Contacts of the helix formed by residues 100 - 109 (chain D) in PDB entry 3KDO
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 ASN 100 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PHE* 6.0 0.3 - - - +
97D GLU* 2.9 49.8 + - + +
98D GLU 3.2 0.8 - - - -
99D ALA* 1.3 78.1 - - - +
101D LEU* 1.3 61.3 + - - +
102D PRO* 3.2 9.2 - - - +
103D GLY* 2.9 21.3 + - - -
104D LEU* 3.1 11.5 + - - +
195J THR* 3.7 12.9 + - - +
231J THR 3.4 20.2 + - - -
232J ALA* 3.4 19.4 - - + +
233J ASP* 4.1 3.4 - - - -
236J GLU* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D ALA 4.0 1.6 - - - -
100D ASN* 1.3 70.0 - - - +
102D PRO* 1.3 77.1 - - + +
104D LEU* 2.9 22.8 + - + +
105D LEU* 2.9 39.2 + - + +
128D PHE* 4.5 3.8 - - + -
136D PHE* 4.2 28.4 - - + -
261D TRP* 4.0 27.4 - - + -
265D ARG* 5.9 1.8 - - - +
304D LEU* 4.2 25.8 - - + -
308D ILE* 4.1 17.9 - - + -
233J ASP* 4.4 4.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ASN* 3.2 9.9 - - - +
101D LEU* 1.3 96.7 - - + +
103D GLY* 1.3 55.0 + - - +
105D LEU* 3.5 5.9 + - + -
106D ALA* 3.1 26.2 + - - +
261D TRP* 3.9 25.4 - - + +
262D GLY* 4.5 1.3 - - - +
231J THR* 4.1 12.8 - - + +
232J ALA 3.6 25.6 - - - +
233J ASP* 3.6 13.7 - - - +
258J ILE* 3.7 30.2 - - + +
259J THR* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D PHE* 4.9 3.8 - - - -
100D ASN* 2.9 24.9 + - - -
102D PRO* 1.3 75.5 - - - +
104D LEU* 1.3 63.8 + - - +
106D ALA* 3.3 17.8 + - - +
107D SER* 3.5 9.0 + - - -
193J ASN 4.7 5.8 - - - +
195J THR* 4.0 20.2 - - - -
231J THR* 4.6 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ILE* 4.9 7.9 - - + -
96D PHE* 3.2 55.5 - - + +
100D ASN 3.1 9.3 + - - +
101D LEU* 2.9 17.1 + - + +
103D GLY* 1.3 74.6 - - - +
105D LEU* 1.3 58.8 + - - +
107D SER* 2.9 18.4 + - - -
108D ILE* 3.0 28.1 + - + +
126D LEU* 4.5 4.9 - - + -
128D PHE* 3.3 41.3 - - + -
132D LEU* 4.4 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101D LEU* 2.9 36.1 + - + +
102D PRO* 3.8 5.6 - - + +
104D LEU* 1.3 77.3 - - + +
106D ALA* 1.3 63.1 + - - +
108D ILE* 3.9 19.3 - - + -
109D ALA* 3.0 36.8 + - + +
123D LEU* 5.6 0.7 - - + -
126D LEU* 4.9 5.4 - - + -
261D TRP* 3.5 52.5 - - + +
296D ILE* 6.0 1.6 - - + -
300D VAL* 5.5 3.1 - - + -
304D LEU* 3.9 20.0 - - + -
258J ILE* 4.0 5.6 - - + -
284J MET* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PRO 3.1 10.7 + - - +
103D GLY* 3.5 13.9 - - - +
105D LEU* 1.3 76.0 - - - +
107D SER* 1.3 60.4 + - - +
110D GLY* 3.5 17.2 - - - -
111D ASN 4.6 0.9 + - - -
192J GLU* 3.6 28.4 - - + +
193J ASN* 4.1 4.9 - - - +
231J THR* 5.3 0.2 - - + -
255J ASP* 3.5 25.1 - - - +
258J ILE* 3.3 18.1 - - + +
283J ALA* 5.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D GLU 4.7 0.9 - - - +
50D SER* 3.0 40.4 + - - +
96D PHE* 3.6 24.9 - - - -
103D GLY 3.5 4.7 + - - -
104D LEU 2.9 10.6 + - - -
106D ALA* 1.3 81.2 - - - +
108D ILE* 1.3 60.7 + - - -
109D ALA 3.3 2.9 + - - -
110D GLY* 4.2 3.1 + - - -
112D ILE* 4.3 3.3 - - - +
193J ASN* 3.0 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ILE* 5.4 1.1 - - + -
27D ALA* 4.5 10.8 - - + -
29D PHE* 3.5 20.8 - - + -
50D SER* 4.4 2.5 - - - -
91D TYR* 3.7 41.5 - - + +
96D PHE* 4.6 0.2 - - + -
104D LEU* 3.0 33.1 + - + +
105D LEU* 3.9 20.2 - - + -
107D SER* 1.3 79.8 - - - +
109D ALA* 1.3 72.8 + - + +
112D ILE* 3.5 9.3 - - - +
123D LEU* 3.9 16.3 - - + +
126D LEU* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LEU* 3.0 17.4 + - + +
108D ILE* 1.3 91.9 - - + +
110D GLY* 1.3 58.8 + - - +
112D ILE* 4.2 2.0 - - - -
113D PHE* 3.5 26.1 - - + -
123D LEU* 4.2 10.8 - - + -
296D ILE* 4.2 4.0 - - + -
284J MET* 3.3 41.7 - - + +
----------------------------------------------------------
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