Contacts of the strand formed by residues 32 - 36 (chain K) in PDB entry 2I2X
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 LEU 32 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K VAL 4.6 0.2 - - - -
27K LYS* 3.5 4.9 - - - +
28K ALA 3.0 37.7 + - - +
30K LEU 4.4 0.9 - - - +
31K ASP* 1.3 78.3 - - - +
33K GLU* 1.3 67.9 + - - +
34K ILE* 4.2 9.4 - - + -
38K TYR* 4.1 4.0 - - - +
40K ILE* 3.9 22.0 - - + -
80K ALA* 3.8 29.4 - - + -
81K ILE 4.7 0.2 - - - +
82K ILE* 3.6 26.9 - - + -
119K LYS* 3.8 14.1 - - + +
120K CYS* 4.0 9.9 - - - +
121K ALA* 3.5 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E LYS* 4.4 12.5 + - - -
33E GLU* 4.2 16.8 - - - +
25K PRO* 5.0 5.7 - - - +
26K VAL 3.4 4.9 - - - +
27K LYS* 3.1 44.4 + - + +
31K ASP 5.2 2.7 - - - +
32K LEU* 1.3 80.5 - - - +
34K ILE* 1.3 64.2 + - - +
35K GLY 4.0 1.4 + - - -
36K ALA* 3.8 26.2 + - + +
38K TYR* 3.0 35.8 + - + +
40K ILE* 3.4 9.5 - - - +
119K LYS* 6.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 34 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K PRO* 3.2 6.8 - - - +
26K VAL* 2.7 47.0 + - + +
28K ALA* 4.8 6.5 - - + -
32K LEU* 4.2 11.4 - - + -
33K GLU* 1.3 75.8 - - - +
35K GLY* 1.3 63.1 + - - +
36K ALA* 3.4 0.4 - - - -
40K ILE* 3.8 17.5 - - + -
82K ILE* 4.2 13.9 - - + -
121K ALA* 5.5 0.2 - - + -
160K LEU* 4.3 14.8 - - + -
265K PRO* 3.8 29.2 - - + -
283K PRO* 3.7 24.1 - - + +
308K ASP* 4.2 3.8 - - + -
309K CYS* 3.7 23.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 35 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20K GLY 3.3 11.1 + - - -
21K VAL* 3.5 2.6 - - - +
22K SER* 3.0 36.3 + - - +
25K PRO* 3.6 7.6 - - - +
33K GLU 4.0 0.6 + - - -
34K ILE* 1.3 77.0 - - - +
36K ALA* 1.3 58.2 + - - +
38K TYR 4.7 4.8 + - - -
40K ILE* 5.3 0.2 - - - +
283K PRO* 4.4 0.2 - - - -
308K ASP* 3.3 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J LYS* 4.8 4.3 + - - -
20K GLY 3.2 1.2 + - - -
21K VAL* 5.1 1.1 - - - -
25K PRO* 4.4 12.8 - - + -
33K GLU* 3.8 42.9 + - + +
35K GLY* 1.3 78.0 - - - +
37K GLY* 1.3 59.2 + - - +
38K TYR* 3.5 13.4 - - + +
----------------------------------------------------------
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