Contacts of the helix formed by residues 982 - 992 (chain r) in PDB entry 6FF7
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 982 (chain r).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968r ASN 4.0 19.7 - - - -
969r LEU 3.4 12.2 + - - -
970r VAL* 5.1 1.8 - - - -
980r GLN 3.8 1.0 + - - -
981r VAL* 1.3 77.5 - - - +
983r GLU* 1.3 58.9 + - - +
984r LEU* 3.0 7.9 - - - -
985r GLY* 2.7 21.0 + - - -
986r ARG* 3.0 11.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 983 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
982r THR* 1.3 73.2 - - - +
984r LEU* 1.3 57.8 + - - +
986r ARG* 3.3 9.1 + - - +
987r ILE* 2.9 29.6 + - - +
1101r ASN* 5.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 984 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967r ASN 5.8 1.1 - - - +
968r ASN* 3.9 19.7 - - + +
969r LEU* 5.1 0.9 - - - -
982r THR* 3.0 3.9 - - - -
983r GLU* 1.3 77.1 - - - +
985r GLY* 1.3 58.7 + - - +
987r ILE* 3.3 7.1 + - - +
988r ALA* 2.9 29.5 + - - +
998r VAL* 5.1 9.6 - - + +
1002r ASN* 6.1 5.4 - - + -
1098r ILE* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 985 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902r ASN* 5.5 6.0 - - - +
906r VAL* 5.2 3.4 - - - -
969r LEU* 3.7 32.1 + - - +
981r VAL* 6.1 0.9 - - - -
982r THR 2.7 10.8 + - - -
984r LEU* 1.3 76.9 - - - +
986r ARG* 1.3 58.5 + - - -
988r ALA* 3.1 6.8 + - - +
989r SER* 2.9 29.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 986 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906r VAL* 4.7 10.7 - - + +
981r VAL* 5.8 4.3 - - + +
982r THR 3.0 10.1 + - - +
983r GLU* 3.3 11.4 + - - +
985r GLY* 1.3 73.7 - - - +
987r ILE* 1.3 63.4 + - - +
989r SER* 3.3 6.6 + - - -
990r HIS* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 987 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
983r GLU 2.9 17.2 + - - +
984r LEU* 3.6 7.0 - - - +
986r ARG* 1.3 75.7 - - - +
988r ALA* 1.3 63.8 + - - +
990r HIS* 3.4 5.0 + - - +
991r TYR* 3.0 27.0 + - - +
1094r ALA* 4.5 20.7 - - + +
1097r GLU* 4.9 13.9 - - + -
1098r ILE* 5.3 7.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 988 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902r ASN* 6.2 2.9 - - + -
969r LEU* 5.7 4.0 - - + -
984r LEU 2.9 14.8 + - - +
985r GLY* 3.3 12.8 - - - +
987r ILE* 1.3 79.4 - - - +
989r SER* 1.3 61.6 + - - +
992r TYR* 3.1 18.4 + - - -
993r ILE* 3.2 31.5 + - - +
994r THR 5.3 1.1 - - - +
995r ASN* 5.7 3.6 - - + -
998r VAL* 4.4 18.2 - - + -
1094r ALA* 5.8 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 989 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595r ILE* 5.5 2.4 - - - -
598r ARG* 4.2 17.2 - - - +
902r ASN* 5.1 2.6 - - - +
903r ALA* 3.9 35.8 - - - +
906r VAL* 3.9 13.7 - - - -
985r GLY 2.9 15.6 + - - -
986r ARG 3.7 3.6 - - - -
988r ALA* 1.3 77.1 - - - +
990r HIS* 1.3 63.2 + - - +
992r TYR* 3.1 14.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 990 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595r ILE* 4.7 13.7 - - - +
598r ARG* 4.8 11.4 - - - +
599r LYS* 5.3 15.9 - - + +
986r ARG 2.9 17.9 + - - +
987r ILE* 3.8 5.8 - - - +
989r SER* 1.3 77.2 - - - +
991r TYR* 1.3 60.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 991 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595r ILE* 6.2 0.2 - - - -
987r ILE 3.0 16.5 + - - +
990r HIS* 1.3 77.1 - - + +
992r TYR* 1.3 71.5 + - - +
993r ILE* 3.1 6.3 + - + +
1090r ARG* 3.4 45.3 - - + +
1093r ARG* 5.5 2.5 - - + -
1094r ALA* 4.0 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 992 (chain r).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595r ILE* 5.3 12.6 - - + -
988r ALA 3.1 7.3 + - - -
989r SER* 3.1 11.0 + - - +
990r HIS 3.5 0.2 - - - -
991r TYR* 1.3 80.1 - - - +
993r ILE* 1.3 61.0 + - - +
994r THR 4.0 1.0 + - - -
----------------------------------------------------------
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