Contacts of the strand formed by residues 243 - 247 (chain A) in PDB entry 1DJ9
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 ALA 243 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 3.4 3.5 - - - +
105A PHE* 2.8 28.4 + - + +
107A SER 3.5 7.0 - - - +
108A GLY* 3.5 29.4 - - - +
111A ALA* 4.0 10.5 - - + -
231A VAL* 4.8 0.9 - - + -
232A VAL 3.2 14.1 - - - +
233A THR* 3.7 1.6 - - - +
234A PHE* 3.2 16.1 - - - -
242A GLY* 1.3 75.8 - - - +
244A ALA* 1.3 66.2 + - - +
268A MET* 5.1 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.9 28.0 - - + -
102A ALA* 4.6 0.7 - - + -
103A LEU 3.1 21.3 - - - +
104A LEU* 4.1 2.5 - - + -
105A PHE* 4.5 1.8 - - - +
111A ALA* 5.0 0.2 - - - -
230A LEU 3.8 0.5 - - - +
231A VAL* 3.5 6.8 - - - +
232A VAL* 2.7 37.5 + - + +
234A PHE* 3.9 4.0 - - + -
243A ALA* 1.3 78.6 - - - +
245A VAL* 1.3 63.1 + - - +
246A LEU* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG 4.0 0.2 - - - +
102A ALA* 3.3 3.5 - - - -
103A LEU* 3.0 28.5 + - + +
105A PHE* 3.3 32.3 - - + -
111A ALA* 4.1 10.5 - - + -
115A VAL* 3.7 21.1 - - + -
229A LEU* 3.8 29.4 - - + -
230A LEU 3.6 6.1 - - - +
231A VAL* 4.7 7.6 - - + +
244A ALA* 1.3 73.8 - - - +
246A LEU* 1.3 67.2 + - - +
247A CYS* 4.0 4.4 + - - -
255A LEU* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.8 5.4 - - + +
94A ALA* 3.8 28.5 - - - -
97A LEU* 3.6 27.8 - - + -
99A TYR* 3.7 28.0 - - + -
101A ARG 3.5 7.6 - - - +
102A ALA* 4.0 6.7 - - + -
228A GLU 3.9 0.2 - - - +
229A LEU* 3.7 3.1 - - - -
230A LEU* 2.8 40.5 + - + +
232A VAL* 3.8 28.9 - - + -
244A ALA* 4.0 11.0 - - + +
245A VAL* 1.3 77.7 - - - +
247A CYS* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR* 3.4 16.2 - - - -
100A SER 3.8 4.3 + - - -
101A ARG* 3.1 34.6 + - - +
103A LEU* 4.6 3.4 - - - -
228A GLU 3.8 13.0 - - - +
229A LEU* 3.9 13.5 - - + -
245A VAL* 4.2 8.7 - - + -
246A LEU* 1.3 76.7 - - - +
248A SER* 1.3 63.4 + - - +
251A VAL* 3.9 10.5 - - + -
252A ALA* 3.6 34.8 - - - -
255A LEU* 4.1 11.9 - - - -
----------------------------------------------------------
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