Contacts of the helix formed by residues 976 - 987 (chain O) in PDB entry 6IY3
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 976 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958O THR 5.5 1.3 - - - +
959O PRO* 3.7 27.6 - - + +
971O LEU* 2.3 40.7 + - + +
972O SER* 3.3 11.8 + - - -
975O GLU* 1.3 87.9 - - + +
977O LEU* 1.3 60.8 + - - +
978O LEU 3.1 0.7 - - - -
979O VAL* 3.3 20.1 - - + +
980O ILE* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 977 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972O SER 4.3 4.4 + - - +
973O GLU* 3.4 30.4 + - - +
974O GLU 4.1 5.4 + - - +
975O GLU 3.2 1.0 - - - -
976O THR* 1.3 77.4 + - - +
978O LEU* 1.3 57.5 + - - +
980O ILE* 3.3 11.5 + - + +
981O ARG* 2.9 56.9 + - + +
1254O LEU* 4.8 11.2 - - + -
1255O ARG* 4.1 18.8 - - - +
1258O LEU* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 978 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670O LEU* 3.8 30.3 - - + -
974O GLU 5.0 0.2 + - - -
975O GLU 3.3 14.1 + - - +
976O THR 3.1 0.4 - - - -
977O LEU* 1.3 77.6 - - - +
979O VAL* 1.3 59.0 + - + +
981O ARG* 3.3 12.3 + - + -
982O ARG* 2.9 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 979 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955O TRP* 4.5 7.6 - - - +
956O PHE* 3.6 40.3 - - + +
959O PRO* 4.5 11.0 - - + -
975O GLU 4.5 2.5 - - - +
976O THR* 3.1 33.3 + - + +
978O LEU* 1.3 73.1 - - + +
980O ILE* 1.3 61.3 + - - +
982O ARG* 3.2 28.3 + - - +
983O LEU* 3.0 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 980 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959O PRO* 4.2 20.0 - - + -
960O PHE 5.7 1.8 - - - +
972O SER 5.3 5.2 - - - +
976O THR 2.9 19.9 + - - +
977O LEU* 3.3 12.8 + - + +
979O VAL* 1.3 75.9 - - - +
981O ARG* 1.3 56.7 + - - +
983O LEU* 3.1 20.4 + - + +
984O HIS* 2.9 54.7 + - + +
1234O LYS* 4.0 34.5 - - + -
1254O LEU* 4.6 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 981 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977O LEU* 2.9 39.3 + - + +
978O LEU* 3.6 16.8 - - + +
979O VAL 3.3 0.2 - - - -
980O ILE* 1.3 75.6 - - + +
982O ARG* 1.3 57.3 + - - +
984O HIS* 3.3 6.2 + - - +
985O LYS* 2.9 28.1 + - - +
1250O GLN* 3.3 46.7 + - - +
1251O GLU* 2.5 49.3 + - - +
1254O LEU* 4.3 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 982 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670O LEU* 3.6 39.1 - - + +
671O LEU 4.1 2.4 - - - +
672O ASP* 3.3 35.9 - - - +
955O TRP* 4.3 11.3 - - - +
956O PHE* 3.3 34.4 - - + -
978O LEU* 2.9 54.6 + - + +
979O VAL* 3.2 32.6 + - - +
981O ARG* 1.3 73.7 - - - +
983O LEU* 1.3 62.3 + - - +
985O LYS* 3.2 3.3 + - - +
986O VAL* 2.9 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 983 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932O PRO* 5.4 15.3 - - + -
956O PHE* 3.5 48.9 - - + +
979O VAL* 3.0 19.5 + - + +
980O ILE* 3.1 24.0 + - + +
982O ARG* 1.3 76.9 - - - +
984O HIS* 1.3 57.5 + - + +
986O VAL* 3.3 13.2 - - + +
987O LEU* 2.9 46.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 984 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
980O ILE* 2.9 48.4 + - + +
981O ARG* 3.5 9.6 - - - +
983O LEU* 1.3 78.0 - - + +
985O LYS* 1.3 55.8 + - - +
987O LEU* 3.4 4.5 - - - -
988O ARG* 3.0 33.9 + - - +
1234O LYS* 3.1 37.4 - - + +
1237O GLN* 4.9 1.3 - - + -
1238O ALA* 3.5 12.5 - - + +
1241O PHE* 3.2 22.9 - + + -
1250O GLN* 3.4 17.9 - - - +
1254O LEU* 3.4 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 985 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672O ASP* 3.3 38.2 + - - +
673O GLN* 5.8 4.8 - - - +
676O ASP* 5.1 3.5 + - - -
743O ASP* 4.7 4.5 + - - -
744O TYR* 3.6 47.0 - - + +
981O ARG 2.9 17.2 + - - +
982O ARG* 3.2 6.3 + - - +
984O HIS* 1.3 77.4 - - - +
986O VAL* 1.3 61.8 + - - +
987O LEU 3.5 0.3 + - - -
988O ARG* 3.6 15.8 + - - +
989O PRO* 3.7 9.9 - - - +
1250O GLN* 5.2 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 986 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672O ASP* 4.9 7.2 + - - +
675O LYS* 5.0 22.2 - - + +
676O ASP* 6.1 0.4 - - - +
744O TYR* 5.8 2.5 - - - -
945O ILE* 6.4 1.3 - - + -
949O VAL* 6.5 0.4 - - + -
982O ARG 2.9 16.5 + - - +
983O LEU* 3.3 27.4 - - + +
985O LYS* 1.3 77.0 - - - +
987O LEU* 1.3 71.1 + - + +
988O ARG 3.5 0.4 - - - -
989O PRO* 3.7 11.3 - - - +
990O PHE* 3.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 987 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932O PRO* 6.3 2.0 - - + -
933O GLU* 4.9 16.2 - - + +
937O LEU* 5.0 16.2 - - + +
983O LEU* 2.9 30.0 + - + +
984O HIS* 3.4 7.0 - - - +
985O LYS 3.3 0.2 - - - -
986O VAL* 1.3 92.9 - - + +
988O ARG* 1.3 60.6 + - - +
989O PRO* 4.5 0.2 - - - -
990O PHE* 5.0 6.3 - - + -
991O LEU* 3.7 45.4 - - + +
1235O VAL* 5.9 7.4 - - + -
1238O ALA* 5.5 9.0 - - + +
1241O PHE* 5.6 1.4 - - - -
1242O ASP* 4.4 6.4 - - - +
----------------------------------------------------------
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