Contacts of the strand formed by residues 50 - 58 (chain C) in PDB entry 5IXG
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 50 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU* 3.8 1.7 - - - +
45C ASP* 2.8 50.2 + - + +
48C ALA* 4.0 15.5 - - + +
49C LYS* 1.3 80.4 - - - +
51C GLY* 1.3 61.1 + - - +
92C THR* 3.6 22.5 - - - +
93C ILE 3.6 6.1 + - - -
95C PHE* 3.2 16.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C THR* 2.9 20.4 - - - -
44C LEU* 4.3 0.2 - - - -
45C ASP* 4.4 1.1 - - - -
50C THR* 1.3 83.3 + - - +
52C THR* 1.3 58.9 - - - -
92C THR* 3.3 10.6 - - - +
93C ILE* 2.8 36.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C THR* 4.1 1.1 - - - +
42C VAL* 3.2 7.4 - - - +
43C THR* 2.9 51.1 + - + +
51C GLY* 1.3 74.5 - - - -
53C VAL* 1.3 71.7 + - - +
54C ASP* 5.7 1.5 - - + +
91C GLY 3.2 11.7 + - - -
92C THR* 5.3 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 4.3 5.8 - - + -
41C THR 3.6 7.0 - - - +
42C VAL* 4.1 11.2 - - + -
52C THR* 1.3 84.6 + - - +
54C ASP* 1.4 64.7 + - - +
55C VAL* 4.1 19.1 - - + -
89C TYR* 4.3 8.1 - - + -
90C LYS* 3.3 5.5 - - - +
91C GLY 2.8 34.0 + - - +
93C ILE* 4.1 21.5 - - + -
103C VAL* 4.2 12.1 - - + -
201C OTP 4.0 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C GLY* 3.1 4.7 - - - -
41C THR* 2.9 45.8 + - - +
52C THR* 5.7 1.6 - - + +
53C VAL* 1.4 75.4 - - - +
55C VAL* 1.3 61.8 + - - +
56C THR* 4.6 1.7 + - - -
88C ASN* 3.1 24.4 + - - -
89C TYR 3.5 3.4 - - - -
90C LYS* 3.8 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 4.2 15.5 - - + -
16C THR* 5.0 0.9 - - + -
38C SER* 4.3 9.0 - - - -
39C SER 3.4 15.9 - - - +
40C GLY* 4.2 0.2 - - - -
53C VAL* 4.1 9.6 - - + -
54C ASP* 1.3 76.4 - - - +
56C THR* 1.4 67.7 + - - +
57C THR* 4.6 2.7 - - - +
88C ASN* 2.8 20.7 + - - -
89C TYR* 2.9 44.1 + - + +
201C OTP 3.7 44.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C SER* 3.1 4.3 - - - -
39C SER* 2.9 40.3 + - - -
54C ASP* 4.6 1.7 + - - -
55C VAL* 1.4 70.4 - - - +
57C THR* 1.3 64.3 + - - +
58C ASP* 4.5 1.5 + - - +
86C GLN* 3.5 42.4 - - + +
87C ALA 3.3 13.0 - - - +
88C ASN* 3.3 20.8 + - + +
201C OTP 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PRO* 3.8 9.9 - - + +
35C PHE* 3.4 43.3 - - + -
37C LYS 3.4 8.1 - - - +
38C SER* 2.8 17.2 + - - +
55C VAL* 4.6 2.4 - - - +
56C THR* 1.3 75.2 - - - +
58C ASP* 1.3 64.6 + - - +
59C ILE 3.6 0.3 + - - -
86C GLN* 3.2 5.0 - - - -
87C ALA* 2.9 32.9 + - - +
201C OTP 3.5 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 3.6 5.2 - - - -
37C LYS* 3.0 42.1 + - + +
56C THR* 4.8 1.2 - - - +
57C THR* 1.3 71.2 - - - +
59C ILE* 1.3 65.2 + - - +
60C ALA* 4.5 6.3 - - + +
61C SER* 2.6 33.4 + - - +
85C PRO 3.7 5.8 - - - +
86C GLN* 2.9 32.3 + - - -
----------------------------------------------------------
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