Contacts of the helix formed by residues 971 - 982 (chain D) in PDB entry 6GHM
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 HIS 971 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040C TYR* 5.6 2.2 - - - -
1041C THR* 5.6 6.8 - - + +
1045C GLN* 5.1 7.1 + - - -
934D SER 3.4 23.8 - - - +
935D LEU 3.2 16.1 + - - -
936D GLU 3.5 4.8 - - - -
937D GLY* 3.3 26.5 + - - -
966D ALA 3.1 8.1 + - - +
969D ALA* 3.4 29.6 + - + +
970D GLY* 1.3 73.6 - - - +
972D THR* 1.3 66.4 + - - +
973D GLU 3.3 2.5 - - - -
974D ILE* 3.1 22.0 + - + +
975D VAL* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 972 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035C GLU* 3.4 32.9 - - + +
1036C MET* 3.4 39.5 - - + -
1040C TYR* 4.6 6.5 - - - -
970D GLY 3.0 11.3 + - - -
971D HIS* 1.3 71.8 - - - +
973D GLU* 1.3 63.1 + - - +
975D VAL* 3.1 10.7 + - + +
976D LYS* 2.9 24.3 + - + +
1004D ASN* 5.2 1.9 + - - -
1007D VAL* 4.2 21.4 - - + +
1010D PHE* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 973 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035C GLU 4.0 6.1 + - - +
1037C GLU 4.4 5.8 - - - +
1038C GLU* 3.8 9.5 - - - +
1039C GLY* 2.9 28.0 + - - -
1040C TYR* 3.2 13.6 + - + -
1041C THR* 2.8 46.1 + - - +
1042C GLN 4.6 0.2 + - - -
939D PHE* 3.3 33.5 - - + -
971D HIS 3.3 0.8 - - - -
972D THR* 1.3 79.4 - - - +
974D ILE* 1.3 57.2 + - - +
976D LYS* 3.5 7.6 + - + +
977D PHE* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 974 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1041C THR* 4.6 4.3 - - - +
933D SER 4.0 9.4 - - - +
934D SER* 4.0 19.1 - - - +
937D GLY* 3.7 36.3 - - - +
939D PHE* 3.7 35.0 - - + +
942D VAL* 4.1 15.3 - - + -
966D ALA* 3.9 14.6 - - + -
971D HIS* 3.1 19.6 + - + +
973D GLU* 1.3 73.5 - - - +
975D VAL* 1.3 65.6 + - - +
977D PHE* 4.4 1.1 - - - -
978D LEU* 2.9 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 975 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963D LEU* 4.0 12.8 - - + -
966D ALA* 3.5 29.8 - - + +
967D VAL* 3.8 24.7 - - + +
970D GLY 5.5 0.4 - - - -
971D HIS 2.9 23.4 + - - +
972D THR* 3.1 12.3 + - + +
974D ILE* 1.3 75.6 - - - +
976D LYS* 1.3 63.0 + - + +
978D LEU* 3.9 1.4 - - - +
979D VAL* 3.0 28.1 + - - +
1007D VAL* 4.3 19.3 - - + -
1010D PHE* 4.3 16.6 - - + -
1011D LEU* 4.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 976 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1035C GLU 5.0 0.4 - - - +
1036C MET* 2.7 59.1 + - + +
1037C GLU* 5.4 0.4 + - - -
972D THR* 2.9 15.0 + - + +
973D GLU* 3.8 9.4 - - + +
975D VAL* 1.3 76.7 - - + +
977D PHE* 1.3 54.1 + - - +
979D VAL* 2.9 2.9 + - - +
980D GLN* 2.6 57.7 + - + +
1010D PHE* 3.7 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 977 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939D PHE* 3.5 26.0 - + + -
942D VAL* 4.0 24.0 - - + -
943D GLN* 4.0 30.7 - - + -
946D ILE* 4.1 30.5 - - + -
947D TYR* 4.9 7.6 - + - -
973D GLU 3.0 18.4 + - - +
974D ILE 3.3 2.2 + - - +
976D LYS* 1.3 75.4 - - - +
978D LEU* 1.3 61.9 + - + +
980D GLN* 3.3 9.4 + - + +
981D PHE* 2.8 49.2 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 978 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930D LEU* 4.5 7.9 - - + -
934D SER* 3.8 11.4 - - - +
942D VAL* 4.1 16.2 - - + -
946D ILE* 3.7 28.0 - - + -
962D ALA* 3.7 15.5 - - + +
963D LEU* 3.7 32.8 - - + +
966D ALA* 4.3 2.9 - - + -
974D ILE* 2.9 28.0 + - + +
975D VAL 3.9 2.7 - - - +
977D PHE* 1.3 78.1 - - + +
979D VAL* 1.3 62.4 + - - +
981D PHE* 3.1 17.5 + - - +
983D VAL* 3.2 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 979 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963D LEU* 3.9 29.8 - - + -
975D VAL 3.0 17.6 + - - +
976D LYS 2.9 4.2 + - - +
978D LEU* 1.3 73.1 - - - +
980D GLN* 1.3 66.2 + - - +
982D GLY* 3.1 14.0 + - - -
983D VAL* 4.3 6.8 + - + +
985D VAL* 4.3 8.5 - - + -
1010D PHE* 3.7 17.3 - - + -
1011D LEU* 4.2 9.6 - - + -
1014D SER* 3.5 36.3 - - - +
1120D ILE* 3.8 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 980 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976D LYS* 2.6 55.8 + - + +
977D PHE* 3.8 8.5 - - + +
979D VAL* 1.3 75.1 - - - +
981D PHE* 1.3 60.7 + - - +
982D GLY 3.3 0.7 + - - -
1010D PHE* 4.0 18.4 - - - -
1120D ILE* 3.7 23.7 - - - +
1121D LYS 5.3 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 981 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946D ILE* 3.6 43.3 - - + -
947D TYR* 3.8 40.2 - + - -
952D PRO* 4.1 20.2 - - + -
977D PHE* 2.8 32.3 + + + +
978D LEU* 3.3 12.1 - - - +
979D VAL 3.1 0.6 - - - -
980D GLN* 1.3 76.4 - - - +
982D GLY* 1.3 57.7 + - - +
983D VAL* 4.6 2.7 - - + -
1121D LYS 5.2 0.9 - - - -
1122D PRO* 3.9 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 982 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952D PRO* 6.2 0.4 - - - -
953D SER* 4.8 0.3 + - - -
979D VAL 3.1 12.9 + - - -
980D GLN 3.2 1.8 - - - -
981D PHE* 1.3 79.4 - - - +
983D VAL* 1.3 67.4 + - - +
984D ASN* 4.7 0.2 - - - -
1120D ILE* 3.9 14.6 - - - +
1121D LYS 4.3 1.3 - - - -
1122D PRO* 3.3 38.3 - - - +
----------------------------------------------------------
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