.3 76.8 - - - +
970D ALA* 1.3 56.4 + - - +
972D TYR* 3.3 7.2 + - - +
973D HIS* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 970 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949D GLY* 5.2 4.9 - - - +
952D LYS* 5.9 0.6 - - + -
953D GLN* 3.7 32.1 - - + +
966D LEU 2.9 17.8 + - - +
967D PHE* 3.8 4.9 - - - +
969D GLY* 1.3 72.2 - - - +
971D VAL* 1.3 60.0 + - - +
973D HIS* 3.7 8.0 - - - +
974D SER* 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 971 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967D PHE 2.9 18.3 + - - +
968D ARG* 3.6 9.4 - - - +
969D GLY 3.2 0.4 - - - -
970D ALA* 1.3 76.8 - - - +
972D TYR* 1.3 55.9 + - - +
974D SER* 3.9 5.1 - - - -
975D TYR* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 972 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968D ARG 2.9 16.7 + - - +
969D GLY* 3.3 7.4 + - - +
971D VAL* 1.3 73.7 - - - +
973D HIS* 1.3 59.8 + - - +
975D TYR* 3.4 6.1 + - - +
976D LEU* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 973 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952D LYS* 4.3 24.3 + - - +
969D GLY 2.9 16.1 + - - +
970D ALA* 3.7 9.0 - - - +
972D TYR* 1.3 76.8 - - - +
974D SER* 1.3 56.6 + - - +
976D LEU* 3.3 7.2 + - - +
977D THR* 2.9 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 974 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945D VAL* 4.7 17.6 - - - +
949D GLY* 4.6 20.4 - - - -
952D LYS* 5.2 4.2 - - - +
970D ALA 2.9 17.9 + - - -
971D VAL* 3.9 5.4 - - - -
973D HIS* 1.3 73.4 - - - +
975D TYR* 1.3 59.9 + - - +
977D THR* 3.3 7.8 + - - -
978D ILE* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 975 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029C LEU* 4.7 20.4 - - + -
971D VAL 2.9 18.8 + - - +
972D TYR* 3.8 6.3 - - - +
974D SER* 1.3 72.3 - - - +
976D LEU* 1.3 60.9 + - - +
978D ILE* 3.3 7.4 + - - +
979D PHE* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 976 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972D TYR 2.9 18.1 + - - +
973D HIS* 3.6 7.9 - - - +
975D TYR* 1.3 76.8 - - - +
977D THR* 1.3 61.9 + - - +
979D PHE* 3.4 14.3 + - - +
980D GLY* 3.5 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 977 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952D LYS* 4.9 11.2 - - - -
973D HIS 2.9 17.0 + - - -
974D SER* 3.7 8.1 - - - -
975D TYR 3.3 0.2 - - - -
976D LEU* 1.3 77.4 - - - +
978D ILE* 1.3 62.0 + - - +
979D PHE 3.6 0.3 + - - -
980D GLY* 3.6 13.6 + - - +
1036D THR* 5.7 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 978 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033C LEU* 4.7 19.4 - - + +
1037C ASN* 5.8 0.3 + - - -
945D VAL* 4.6 22.9 - - + -
974D SER 2.9 16.6 + - - +
975D TYR* 3.8 8.1 - - - +
976D LEU 3.3 0.4 - - - -
977D THR* 1.3 75.0 - - - +
979D PHE* 1.3 64.3 + - - +
980D GLY* 3.3 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 979 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980C GLY* 6.1 0.7 - - - -
1033C LEU* 5.7 5.6 - - + -
1037C ASN* 5.7 4.0 + - - +
975D TYR 2.9 16.6 + - - +
976D LEU* 3.7 9.4 - - - +
977D THR 3.3 0.4 - - - -
978D ILE* 1.3 78.9 - - - +
980D GLY* 1.3 63.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 980 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
979A PHE 6.1 1.1 - - - -
976D LEU 3.5 9.7 + - - -
977D THR 3.6 11.1 + - - -
978D ILE 3.3 5.0 - - - -
979D PHE* 1.3 83.2 - - - +
1037D ASN* 5.1 12.7 + - - -
----------------------------------------------------------
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