Contacts of the strand formed by residues 46 - 50 (chain C) in PDB entry 6BA5
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 THR 46 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C PHE* 3.2 7.2 - - - -
38C GLN* 2.8 53.9 + - - +
44C PRO* 4.2 6.7 - - + +
45C PRO* 1.3 80.1 - - - +
47C LEU* 1.3 66.8 + - - +
48C LEU* 4.1 3.6 - - - +
104D ASN 6.0 1.1 - - - -
106D TRP* 5.0 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ALA* 4.0 6.1 - - + -
36C TRP 3.9 2.0 - - - +
37C PHE* 3.7 27.2 - - + -
46C THR* 1.3 74.9 + - - +
48C LEU* 1.3 63.5 + - - +
49C ILE 3.5 25.6 - - - +
50C TYR* 4.3 5.8 - - + -
56C ALA* 3.9 22.9 - - + +
59C VAL* 3.5 17.2 - - - +
101D GLY* 3.8 26.2 - - - +
102D ASP 3.5 19.3 - - - +
103D PHE 3.7 15.9 + - - +
104D ASN* 4.3 13.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C TRP 2.8 14.7 + - - +
37C PHE* 3.7 14.6 - - - +
38C GLN* 3.8 20.6 - - + +
46C THR* 4.7 3.1 - - - +
47C LEU* 1.3 78.4 - - - +
49C ILE* 1.3 72.8 - - + +
55C LEU* 3.9 3.5 - - - +
56C ALA* 2.9 26.9 + - - +
59C VAL* 3.9 28.1 - - + +
60C PRO* 5.9 0.2 - - + -
63C PHE* 4.2 28.0 - - + -
74C LEU* 4.2 9.4 - - + -
87C TYR* 3.6 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU 5.1 0.4 - - - +
35C ALA* 3.1 7.2 - - - +
36C TRP* 2.9 40.0 + - + -
47C LEU* 3.5 5.7 - - - +
48C LEU* 1.3 79.9 - - + +
50C TYR* 1.3 64.4 + - - +
52C ALA* 3.4 34.3 - - - +
53C SER* 3.7 6.3 - - - +
54C ASN 3.3 11.0 - - - +
55C LEU* 3.7 38.1 - - + +
56C ALA 4.4 0.2 - - - +
63C PHE* 3.9 12.6 - - + +
64C SER* 4.0 1.1 - - - -
65C GLY* 4.0 14.4 - - - +
74C LEU* 4.1 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LEU 3.8 5.4 - - - -
35C ALA* 4.2 2.9 - - + -
47C LEU* 4.3 14.8 - - + -
49C ILE* 1.3 75.0 - - - +
51C ARG* 1.3 71.5 + - + +
52C ALA 3.1 3.3 + - - -
53C SER 3.4 0.3 + - - -
54C ASN* 2.8 70.1 + - + +
55C LEU 4.3 9.9 + - - -
56C ALA* 4.3 9.2 - - - -
98D THR 3.6 4.3 - - - +
99D TYR 3.5 15.0 - - - -
100D TYR* 3.2 33.0 - - - +
101D GLY* 3.6 25.4 - - - -
329N LYS 5.3 2.7 + - - -
330N SER 4.3 7.5 + - - -
331N GLY* 4.4 8.7 + - - -
----------------------------------------------------------
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