Contacts of the helix formed by residues 110 - 115 (chain E) 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 GLY 110 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105E LEU 3.5 1.8 + - - -
106E ALA* 3.4 18.1 + - - -
107E SER 4.3 1.6 + - - -
108E ILE 3.9 0.4 - - - -
109E ALA* 1.3 78.5 - - - +
111E ASN* 1.3 66.6 + - - -
112E ILE* 2.9 9.1 + - - +
113E PHE* 3.3 20.6 + - - +
283I ALA* 4.0 5.6 - - - -
284I MET* 3.4 20.0 + - - -
286I ALA* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E GLU* 5.2 12.3 + - + +
106E ALA 4.5 1.8 + - - -
110E GLY* 1.3 71.4 - - - -
112E ILE* 1.3 63.7 + - - +
114E GLY* 2.9 18.0 + - - -
115E MET* 4.0 3.8 + - + -
165I LYS* 4.3 1.0 - - - +
192I GLU* 3.0 36.6 + - - +
281I HIS* 3.2 21.6 - - - -
283I ALA* 4.0 6.2 - - - +
284I MET 4.2 1.1 - - - +
285I HIS* 6.2 1.1 - - - -
286I ALA* 5.2 0.7 - - - +
322I LYS* 6.5 0.2 - - - -
323I LEU* 4.1 14.8 - - + +
600I CAP 3.1 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E PHE* 3.6 24.9 - - + -
46E VAL* 3.7 28.8 - - + +
49E GLU* 4.0 18.6 - - + +
50E SER* 3.9 17.7 - - - +
107E SER 4.4 1.3 - - - +
108E ILE 3.5 31.2 - - - +
109E ALA* 4.3 1.6 - - - +
110E GLY 2.9 12.8 + - - +
111E ASN* 1.3 77.9 - - - +
113E PHE* 1.3 68.8 + - + +
114E GLY 3.1 1.4 + - - -
115E MET* 3.3 25.4 + - - +
118E VAL* 4.2 4.5 - - - +
121E LEU* 3.6 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E PHE* 5.0 2.2 - + - -
109E ALA* 3.3 38.1 - - + -
110E GLY 3.3 17.5 + - - +
111E ASN 3.0 1.2 + - - -
112E ILE* 1.3 79.7 - - + +
114E GLY* 1.3 56.7 + - - +
115E MET 3.5 0.2 - - - -
118E VAL* 4.7 1.0 - - - +
121E LEU* 3.4 35.7 - - + -
123E LEU* 4.3 11.0 - - + -
294E HIS* 3.4 17.7 - + + -
295E GLY* 3.2 27.8 - - - -
296E ILE* 3.6 25.6 - - + -
284I MET 4.3 2.9 - - - -
286I ALA* 3.5 23.5 - - + +
287I ALA* 4.0 15.7 - - + -
290I ARG* 2.8 20.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E ASN 2.9 9.5 + - - -
113E PHE* 1.3 78.6 - - - +
115E MET* 1.3 58.2 + - - +
285I HIS* 5.9 1.6 - - - -
286I ALA* 3.5 17.4 - - - +
290I ARG* 3.5 9.4 - - - -
323I LEU* 3.2 13.5 - - - -
324I GLU* 2.7 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E TYR* 3.7 16.4 - - + +
45E ALA* 3.7 27.4 - - + +
46E VAL* 4.6 4.9 - - - -
49E GLU* 3.4 40.8 - - + +
111E ASN* 4.2 1.1 - - + +
112E ILE* 3.3 27.1 + - - +
113E PHE 3.5 0.6 - - - -
114E GLY* 1.3 75.8 - - - +
116E LYS* 1.3 63.5 + - - +
117E ARG* 2.9 16.7 + - + +
118E VAL* 3.0 20.0 + - + +
290I ARG* 3.1 14.8 + - - -
322I LYS* 3.9 13.5 - - + +
323I LEU* 3.7 17.7 - - + -
444I VAL 5.6 2.7 - - - -
----------------------------------------------------------
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