Contacts of the helix formed by residues 738 - 746 (chain A) in PDB entry 1OFD
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 GLY 738 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A LEU* 1.3 76.3 - - - +
739A ALA* 1.3 65.8 + - - -
740A GLU* 3.3 4.7 - - - -
741A LEU* 3.3 4.6 + - - +
742A VAL* 3.0 19.9 + - - +
754A GLY* 3.8 2.7 - - - -
755A GLY 3.7 18.2 - - - -
756A LEU 2.8 25.4 + - - +
757A THR* 5.6 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 739 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A LEU 4.8 0.2 - - - -
738A GLY* 1.3 72.3 - - - -
740A GLU* 1.3 71.6 + - - +
742A VAL* 3.3 7.1 + - - +
743A GLU* 2.8 32.3 + - - +
751A SER* 6.3 0.4 - - - -
754A GLY* 5.1 3.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 740 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738A GLY* 3.3 2.1 - - - -
739A ALA* 1.3 90.3 + - - +
741A LEU* 1.3 61.8 + - - +
743A GLU* 3.4 5.9 + - - +
744A TYR* 3.1 23.8 + - - +
757A THR* 6.0 7.2 - - + +
758A ILE* 5.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 741 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LEU* 4.7 2.9 - - + -
620A LEU* 3.7 30.1 - - + -
737A LEU* 3.9 31.6 - - + -
738A GLY 3.3 7.8 + - - +
740A GLU* 1.3 74.1 - - - +
742A VAL* 1.3 66.4 + - - +
744A TYR* 3.1 14.8 + - + +
745A ALA 3.2 10.7 + - - -
746A PHE* 4.0 14.5 - - + -
756A LEU* 3.8 22.2 + - + +
757A THR* 4.7 1.2 - - - +
758A ILE* 4.3 27.6 - - + +
761A VAL* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 742 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A ALA* 4.9 3.1 - - + -
737A LEU* 3.7 28.7 - - + +
738A GLY 3.0 21.1 + - - +
739A ALA* 3.8 7.0 - - - +
741A LEU* 1.3 75.7 - - - +
743A GLU* 1.3 57.6 + - - +
746A PHE* 2.8 48.0 + - + +
747A ALA* 2.9 12.6 + - - +
748A GLY 4.9 1.3 - - - +
749A THR* 3.5 27.1 - - - +
751A SER* 3.8 19.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 743 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A ARG* 2.7 59.5 + - - -
739A ALA 2.8 18.0 + - - +
740A GLU* 3.7 6.7 - - - +
742A VAL* 1.3 79.5 - - - +
744A TYR* 1.3 57.8 + - - +
745A ALA 3.6 0.2 + - - -
747A ALA* 3.8 14.8 - - - +
748A GLY 5.6 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 744 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A GLU* 5.4 4.7 - - + -
580A LEU* 3.4 52.1 + - + -
581A THR* 3.5 14.2 + - - -
584A VAL* 4.2 5.2 - - + +
620A LEU* 5.1 2.7 - - + -
624A ALA* 3.8 18.4 - - + -
627A HIS* 4.2 7.3 - - - +
628A HIS* 3.4 47.9 + + - -
631A ARG* 4.2 1.6 + - - +
740A GLU 3.1 16.6 + - - +
741A LEU* 3.1 9.8 + - + +
743A GLU* 1.3 79.6 - - - +
745A ALA* 1.3 60.8 + - + +
758A ILE* 4.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 745 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620A LEU* 3.7 30.5 - - + +
623A GLY* 3.1 25.3 - - - +
624A ALA* 3.4 22.9 - - + +
627A HIS* 3.3 11.4 - - - -
659A TYR* 4.3 1.2 - - - -
741A LEU 3.2 4.4 + - - +
744A TYR* 1.3 79.6 - - + +
746A PHE* 1.3 77.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 746 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A LEU* 3.9 22.4 - - + -
495A PHE* 3.8 32.1 - + + -
619A LEU* 3.5 30.3 - - + -
620A LEU* 4.1 3.1 - - - -
623A GLY* 4.6 0.4 - - - -
627A HIS* 4.1 2.5 - - - -
659A TYR* 3.7 31.0 - + + -
730A GLN* 4.2 0.9 - - - -
737A LEU* 4.0 16.8 - - + -
741A LEU* 4.0 26.0 - - + -
742A VAL* 2.8 22.8 + - + +
745A ALA* 1.3 100.2 - - + +
747A ALA* 1.3 65.5 + - - +
749A THR* 2.8 31.0 + - - +
----------------------------------------------------------
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