Contacts of the strand formed by residues 26 - 31 (chain A) in PDB entry 2R8J
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 ILE 26 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 5.4 0.2 - - - +
19A TYR* 4.6 9.2 - - + -
24A ALA* 4.5 9.0 - - + -
25A CYS* 1.3 84.2 - - - +
27A ALA* 1.3 71.4 - - - +
158A PHE* 4.2 9.2 - - + -
159A LEU 3.3 10.1 - - - +
160A ASP* 4.1 17.3 - - - +
161A LEU* 5.0 0.2 - - - -
264A LEU* 3.6 7.4 - - - +
265A SER 3.0 20.4 + - - +
266A SER 4.1 21.8 - - - +
267A THR* 4.2 5.8 - - - +
268A LYS* 3.8 25.1 - - + +
271A CYS* 3.4 22.1 - - - -
386A LEU* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 1.3 80.0 - - - +
28A HIS* 1.3 60.7 + - - +
29A ILE* 5.0 1.3 - - + -
157A VAL 3.6 0.3 - - - +
158A PHE* 3.0 7.8 - - - +
159A LEU* 2.7 45.0 + - + +
161A LEU* 4.1 16.2 - - + -
245A CYS* 4.1 22.7 - - - -
262A CYS* 4.4 2.0 - - - -
263A GLY 3.4 9.2 - - - +
264A LEU* 4.3 6.3 - - + -
271A CYS* 3.9 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA* 1.3 73.6 - - - +
29A ILE* 1.3 65.2 + - - +
30A ASP* 4.1 9.2 - - + -
156A GLU* 3.2 46.4 + - + +
157A VAL 3.3 5.8 - - - -
158A PHE* 3.2 41.2 - + + -
262A CYS* 3.2 5.2 - - - -
263A GLY 3.1 29.8 + - - -
271A CYS* 3.8 25.8 - - + +
272A LYS* 3.3 22.5 - - + +
275A SER* 3.2 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ALA 5.0 0.4 - - - -
28A HIS* 1.3 84.0 + - - +
30A ASP* 1.3 61.1 + - - +
31A MET* 4.2 1.4 + - + +
142A PHE* 3.9 32.0 - - + -
155A ASP 3.6 1.6 - - - +
156A GLU* 3.3 5.4 - - - -
157A VAL* 2.9 39.3 + - + +
159A LEU* 3.9 22.0 - - + -
245A CYS* 4.5 4.9 - - - -
248A ILE* 5.1 2.2 - - + -
249A ARG* 4.0 22.0 - - + -
252A ILE* 5.4 0.7 - - + -
260A THR* 3.8 32.1 - - + +
261A SER 3.4 5.2 - - - +
262A CYS* 3.8 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 4.1 15.0 - - + +
29A ILE* 1.3 72.1 - - - +
31A MET* 1.3 78.6 + - - +
32A ASN* 3.2 6.1 + - - +
155A ASP 3.4 3.1 - - - -
156A GLU* 2.9 16.5 - - + +
260A THR* 4.0 2.9 - - - -
261A SER* 3.0 32.5 + - - +
275A SER* 4.8 7.4 - - - +
276A ASN* 5.5 1.8 + - - -
279A LYS* 6.1 3.4 - - + -
1501A CA 2.7 28.4 - - - -
1502A CA 2.1 30.1 - - - -
2001A DCP 3.1 8.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.1 1.7 - - + +
30A ASP* 1.3 70.8 - - - +
32A ASN* 1.3 60.5 + - - +
34A PHE* 3.7 32.9 + - + -
37A GLN* 4.9 1.3 - - - +
134A GLU 5.2 0.4 - - - +
135A SER* 5.6 0.9 - - - -
138A ALA* 3.7 28.7 - - + -
142A PHE* 5.7 4.5 - - + -
155A ASP* 3.0 29.7 + - + +
252A ILE* 4.6 8.5 - - + -
258A TYR* 3.3 43.1 - - + -
259A THR 4.5 0.2 - - - +
260A THR* 3.3 34.2 - - + +
1502A CA 2.5 29.8 - - - -
2001A DCP 3.1 0.9 + - - -
----------------------------------------------------------
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