Contacts of the helix formed by residues 20 - 29 (chain B) in PDB entry 2PX8
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 20 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ALA 3.6 3.2 + - - -
19B MET* 1.3 75.3 - - - +
21B LYS* 1.3 60.3 + - - -
22B GLU* 3.3 3.1 - - - -
23B GLU* 3.2 12.7 + - - -
24B PHE* 2.8 26.9 + - - +
468B GOL 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET 3.9 0.4 + - - -
20B GLY* 1.3 70.4 - - - +
22B GLU* 1.3 64.8 + - + +
24B PHE* 3.4 5.0 + - - +
25B PHE* 3.2 44.4 + - + -
402B MGT 3.2 27.3 + - - +
403B MGT 3.9 40.6 + - + +
468B GOL 3.9 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY 3.3 0.8 - - - -
21B LYS* 1.3 77.4 - - + +
23B GLU* 1.3 64.1 + - - +
25B PHE* 3.4 2.1 + - - +
26B SER* 3.2 27.2 + - - -
403B MGT 2.8 54.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B MET* 3.9 34.9 - - + +
20B GLY* 3.2 13.1 + - - +
22B GLU* 1.3 78.3 - - - +
24B PHE* 1.3 57.9 + - - +
26B SER* 3.8 5.4 - - - -
27B TYR* 2.8 33.1 + - - +
245B ASP* 4.0 28.1 + - - +
249B TRP* 4.1 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.9 17.3 - - + -
19B MET* 4.0 10.9 - - + +
20B GLY 2.8 17.7 + - - +
21B LYS 3.7 2.9 - - - +
23B GLU* 1.3 78.0 - - - +
25B PHE* 1.3 85.8 + + - +
27B TYR* 3.6 1.2 - - - +
28B ARG* 2.9 39.8 + - - +
215B SER* 3.6 27.4 - - - -
402B MGT 3.3 95.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 3.2 40.6 + - + +
22B GLU 3.4 2.4 + - - +
24B PHE* 1.3 98.8 - + - +
26B SER* 1.3 67.0 + - - +
28B ARG* 3.5 40.0 - - - +
29B LYS* 3.6 18.1 - - - +
402B MGT 4.4 10.1 - - - -
403B MGT 3.3 91.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU 3.2 18.1 + - - -
23B GLU 3.8 1.8 - - - -
25B PHE* 1.3 75.2 - - - +
27B TYR* 1.3 67.7 + - - +
29B LYS* 3.3 23.1 + - - +
30B GLU* 3.4 11.4 + - - +
249B TRP* 3.7 40.6 + - - +
251B GLY* 5.9 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.0 19.5 + - - -
16B LEU* 3.7 22.9 - - + -
19B MET* 3.7 18.8 - - + -
23B GLU 2.8 22.4 + - - +
24B PHE 3.6 3.1 - - - +
26B SER* 1.3 72.9 - - - +
28B ARG* 1.3 67.0 + - - +
30B GLU* 2.9 14.6 + - - +
214B ASN* 3.0 46.8 + - + +
240B LEU* 2.7 24.6 + - - +
243B ARG* 3.6 25.8 - - + -
244B MET* 3.4 36.1 - - + -
249B TRP* 3.8 17.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 2.9 29.1 + - + +
25B PHE* 3.5 39.4 - - - +
27B TYR* 1.3 77.6 - - - +
29B LYS* 1.3 57.5 + - + +
32B ILE* 3.8 1.2 - - - +
213B ARG* 3.4 36.0 - - - +
214B ASN* 2.8 25.5 + - - +
215B SER* 3.3 30.3 - - - +
402B MGT 2.6 54.5 + - - -
403B MGT 4.6 7.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE 3.6 16.4 - - - +
26B SER* 3.6 15.3 - - - +
27B TYR 3.1 0.4 - - - -
28B ARG* 1.3 77.6 - - + +
30B GLU* 1.3 63.4 + - - +
31B ALA 3.2 3.3 + - - -
32B ILE* 3.4 23.0 - - + +
34B GLU* 4.5 7.2 - - - +
213B ARG* 5.7 2.7 - - + +
251B GLY* 4.4 4.7 - - - -
252B PRO* 3.2 43.5 - - + +
254B TYR* 5.7 2.1 + - - +
403B MGT 3.9 21.0 + - - +
----------------------------------------------------------
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