Contacts of the helix formed by residues 100 - 109 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E THR* 3.6 12.3 + - - +
231E THR 3.4 20.2 + - - -
232E ALA* 3.3 21.0 - - - +
233E ASP* 4.2 1.8 - - - -
96I PHE* 6.0 0.7 - - - +
97I GLU* 2.9 47.8 + - + +
98I GLU 3.1 0.8 + - - -
99I ALA* 1.3 78.0 - - - +
101I LEU* 1.3 62.7 + - - +
102I PRO* 3.2 10.4 - - - +
103I GLY* 2.9 16.7 + - - -
104I LEU* 3.1 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233E ASP* 4.5 4.2 + - - +
99I ALA 3.9 1.6 - - - -
100I ASN* 1.3 73.6 - - - +
102I PRO* 1.3 73.6 - - + +
104I LEU* 3.0 13.7 + - + +
105I LEU* 2.9 39.9 + - + +
126I LEU* 5.8 0.4 - - + -
128I PHE* 4.5 10.8 - - + -
136I PHE* 4.3 25.3 - - + -
261I TRP* 3.9 29.4 - - + -
265I ARG* 5.9 1.8 - - - +
304I LEU* 3.9 27.8 - - + -
308I ILE* 4.0 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 102 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231E THR* 4.1 7.7 - - + +
232E ALA* 3.6 30.5 - - - +
233E ASP* 3.7 13.9 - - - +
258E ILE* 3.6 30.2 - - + +
259E THR* 6.0 0.7 - - - -
100I ASN* 3.2 9.6 - - - +
101I LEU* 1.3 97.8 - - + +
103I GLY* 1.3 59.8 + - - +
105I LEU* 3.4 2.7 + - + +
106I ALA* 3.1 21.3 + - - +
261I TRP* 3.9 28.0 - - + +
262I GLY* 4.7 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E ASN 4.4 7.7 - - - +
195E THR* 3.8 25.6 - - - -
231E THR* 4.5 3.1 - - - +
96I PHE* 4.8 3.6 - - - -
100I ASN* 2.9 21.8 + - - -
102I PRO* 1.3 77.3 - - - +
104I LEU* 1.3 60.2 + - - +
106I ALA* 3.5 15.9 - - - +
107I SER* 3.7 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I ILE* 4.4 15.7 - - + -
96I PHE* 3.2 52.6 - - + +
100I ASN 3.1 11.1 + - - +
101I LEU* 3.0 17.3 + - + +
103I GLY* 1.3 74.1 - - - +
105I LEU* 1.3 65.1 + - + +
106I ALA 3.1 1.8 - - - -
107I SER* 3.0 11.6 + - - -
108I ILE* 3.1 35.0 + - + +
126I LEU* 5.3 2.0 - - + -
128I PHE* 3.5 37.5 - - + -
132I LEU* 4.4 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258E ILE* 4.1 5.2 - - + -
284E MET* 4.0 13.2 - - + +
101I LEU* 2.9 33.8 + - + +
102I PRO* 3.9 4.7 - - + +
104I LEU* 1.3 75.9 - - + +
106I ALA* 1.3 57.5 + - - +
108I ILE* 3.7 21.1 - - + -
109I ALA* 2.8 42.2 + - + +
123I LEU* 5.4 0.7 - - + -
126I LEU* 4.4 5.2 - - + -
261I TRP* 3.5 51.6 - - + +
296I ILE* 6.0 1.8 - - + -
300I VAL* 5.3 3.6 - - + -
304I LEU* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E GLU* 3.4 39.9 - - + +
193E ASN* 4.2 6.0 - - - +
255E ASP* 3.6 4.7 - - - +
258E ILE* 3.3 25.0 - - + +
283E ALA* 5.0 0.7 - - - -
102I PRO 3.1 10.5 + - - +
103I GLY* 3.5 14.4 - - - +
104I LEU 3.1 0.6 - - - -
105I LEU* 1.3 78.1 - - - +
107I SER* 1.3 58.4 + - - +
110I GLY* 3.4 19.4 - - - -
111I ASN 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193E ASN* 3.0 31.3 + - - +
49I GLU 4.6 1.2 - - - +
50I SER* 2.9 43.5 + - - +
96I PHE* 3.7 24.2 - - - -
103I GLY 3.7 3.9 + - - -
104I LEU 3.0 8.9 + - - -
106I ALA* 1.3 80.8 - - - +
108I ILE* 1.3 60.1 + - - +
109I ALA 3.3 2.2 + - - -
110I GLY* 4.2 2.6 + - - -
111I ASN 5.7 0.3 + - - -
112I ILE* 4.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I ILE* 5.7 1.1 - - + -
27I ALA* 4.5 10.5 - - + -
29I PHE* 3.4 20.0 - - + -
50I SER* 4.4 1.8 - - - -
91I TYR* 3.7 42.8 - - + +
96I PHE* 4.7 0.7 - - + -
104I LEU* 3.1 30.3 + - + +
105I LEU* 3.7 23.3 - - + -
107I SER* 1.3 79.3 - - - +
109I ALA* 1.3 71.2 + - + +
112I ILE* 3.6 8.6 - - - +
123I LEU* 3.7 11.2 - - + +
126I LEU* 3.8 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E MET* 3.1 43.9 - - + +
105I LEU* 2.8 17.1 + - + +
108I ILE* 1.3 90.6 - - + +
110I GLY* 1.3 59.1 + - - +
112I ILE* 4.3 1.8 - - - -
113I PHE* 3.5 25.2 - - + -
123I LEU* 4.1 10.3 - - + -
296I ILE* 4.2 4.7 - - + -
----------------------------------------------------------
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