Contacts of the helix formed by residues 129 - 134 (chain J) 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 PRO 129 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J LYS 3.4 19.7 - - - +
22J LYS 3.4 26.5 - - - +
23J ARG 4.4 2.2 - - - +
24J ASP 3.5 30.5 - - - +
25J ILE* 4.1 12.1 - - + -
93J PHE* 4.7 1.6 - - + -
127J TYR* 3.7 6.3 - - + +
128J PHE* 1.3 85.2 - - + +
130J GLU* 1.3 67.0 + - - +
131J LYS* 3.0 2.0 - - + +
132J LEU* 2.9 33.6 + - + +
133J ILE* 3.1 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 130 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG* 2.6 41.3 + - - +
169F SER* 4.3 0.9 - - - -
198F TRP* 4.0 10.3 - - + -
199F TYR 5.1 1.2 - - - +
21J LYS 4.7 0.6 + - - -
22J LYS* 2.8 32.3 + - - +
127J TYR* 5.1 0.6 + - - -
128J PHE 4.0 0.2 + - - -
129J PRO* 1.3 72.5 - - - +
131J LYS* 1.3 62.8 + - - +
133J ILE* 3.5 3.9 - - - +
134J ARG* 2.6 64.5 + - - +
357J TYR* 3.5 33.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 131 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C PHE* 5.9 1.3 - - - -
94C HIS* 4.6 4.0 - - + -
98C GLU* 5.4 4.8 + - - -
198F TRP* 3.6 64.3 - - + +
22J LYS 4.8 10.0 + - - +
93J PHE* 3.7 44.2 - - + -
98J GLU* 4.0 28.3 + - - +
129J PRO* 2.9 3.6 + - + +
130J GLU* 1.3 81.4 - - - +
132J LEU* 1.3 68.5 + - + +
134J ARG* 3.6 7.2 + - - +
135J GLU* 3.2 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 132 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25J ILE* 3.5 32.3 - - + -
93J PHE* 3.7 33.4 - - + +
96J PHE* 5.7 2.9 - - + -
104J LEU* 4.0 11.0 - - + -
128J PHE* 3.8 29.6 - - + -
129J PRO* 2.9 13.2 + - + +
131J LYS* 1.3 81.2 - - + +
133J ILE* 1.3 68.9 + - - +
134J ARG 3.1 1.8 - - - -
135J GLU* 2.8 38.4 + - - +
136J PHE* 3.3 14.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J PHE* 3.7 23.6 - - + +
129J PRO 3.1 15.5 + - - +
130J GLU* 3.5 11.2 - - - +
132J LEU* 1.3 75.3 - - - +
134J ARG* 1.3 61.7 + - + +
136J PHE* 3.1 32.0 + - - +
307J LEU* 3.9 22.4 - - + +
354J GLN* 3.6 23.6 - - - +
355J LYS 3.9 8.7 - - - +
356J PHE* 3.9 17.7 - - + +
357J TYR* 4.3 9.9 - - + -
359J ILE* 3.8 26.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F SER* 3.3 13.7 + - - -
170F PRO* 4.2 9.8 - - - +
171F GLU* 2.8 43.2 + - - -
198F TRP* 4.2 26.9 - - + +
199F TYR* 4.8 4.9 + - - +
204F GLU* 5.2 4.7 + - - +
130J GLU* 2.6 54.6 + - + +
131J LYS* 4.0 6.1 - - - +
132J LEU 3.1 0.4 - - - -
133J ILE* 1.3 79.4 - - + +
135J GLU* 1.3 58.5 + - - +
136J PHE 3.2 11.6 - - - +
357J TYR* 3.6 25.9 - - + +
358J SER* 4.8 2.8 - - - -
----------------------------------------------------------
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