Contacts of the strand formed by residues 36 - 42 (chain A) in PDB entry 2KUL
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 GLU 36 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.3 50.9 - - + +
29A ILE 3.3 2.9 - - - +
30A THR* 3.0 25.0 + - + +
34A LYS 4.1 1.4 + - - -
35A LYS* 1.3 69.7 - - - +
37A TRP* 1.3 63.6 + - - +
38A LYS* 3.6 2.4 + - - +
56A MET* 3.8 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A GLU 3.4 3.5 - - - +
28A ILE* 3.1 2.6 - - - -
29A ILE* 2.7 52.7 + - + +
31A ASP* 2.8 33.0 + - + +
33A ALA* 5.7 0.4 - - + -
35A LYS* 3.1 50.5 + - + +
36A GLU* 1.3 70.5 - - - +
38A LYS* 1.3 62.4 + - - +
39A VAL 3.5 0.4 + - - +
54A ALA* 4.7 3.4 - - + -
56A MET* 3.4 25.4 - - + -
65A ASP* 3.6 22.9 - - + -
68A CYS* 3.6 29.6 - - - -
114A TRP* 3.8 34.1 - + + -
115A GLY 4.2 7.9 - - - -
128A PHE* 4.6 3.1 - + - -
130A ILE* 3.9 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 5.5 4.9 - - - -
26A GLY* 3.8 29.6 - - - +
27A GLU 3.8 0.7 - - - -
28A ILE* 3.6 21.8 - - + -
36A GLU 3.6 2.5 + - - +
37A TRP* 1.3 70.0 - - - +
39A VAL* 1.3 61.2 + - - +
54A ALA* 3.8 4.4 - - - +
55A ASP* 2.7 51.9 + - - -
56A MET* 3.0 44.1 + - - +
57A ASN* 4.1 8.3 - - + +
58A SER* 5.6 2.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 3.1 24.0 - - - +
25A VAL* 4.3 0.2 - - - +
26A GLY* 2.8 28.4 + - - -
27A GLU* 3.1 27.2 + - + +
29A ILE* 5.7 8.7 - - + +
37A TRP 3.5 2.6 + - - +
38A LYS* 1.3 73.4 - - - +
40A GLY* 1.3 68.0 + - - +
52A TYR* 3.5 46.9 - - + -
53A LEU 3.9 4.3 - - - +
54A ALA* 4.7 2.0 - - - +
70A VAL* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA 5.2 0.2 - - - -
25A VAL* 3.3 37.9 - - - +
38A LYS 3.5 1.8 + - - -
39A VAL* 1.3 77.5 - - - +
41A LEU* 1.3 65.7 + - - +
42A PRO* 4.0 1.9 - - - +
53A LEU* 2.8 13.8 + - - -
55A ASP* 3.6 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 5.2 16.2 - - + +
25A VAL* 5.1 9.2 - - + -
40A GLY* 1.3 80.2 - - - +
42A PRO* 1.3 73.8 - - + +
43A ILE* 3.3 2.8 + - + +
52A TYR* 3.7 3.8 - - - -
53A LEU* 2.9 48.4 + - + +
55A ASP* 6.2 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A HIS* 2.7 58.7 + - + +
20A ALA* 5.5 11.4 - - + +
24A ALA* 5.6 4.3 - - + -
25A VAL* 5.1 5.2 - - + -
40A GLY 4.0 5.6 - - - +
41A LEU* 1.3 88.6 - - + +
43A ILE* 1.3 61.8 + - - +
44A GLY* 3.5 2.0 - - - +
51A ILE 4.2 0.4 - - - +
52A TYR* 3.5 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