Contacts of the helix formed by residues 89 - 96 (chain D) in PDB entry 4OGB
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 GLU 89 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLN* 1.3 88.9 + - - +
90D ASP* 1.3 58.0 + - - +
92D LEU* 3.3 12.4 + - + +
93D ALA* 2.7 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLN* 3.2 30.5 + - + +
89D GLU* 1.3 78.9 - - - +
91D VAL* 1.3 66.1 + - + +
93D ALA* 3.7 4.9 - - - +
94D LYS* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLN* 3.9 26.7 - - + +
89D GLU 3.4 0.2 - - - -
90D ASP* 1.3 76.4 - - + +
92D LEU* 1.3 63.4 + - - +
94D LYS* 3.4 5.5 + - - +
95D GLU* 3.0 36.3 + - + +
108D ARG* 4.2 15.9 - - - +
112D LEU* 3.8 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLN 3.3 10.7 + - - +
89D GLU* 3.3 15.5 + - + +
91D VAL* 1.3 78.4 - - - +
93D ALA* 1.3 63.9 + - - +
95D GLU* 3.1 3.3 + - - +
96D LEU* 3.0 41.5 + - + +
109D ILE* 4.1 27.4 - - + +
112D LEU* 3.8 28.1 - - + +
113D SER* 4.0 23.6 - - - -
120D VAL* 4.2 14.8 - - + -
505D EDO 5.7 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D GLU* 2.7 23.0 + - + +
90D ASP* 3.7 5.4 - - - +
92D LEU* 1.3 73.9 - - - +
94D LYS* 1.3 63.0 + - - +
96D LEU* 3.4 16.8 + - - +
97D GLU* 3.6 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D ASP 2.9 16.8 + - - +
91D VAL* 3.8 6.1 - - + +
93D ALA* 1.3 73.0 - - - +
95D GLU* 1.3 67.3 + - + +
96D LEU 3.0 1.1 - - - -
97D GLU* 2.3 65.3 + - - +
98D ASP* 4.1 9.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D VAL* 3.0 25.5 + - + +
92D LEU* 3.1 8.3 + - - +
94D LYS* 1.3 77.6 - - + +
96D LEU* 1.3 56.8 + - - +
97D GLU 3.1 0.2 - - - -
98D ASP* 3.0 37.0 + - - +
104D LEU* 3.5 8.3 - - - +
105D HIS* 4.3 18.7 + - - +
108D ARG* 3.8 22.8 + - + +
109D ILE* 3.8 18.8 - - + +
112D LEU* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D LEU* 3.0 36.6 + - + +
93D ALA* 3.7 11.0 - - - +
94D LYS 3.0 0.8 - - - -
95D GLU* 1.3 73.1 - - - +
97D GLU* 1.3 58.8 + - - +
98D ASP 3.1 5.4 - - - -
99D VAL* 3.3 29.6 - - + +
104D LEU* 4.9 0.7 - - + -
109D ILE* 3.8 20.9 - - + -
120D VAL* 3.8 34.5 - - + -
121D ILE* 4.0 14.1 - - + -
124D THR* 3.8 29.8 - - + +
505D EDO 5.4 2.0 - - - +
----------------------------------------------------------
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