Contacts of the helix formed by residues 634 - 638 (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 LEU 634 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A ILE* 3.8 38.4 - - + +
591A VAL* 4.0 17.7 - - + +
592A GLN* 3.8 28.5 - - + +
629A LEU* 2.9 17.7 + - + +
632A ALA* 3.6 19.7 - - + +
633A GLY* 1.3 82.5 - - - +
635A ARG* 1.3 65.7 + - - +
636A LEU 3.2 2.9 - - - -
637A LYS* 3.0 38.5 + - + +
638A ALA 4.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 635 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.7 36.3 - - + -
242A ALA* 4.6 7.4 - - + +
626A HIS* 2.9 40.3 + - - +
629A LEU* 3.3 20.8 + - - +
630A ILE* 3.7 31.9 - - + +
633A GLY* 3.7 2.2 - - - -
634A LEU* 1.3 77.2 - - - +
636A LEU* 1.3 64.0 + - + +
637A LYS 3.2 0.2 - - - -
638A ALA 2.8 38.8 + - - +
639A SER* 4.3 4.2 - - - +
640A LEU* 3.9 16.6 - - - +
660A GLY 3.0 26.3 + - - -
662A SER* 5.1 1.0 + - - -
727A HIS* 4.0 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 636 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP* 3.9 27.1 - - + +
242A ALA* 3.3 50.6 - - + +
243A ARG* 3.6 24.5 - - + +
246A GLU* 6.5 0.4 - - + -
523A GLY 5.2 0.7 - - - -
524A LYS* 3.2 5.2 - - - +
525A ARG* 2.9 61.3 + - + +
633A GLY 5.5 0.2 + - - -
634A LEU 3.1 1.2 + - - -
635A ARG* 1.3 79.9 - - + +
637A LYS* 1.3 68.8 + - - +
638A ALA 3.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 637 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLU* 3.1 40.2 + - - +
524A LYS* 3.4 31.0 - - + +
591A VAL* 3.7 17.0 - - + +
595A ALA 3.9 2.5 - - - +
596A GLU* 3.7 15.6 - - - +
633A GLY 4.5 13.9 + - - -
634A LEU* 3.0 37.8 + - + +
636A LEU* 1.3 88.0 - - - +
638A ALA* 1.3 59.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 638 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A GLY 4.0 6.8 - - - +
524A LYS* 4.4 0.4 - - - +
591A VAL* 4.0 20.9 - - + -
595A ALA 3.7 10.5 - - - +
596A GLU 3.2 20.0 - - - +
597A ILE* 4.3 0.9 - - - +
598A LEU* 5.0 4.0 - - + -
629A LEU* 5.5 5.1 - - + +
634A LEU 4.2 1.4 + - - +
635A ARG* 2.8 29.1 + - - +
636A LEU 3.4 1.6 - - - -
637A LYS* 1.3 82.0 - - - +
639A SER* 1.3 67.8 + - - +
640A LEU* 5.4 1.1 - - + -
----------------------------------------------------------
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