Contacts of the helix formed by residues 1019 - 1030 (chain U) 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 SER1019 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017U LEU 3.7 0.5 - - - +
1018U ARG* 1.3 82.1 - - - +
1020U GLY* 1.3 64.6 + - - +
1021U LEU* 3.2 10.3 + - - -
1022U ASP* 3.3 13.8 + - - +
1023U ARG* 3.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1020 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898U VAL* 5.1 9.4 - - - +
1018U ARG 3.7 2.2 + - - -
1019U SER* 1.3 71.3 - - - +
1021U LEU* 1.3 56.8 + - - +
1023U ARG* 3.7 8.1 - - - +
1024U SER* 3.0 28.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1021 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019U SER* 3.1 6.8 - - - -
1020U GLY* 1.3 75.6 - - - +
1022U ASP* 1.3 59.8 + - - +
1024U SER* 3.3 6.8 + - - -
1025U LYS* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1022 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208M ARG* 4.7 10.9 - - + +
1017U LEU* 3.9 21.5 - - + +
1018U ARG 5.4 0.2 - - - +
1019U SER* 3.3 16.4 + - - +
1021U LEU* 1.3 79.1 - - - +
1023U ARG* 1.3 62.0 + - - +
1025U LYS* 3.2 10.2 + - - +
1026U TYR* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1023 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898U VAL* 4.7 15.7 - - + -
1013U ALA 5.9 1.1 - - - -
1014U SER* 5.4 11.0 - - - +
1017U LEU* 4.3 15.6 - - + +
1018U ARG 5.5 0.4 - - - +
1019U SER 3.1 17.3 + - - +
1020U GLY* 3.7 9.4 - - - +
1021U LEU 3.2 0.2 - - - -
1022U ASP* 1.3 77.4 - - - +
1024U SER* 1.3 61.1 + - - +
1026U TYR* 3.3 15.6 + - - +
1027U LEU* 3.4 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1024 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894U ARG* 3.6 36.6 - - - +
898U VAL* 5.3 2.2 - - - +
1020U GLY 3.0 18.7 + - - -
1021U LEU* 3.7 7.6 - - - -
1023U ARG* 1.3 73.9 - - - +
1025U LYS* 1.3 65.0 + - - +
1027U LEU* 3.2 8.8 + - - +
1028U LEU* 3.1 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1025 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206M ASP 5.5 2.0 - - - +
207M GLU* 5.2 4.3 - - + +
208M ARG* 3.6 28.5 - - + +
1021U LEU 3.0 12.8 + - - +
1022U ASP* 3.2 12.1 + - - +
1024U SER* 1.3 77.5 - - - +
1026U TYR* 1.3 56.3 + - - +
1028U LEU* 3.2 6.8 + - - +
1029U VAL* 2.9 34.9 + - + +
1052U LEU* 6.2 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1026 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208M ARG* 5.1 2.2 - - - +
1013U ALA* 4.3 23.1 - - + -
1022U ASP 3.1 12.0 + - - +
1023U ARG* 3.5 11.7 - - - +
1024U SER 3.2 0.2 - - - -
1025U LYS* 1.3 77.9 - - - +
1027U LEU* 1.3 56.6 + - - +
1029U VAL* 5.1 1.6 - - - -
1030U LYS* 2.9 31.2 + - + +
1031U GLU* 3.1 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1027 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874U ARG 6.1 0.4 - - - +
877U LEU* 5.5 6.5 - - + -
894U ARG* 6.4 1.3 - - - -
897U ARG* 5.3 13.5 - - + -
898U VAL 6.3 0.2 - - - +
1023U ARG 3.4 8.0 + - - +
1024U SER* 3.2 12.2 + - - +
1026U TYR* 1.3 78.7 - - - +
1028U LEU* 1.3 61.7 + - - +
1031U GLU* 3.4 16.3 + - + -
1032U ALA* 2.8 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1028 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877U LEU* 5.6 4.5 - - - -
1024U SER 3.1 16.1 + - - +
1025U LYS* 3.2 7.4 + - - +
1027U LEU* 1.3 79.7 - - - +
1029U VAL* 1.3 60.6 + - - +
1032U ALA* 5.1 7.0 - - - +
1054U PHE* 5.4 7.2 - - + +
1055U LYS 5.5 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1029 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172M PHE* 5.7 2.1 - - - +
206M ASP* 5.0 4.7 - - - +
208M ARG* 6.4 1.1 - - + -
1025U LYS* 2.9 16.9 + - + +
1026U TYR* 4.6 1.1 - - - +
1028U LEU* 1.3 78.3 - - + +
1030U LYS* 1.3 61.8 + - + +
1032U ALA 6.0 0.4 - - - -
1052U LEU* 4.6 18.6 - - + +
1053U GLY 5.0 6.5 - - - +
1054U PHE* 5.1 9.0 - - - +
1055U LYS* 5.3 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1030 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172M PHE* 3.3 37.1 - - - +
173M LEU* 5.4 0.9 - - - -
174M LYS 5.9 2.7 - - - +
1026U TYR* 2.9 16.4 + - + +
1028U LEU 3.5 0.6 - - - -
1029U VAL* 1.3 82.8 - - + +
1031U GLU* 1.3 65.5 + - + +
1032U ALA 3.7 8.4 - - - +
----------------------------------------------------------
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