Contacts of the helix formed by residues 923 - 930 (chain A) in PDB entry 1FVR
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 ASP 923 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A VAL* 2.7 24.5 + - + +
922A THR* 1.3 79.5 + - - +
924A PRO* 1.3 65.7 - - - +
925A ALA* 3.0 10.7 + - - +
926A PHE* 3.0 36.2 + - - +
927A ALA 3.1 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 924 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A VAL 3.2 7.3 - - - +
920A LEU* 3.7 23.1 - - + +
921A GLU 4.0 6.5 - - - +
922A THR 3.9 4.3 - - - +
923A ASP* 1.3 87.8 - - - +
925A ALA* 1.3 56.9 + - - +
927A ALA* 3.5 7.5 - - + +
928A ILE* 2.8 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 925 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A ASP* 3.0 10.3 + - - +
924A PRO* 1.3 79.5 - - - +
926A PHE* 1.3 54.8 + - - +
928A ILE* 3.8 4.0 - - - +
929A ALA* 2.8 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 926 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A VAL* 3.3 22.7 - - + -
923A ASP* 3.0 30.1 + - - +
925A ALA* 1.3 77.9 - - - +
927A ALA* 1.3 55.3 + - - +
929A ALA* 3.3 3.7 + - - -
930A ASN* 2.8 69.8 + - + +
932A THR* 4.2 15.7 - - + -
935A THR* 4.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 927 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A VAL* 3.8 7.9 - - + -
920A LEU* 3.7 34.3 - - + -
923A ASP 3.1 5.3 + - - +
924A PRO 3.5 8.5 - - - +
926A PHE* 1.3 85.8 - - - +
928A ILE* 1.3 57.1 + - - +
930A ASN 3.3 0.3 + - - -
931A SER* 2.8 25.5 + - - -
932A THR* 2.9 31.9 + - - +
1107A LEU* 3.8 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 928 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920A LEU* 4.4 12.1 - - + -
924A PRO* 2.8 27.5 + - + +
925A ALA* 3.8 4.0 - - - +
927A ALA* 1.3 72.1 - - - +
929A ALA* 1.3 64.6 + - - +
931A SER* 3.1 15.6 + - - +
1107A LEU* 4.3 18.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A ALA 2.8 20.0 + - - +
926A PHE* 3.6 7.0 - - - +
928A ILE* 1.3 79.7 - - - +
930A ASN* 1.3 66.5 + - - +
931A SER* 3.8 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 930 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A PHE* 2.8 64.5 + - + +
929A ALA* 1.3 82.1 - - - +
931A SER* 1.3 72.1 + - - +
932A THR* 3.0 20.5 + - + -
----------------------------------------------------------
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