Contacts of the strand formed by residues 36 - 42 (chain A) in PDB entry 2K9U
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 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLY 4.2 4.5 - - - +
35A VAL* 1.3 97.0 - - + +
37A ALA* 1.3 59.9 + - - +
77A TYR 4.0 5.4 - - - +
78A VAL* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 6.1 1.3 - - + -
27A GLY* 4.5 4.5 - - - -
30A ARG 4.9 5.6 - - - +
31A GLY* 5.0 7.2 - - - -
35A VAL* 3.3 8.4 + - + +
36A PRO* 1.3 76.5 - - - +
38A GLU* 1.3 64.9 + - - +
76A SER* 3.5 2.4 - - - -
77A TYR* 2.7 70.7 + - + +
79A VAL* 5.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A THR* 3.7 11.7 + - + +
27A GLY* 2.9 24.4 + - - -
37A ALA* 1.3 79.4 - - - +
39A PHE* 1.3 68.9 + - - +
66A GLU* 5.6 2.3 - - - +
69A LYS* 4.8 13.9 + - - -
74A GLY* 5.6 3.1 - - - -
75A VAL 3.6 7.0 - - - +
76A SER* 3.5 24.5 - - - +
77A TYR* 3.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 4.6 3.6 - - + -
25A GLY* 3.9 14.6 - - - -
27A GLY 5.1 0.4 - - - -
28A LEU* 3.4 47.8 - - + +
38A GLU* 1.3 83.9 - - - +
40A SER* 1.3 65.9 + - - +
41A ILE* 3.1 35.4 - - + -
69A LYS* 5.6 1.8 - - - -
74A GLY* 3.7 3.2 - - - -
75A VAL* 3.1 53.6 + - + -
77A TYR* 3.8 22.2 - + + -
87A VAL* 6.2 5.2 - - + -
89A ILE* 5.4 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ARG* 6.2 0.2 - - - +
23A ALA* 3.4 0.5 - - - -
24A GLY* 2.4 47.2 + - - -
25A GLY* 4.3 0.8 - - - -
39A PHE* 1.3 77.3 - - - +
41A ILE* 1.3 70.5 + - - +
42A TRP 5.3 1.1 + - - -
69A LYS* 4.4 10.3 - - - +
72A SER* 4.4 17.6 + - - -
73A CYS 3.4 6.7 - - - -
74A GLY* 4.6 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 5.7 4.9 - - + -
22A ARG 3.3 11.2 - - - +
23A ALA* 4.1 9.2 - - + -
39A PHE* 3.1 33.7 - - + -
40A SER* 1.3 84.8 - - - +
42A TRP* 1.3 65.4 + - - +
43A THR* 3.8 6.5 + - + +
51A LEU* 5.3 20.2 - - + -
53A ILE* 6.3 1.3 - - + -
73A CYS* 2.6 43.7 + - + +
75A VAL* 3.3 25.4 - - + -
89A ILE* 4.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 3.7 13.8 + - - +
21A VAL* 4.4 1.2 - - - -
22A ARG* 3.1 48.5 + - + +
40A SER* 4.2 1.0 + - - -
41A ILE* 1.3 76.4 - - - +
43A THR* 1.3 84.3 + - - +
44A ARG* 4.4 26.2 - - + -
45A GLU* 4.3 18.3 + - - +
70A ASP 5.4 0.2 - - - -
71A GLY* 3.2 40.6 - - - -
72A SER* 3.9 22.6 - - - +
73A CYS 4.2 0.2 - - - +
----------------------------------------------------------
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