Contacts of the strand formed by residues 44 - 50 (chain C) in PDB entry 1USK
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 LEU 44 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 3.7 18.2 - - + +
5C VAL* 3.9 26.5 - - + -
30C ILE* 3.3 21.5 - - + +
33C ILE* 3.7 43.5 - - + -
34C ASN* 3.0 31.0 + - - +
39C ILE* 4.1 21.5 - - + -
42C ASP 3.9 1.2 + - - -
43C LYS* 1.3 72.3 - - - +
45C VAL* 1.3 63.0 + - - +
284C VAL* 4.5 12.1 - - + -
287C LEU* 5.3 2.7 - - + -
288C ALA* 4.6 3.8 - - + -
291C LEU* 4.8 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ASP* 3.9 35.9 - - + +
3C ILE 3.1 10.2 + - - +
4C LYS* 3.5 11.2 - - + -
5C VAL* 2.9 28.0 + - - +
30C ILE* 4.8 1.8 - - - -
43C LYS* 4.1 16.2 - - - +
44C LEU* 1.3 77.9 - - - +
46C GLY* 1.3 71.1 + - - +
47C VAL* 3.9 9.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 46 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 3.4 8.7 - - - -
7C VAL* 4.9 3.8 - - - -
30C ILE* 3.8 27.2 - - - +
44C LEU 4.2 0.4 + - - -
45C VAL* 1.3 78.5 - - - +
47C VAL* 1.3 63.5 + - - +
48C GLU* 4.1 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LYS* 4.5 18.2 - - + +
5C VAL 3.0 7.3 + - - +
6C ALA* 3.2 4.3 - - - -
7C VAL 2.9 21.8 + - - -
45C VAL* 4.4 13.5 - - + +
46C GLY* 1.3 75.8 - - - +
48C GLU* 1.3 64.4 + - - +
49C TYR* 3.3 31.3 - - + +
70C ILE* 3.8 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 3.5 10.5 - - + +
11C MET* 4.7 13.3 - - + +
23C PHE* 3.6 27.9 - - + +
26C ALA* 6.1 0.3 - - - +
27C ARG* 2.9 52.6 + - - +
46C GLY* 4.1 8.0 + - - +
47C VAL* 1.3 78.8 - - - +
49C TYR* 1.3 65.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ALA* 3.7 16.8 - - + -
7C VAL 3.1 7.2 + - - +
8C VAL* 3.5 8.9 - - + +
9C GLY 3.3 23.9 + - - +
11C MET* 4.4 3.6 - - - -
23C PHE* 3.7 4.2 - - - -
47C VAL* 3.3 41.2 - - + +
48C GLU* 1.3 74.4 - - - +
50C ASP* 1.3 60.0 + - - +
51C ASP 4.0 0.2 - - - -
61C VAL* 3.5 33.2 - - + -
64C LYS* 4.0 27.8 - - + -
65C ILE* 3.6 22.4 - - + +
68C ASP* 2.5 36.5 + - - +
70C ILE* 3.9 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLY 3.4 4.3 - - - -
11C MET* 3.0 41.6 + - + +
12C SER* 2.6 26.7 + - - -
49C TYR* 1.3 71.5 - - - +
51C ASP* 1.3 59.0 + - - +
52C ALA* 2.8 25.4 + - - -
57C GLN* 3.7 16.8 + - - +
61C VAL* 3.5 13.7 - - - +
----------------------------------------------------------
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