Contacts of the strand formed by residues 47 - 52 (chain C) in PDB entry 1K9A
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 TRP 47 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 4.0 7.2 - + - -
23C THR* 4.3 15.5 - - + -
26C GLN* 5.7 2.0 - - - -
27C ASP* 3.8 25.6 - - - -
41C VAL* 3.8 1.4 - - - +
42C THR* 2.8 39.0 + - + +
44C ASP* 2.8 34.3 + - + +
45C PRO 3.1 1.2 - - - -
46C ASN* 1.3 93.3 + - + +
48C TYR* 1.3 69.4 + - - +
59C ILE* 3.6 22.7 - - + -
60C ILE* 3.4 21.8 - - - -
61C PRO* 3.6 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER* 3.1 12.8 - - - -
8C TRP* 2.7 65.1 + + + +
38C ILE* 3.5 28.3 - - + -
40C ALA 3.5 3.4 - - - +
41C VAL* 3.6 30.0 - - + +
42C THR* 4.0 5.4 - - - -
45C PRO 3.8 19.1 + - - -
47C TRP* 1.3 79.7 - - - +
49C LYS* 1.3 64.0 + - - +
59C ILE* 3.1 5.9 - - - +
60C ILE* 2.7 46.0 + - + -
62C ALA* 3.9 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ILE* 3.8 1.6 - - - -
39C VAL* 2.8 43.8 + - + +
40C ALA* 2.8 24.0 + - + +
42C THR* 4.3 3.9 - - + +
48C TYR* 1.3 76.4 - - - +
50C ALA* 1.3 62.9 + - - +
57C GLU* 3.6 36.2 + - + +
58C GLY* 3.3 7.9 - - - +
59C ILE* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.4 5.6 - - + +
36C LEU* 4.6 4.9 - - + -
37C THR 3.3 18.4 - - - +
38C ILE* 4.3 2.9 - - + -
39C VAL* 4.0 3.6 - - - -
49C LYS* 1.3 78.4 - - - +
51C LYS* 1.3 68.1 + - - +
57C GLU* 3.0 5.5 - - - -
58C GLY 2.7 31.1 + - - -
60C ILE* 3.9 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A LYS* 5.3 3.2 - - - +
446B HIS* 2.9 39.8 + - + +
447B GLU* 3.5 27.4 + - - +
448B LEU* 5.3 1.1 - - + -
28C LEU* 4.2 3.4 - - - -
36C LEU* 3.6 4.5 - - - +
37C THR* 2.8 43.2 + - + +
39C VAL* 3.8 15.9 - - + -
50C ALA* 1.3 78.1 - - - +
52C ASN* 1.3 62.7 + - - +
55C GLY* 3.9 22.1 + - - +
56C ARG 2.9 11.2 - - - +
57C GLU* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 4.1 15.4 - - + +
29C PRO 5.1 4.3 + - - +
30C PHE* 5.9 1.3 - - + -
34C ASP* 6.6 0.4 - - + -
35C VAL 4.2 7.2 - - - +
36C LEU* 4.3 10.1 - - + -
51C LYS* 1.3 76.2 - - - +
53C LYS* 1.3 61.6 + - + +
54C VAL* 2.8 15.9 + - - +
55C GLY* 2.6 31.9 + - - -
56C ARG* 2.9 57.7 + - - +
----------------------------------------------------------
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