Contacts of the strand formed by residues 28 - 33 (chain G) in PDB entry 2PWZ
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 SER 28 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 3.2 24.9 + - - +
3G VAL* 6.2 0.2 - - - -
24G LEU* 3.7 26.0 - - - +
25G PRO* 2.6 40.4 + - - +
26G SER 3.3 0.2 - - - -
27G GLY* 1.3 79.4 - - - +
29G GLU* 1.3 60.7 + - - +
52G ALA 3.9 0.4 + - - -
53G VAL* 3.3 9.1 - - - -
54G LYS* 3.1 23.4 + - - +
243G GLN* 5.2 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET 2.7 11.4 + - - +
2G LYS* 3.5 37.0 + - + +
3G VAL* 2.9 27.0 + - - +
24G LEU* 4.2 4.7 - - - +
27G GLY 3.9 1.5 + - - +
28G SER* 1.3 74.1 - - - +
30G LEU* 1.3 61.1 + - - +
53G VAL* 4.5 1.1 - - - -
54G LYS* 3.3 42.2 + - + +
56G LYS* 4.6 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G VAL* 3.3 20.6 - - + +
5G VAL* 4.0 24.5 - - + -
17G ALA* 3.7 23.6 - - - +
20G LEU* 3.8 17.9 - - + -
21G LYS* 3.7 20.0 - - + +
24G LEU* 4.4 1.8 - - + -
29G GLU* 1.3 76.1 - - - +
31G SER* 1.3 62.2 + - - +
32G LEU* 4.1 5.4 - - + -
53G VAL* 3.9 11.4 - - + -
54G LYS 2.7 12.6 + - - +
55G ILE* 2.9 55.1 - - + +
56G LYS 3.0 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G LYS* 3.6 14.9 - - - +
3G VAL 2.9 7.6 + - - +
4G ALA* 3.4 8.3 - - - +
5G VAL 2.9 26.9 + - - +
29G GLU 4.4 0.2 - - - -
30G LEU* 1.3 75.3 - - - +
32G LEU* 1.3 66.2 + - - +
56G LYS* 3.2 8.7 - - - -
58G PHE* 4.0 7.9 - - - -
66G ALA* 2.6 43.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G VAL* 3.6 12.1 - - + -
8G ALA* 3.4 19.1 - - + -
17G ALA* 3.7 26.0 - - + -
30G LEU* 4.1 15.9 - - + -
31G SER* 1.3 83.3 - - - +
33G TYR* 1.3 59.0 + - - +
39G THR* 3.9 7.6 - - + +
42G VAL* 3.8 30.5 - - + -
43G ALA* 4.0 11.9 - - - +
46G LEU* 4.1 0.7 - - + -
55G ILE* 3.8 23.1 - - + -
56G LYS 2.9 10.7 + - - +
57G GLY* 3.4 2.6 - - - -
58G PHE* 2.9 31.2 + - - -
66G ALA* 4.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G VAL 2.8 9.7 + - - -
6G LEU* 3.7 25.8 - - + -
7G GLY 2.7 32.5 + - - -
8G ALA 3.1 4.8 + - - -
32G LEU* 1.3 76.6 - - - +
34G ASP* 1.3 70.2 + - - +
35G ILE* 4.0 8.0 - - + +
39G THR* 4.0 1.6 - - - -
58G PHE* 3.3 20.2 - - + -
59G SER 4.1 3.6 - - - -
60G GLY 2.5 29.6 + - - -
61G GLU* 3.4 16.2 + - - -
62G ASP 3.6 18.6 - - - -
63G ALA* 3.9 29.8 - - + -
66G ALA* 3.8 12.1 - - + +
100G ASN* 5.7 0.3 + - - -
101G LEU* 4.0 19.8 - - + +
104G GLN* 5.0 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