Contacts of the helix formed by residues 20 - 29 (chain A) in PDB entry 2PXC
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 3.9 1.6 + - - -
19A MET* 1.3 76.2 - - - +
21A LYS* 1.3 57.6 + - - -
22A GLU 3.5 2.0 - - - -
23A GLU* 3.8 14.0 + - - -
24A PHE* 2.8 32.8 + - - +
501A G3A 5.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLY* 1.3 70.3 - - - -
22A GLU* 1.3 65.3 + - - +
24A PHE* 3.1 4.9 + - - +
25A PHE* 2.9 53.7 + - + -
501A G3A 5.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLY 3.5 0.2 - - - -
21A LYS* 1.3 77.6 - - - +
23A GLU* 1.3 60.7 + - - +
25A PHE* 4.5 4.2 - - - +
26A SER* 3.1 26.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET* 3.2 46.4 - - + +
20A GLY* 3.4 13.1 + - - +
21A LYS 3.2 0.6 - - - -
22A GLU* 1.3 75.8 + - - +
24A PHE* 1.3 55.6 + - - +
26A SER* 3.3 4.6 + - - -
27A TYR* 2.7 38.0 + - - +
245A ASP* 4.5 18.5 + - - +
249A TRP* 4.2 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.6 26.9 - - + -
19A MET* 4.1 13.8 - - + +
20A GLY 2.8 24.4 + - - +
21A LYS* 3.5 2.9 - - - +
23A GLU* 1.3 71.7 - - - +
25A PHE* 1.3 90.4 + + - +
27A TYR* 2.8 23.2 + - - +
28A ARG* 2.8 28.4 + - + +
215A SER* 3.8 18.2 - - - -
501A G3A 3.2 85.5 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 2.9 49.1 + - + +
22A GLU* 4.5 3.6 - - - +
24A PHE* 1.3 100.7 - + - +
26A SER* 1.3 60.2 + - - +
28A ARG* 3.6 31.6 - - - +
29A LYS* 3.6 23.0 + - - +
501A G3A 4.8 11.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLU* 3.1 21.2 + - - -
23A GLU* 3.6 3.1 - - - -
24A PHE 3.1 0.4 - - - -
25A PHE* 1.3 78.9 - - - +
27A TYR* 1.3 63.9 + - - +
28A ARG 3.6 0.2 + - - -
29A LYS* 3.7 20.3 + - - +
30A GLU* 3.7 14.0 + - - +
249A TRP* 3.0 48.1 - - - +
251A GLY* 5.7 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TRP* 3.3 17.5 + - - -
16A LEU* 3.8 19.1 - - + -
19A MET* 3.8 23.6 - - + -
23A GLU 2.7 21.0 + - - +
24A PHE* 2.8 6.1 + - - +
26A SER* 1.3 68.9 - - - +
28A ARG* 1.3 69.6 + - - +
29A LYS 3.0 4.6 + - - -
30A GLU* 3.0 11.1 + - + +
214A ASN* 3.0 41.5 + - + +
240A LEU* 2.7 31.0 + - - -
243A ARG* 3.7 30.1 - - + -
244A MET* 3.6 25.5 - - + +
249A TRP* 3.5 19.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PHE* 2.8 25.9 + - + +
25A PHE* 3.6 37.0 - - - +
26A SER 3.4 0.4 - - - -
27A TYR* 1.3 75.8 - - + +
29A LYS* 1.3 60.9 + - + +
30A GLU 3.5 0.2 - - - -
32A ILE* 3.7 1.6 - - - +
213A ARG* 3.4 45.0 - - - +
214A ASN* 2.8 33.1 + - - +
215A SER* 3.6 33.0 - - - +
501A G3A 3.1 48.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PHE* 3.6 21.1 + - - +
26A SER* 3.8 18.9 + - - +
27A TYR 3.0 0.6 - - - -
28A ARG* 1.3 82.2 - - + +
30A GLU* 1.3 60.0 + - - +
31A ALA 3.3 0.3 + - - -
32A ILE* 3.6 21.5 - - + +
34A GLU* 5.6 5.2 - - - +
213A ARG* 5.8 2.2 - - - -
251A GLY* 4.4 4.3 - - - -
252A PRO* 3.1 52.5 - - + +
254A TYR* 5.4 4.0 - - - +
----------------------------------------------------------
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