Contacts of the helix formed by residues 41 - 48 (chain K) in PDB entry 5OA3
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 PRO 41 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7K ASN* 3.4 18.4 - - - +
29K MET 4.9 2.0 - - - +
30K PRO 3.5 21.1 - - - +
39K ASN 3.2 11.6 - - - +
40K VAL* 1.3 87.6 - - - +
42K ASN* 1.3 64.2 + - - +
43K LEU* 3.3 4.9 - - + +
44K HIS* 3.1 45.1 + - + +
45K VAL* 3.6 3.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 42 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K ALA* 4.9 3.9 - - - +
24K LYS* 4.5 20.6 - - - +
25K LYS 5.1 0.2 - - - +
26K ASP* 3.8 16.5 + - - +
29K MET* 3.7 48.9 + - + +
31K LYS* 4.0 4.7 - - - +
32K HIS* 2.4 39.8 + - - +
33K PRO* 4.8 4.8 - - - +
40K VAL 3.6 3.0 + - - -
41K PRO* 1.3 69.0 - - - +
43K LEU* 1.3 65.6 + - - +
44K HIS 3.1 2.2 - - - -
45K VAL* 3.3 3.8 + - - +
46K MET* 2.9 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12742 G 3.4 55.4 - - + +
26K ASP 4.2 4.9 + - - -
27K VAL* 3.6 35.7 + - + +
29K MET 4.8 0.6 + - - -
41K PRO* 3.3 3.5 - - + +
42K ASN* 1.3 78.4 - - - +
44K HIS* 1.3 69.3 + - + +
46K MET* 3.3 18.5 - - + +
47K LYS* 2.9 44.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K MET* 3.5 51.8 - - + +
4K PRO* 4.6 4.0 - - + +
7K ASN* 4.6 10.1 - - + +
11K ILE* 4.0 5.8 - - + -
40K VAL* 4.3 11.2 - - + -
41K PRO* 3.1 49.4 + - + +
42K ASN 3.1 0.6 - - - -
43K LEU* 1.3 83.5 - - + +
45K VAL* 1.3 57.9 + - - +
46K MET 2.9 4.3 - - - -
47K LYS* 5.4 0.4 - - - -
48K ALA* 2.9 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K ILE* 3.6 31.2 - - + +
21K MET* 4.1 22.0 - - + -
22K VAL 4.5 1.6 - - - +
23K ALA* 5.4 0.9 - - + -
32K HIS* 3.7 49.1 - - + +
35K LEU* 4.1 3.6 - - + -
40K VAL* 3.9 17.7 - - + -
41K PRO 3.9 5.8 - - - +
42K ASN* 3.3 6.0 + - - +
44K HIS* 1.3 74.8 - - - +
46K MET* 1.3 61.4 + - - +
48K ALA 4.5 0.2 - - - -
49K MET* 4.1 10.8 + - + +
69K TRP* 3.4 15.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 46 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23K ALA* 4.5 7.2 - - + -
25K LYS* 3.8 13.2 - - + -
26K ASP 3.7 37.2 - - - +
27K VAL* 3.9 21.1 - - + -
42K ASN* 2.9 12.5 + - - +
43K LEU* 3.3 19.3 - - + +
44K HIS 2.9 0.8 - - - -
45K VAL* 1.3 80.7 - - - +
47K LYS* 1.3 72.5 + - + +
48K ALA 3.5 0.7 + - - -
49K MET 3.7 5.7 + - - -
50K GLN* 4.0 4.9 + - - +
67K PHE* 4.1 28.9 - - + -
69K TRP* 3.8 18.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12742 G 3.5 49.4 + - - +
12752 G 3.6 14.3 + - - -
13232 U 4.5 10.9 + - - +
13242 G 6.3 0.6 - - - -
3K MET* 6.0 1.6 - - + -
43K LEU* 2.9 31.2 + - + +
44K HIS* 5.4 0.9 - - - -
46K MET* 1.3 79.2 - - + +
48K ALA* 1.3 60.4 + - - +
49K MET 3.3 1.3 - - - -
50K GLN* 3.1 50.6 - - - +
51K SER* 3.9 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K MET* 4.3 25.9 - - + +
8K ARG* 5.4 7.6 - - + +
11K ILE* 4.6 15.3 - - + -
12K TYR* 4.2 19.1 + - + +
44K HIS* 2.9 21.1 + - - +
47K LYS* 1.3 75.0 - - - +
49K MET* 1.3 59.6 + - - +
50K GLN 3.1 4.9 - - - -
51K SER* 3.5 19.0 + - - -
52K LEU* 3.9 3.6 + - - +
----------------------------------------------------------
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