Contacts of the strand formed by residues 46 - 53 (chain J) in PDB entry 1KYO
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 46 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J ILE* 3.6 22.4 - - + -
39J ARG 3.4 16.2 - - - +
40J LEU* 3.5 24.7 - - + -
44J ASN 4.2 1.0 + - - -
45J LYS* 1.3 75.5 - - - +
47J GLU* 1.3 61.5 + - - +
95J TYR* 5.1 1.8 - - + -
36K TYR* 5.9 0.7 - - + -
44K ILE* 4.4 14.6 - - + -
87K PHE* 3.6 41.9 - - + -
97K THR* 5.5 2.1 - - - +
98K PHE* 3.5 56.3 + - + +
99K GLY 4.5 3.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 47 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38J ILE* 3.4 7.2 - - - +
39J ARG* 2.7 71.0 + - - -
41J PHE* 4.1 14.5 - - + -
45J LYS* 3.9 2.4 + - + +
46J LEU* 1.3 75.5 - - - +
48J TRP* 1.3 65.4 + - - +
49J VAL* 3.4 1.7 + - - +
61J ASN* 4.2 16.3 - - - +
63J SER* 4.7 8.4 + - - -
64J LEU* 3.4 23.9 - - - +
98K PHE* 4.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 48 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ASN* 3.3 20.9 + - + +
37J TRP 4.2 1.3 - - - -
38J ILE* 4.1 20.0 - - + -
47J GLU* 1.3 73.3 - - - +
49J VAL* 1.3 59.6 + - - +
50J GLY* 3.3 24.6 - - - +
51J TYR* 3.8 14.8 - + - -
59J ASN* 3.0 39.7 - - - -
60J TYR 3.8 1.8 - - - -
61J ASN* 2.9 55.1 + - + +
62J PRO* 5.1 0.2 - - + -
109J MET* 5.1 1.8 - - + -
94K PHE* 4.2 7.6 - + + -
95K PRO* 3.6 31.9 - - + -
96K TRP* 3.4 48.7 + + + +
98K PHE* 4.2 10.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J TRP* 3.0 25.5 + - + +
38J ILE* 3.8 14.4 - - - +
39J ARG* 4.0 24.9 - - + +
47J GLU* 4.0 4.9 - - - +
48J TRP* 1.3 73.3 - - - +
50J GLY* 1.3 58.9 + - - +
60J TYR* 3.8 0.2 - - - -
61J ASN* 3.1 21.8 + - - +
64J LEU* 3.5 16.6 - - + -
68J LEU* 3.2 36.3 - - + +
70J ILE* 5.3 1.1 - - + -
81J LEU* 4.2 18.8 - - + -
83J LEU* 5.9 1.6 - - + -
94J TYR* 4.8 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 50 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36J ASN* 3.4 1.4 - - - +
37J TRP* 3.0 26.9 + - - +
48J TRP* 3.3 24.4 - - - -
49J VAL* 1.3 81.3 - - - +
51J TYR* 1.3 60.4 + - - -
59J ASN 3.4 7.2 - - - -
60J TYR* 4.0 3.4 - - - -
70J ILE* 3.6 15.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 51 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34J TYR* 4.1 41.0 + + + -
35J TRP 3.1 18.4 - - - +
36J ASN* 3.6 24.0 - - - +
48J TRP* 3.9 12.1 - + - -
50J GLY* 1.3 75.0 - - - +
52J ILE* 1.3 72.1 + - - +
53J SER* 4.0 1.8 - - - -
57J ASP* 3.9 13.9 - - + -
58J ASN* 3.5 21.3 + - - +
59J ASN* 3.2 33.6 + - + +
70J ILE* 3.7 10.3 - - - +
107J TYR* 5.2 0.5 + - - -
94K PHE* 3.6 40.1 - + - -
96K TRP* 4.6 3.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 52 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ILE* 5.5 1.6 - - + -
35J TRP* 3.0 43.3 + - + +
51J TYR* 1.3 80.8 - - - +
53J SER* 1.3 70.2 + - - +
56J GLY* 4.2 14.1 - - - +
57J ASP 3.4 8.5 - - - +
58J ASN* 3.8 13.5 - - - +
70J ILE* 3.9 28.9 - - + +
71J THR* 4.1 4.5 - - - -
72J ARG* 3.8 38.8 - - + +
79J PHE* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 53 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ILE* 4.8 0.2 - - - +
33J TYR 3.9 1.8 - - - -
34J TYR* 3.5 34.5 - - - -
35J TRP* 4.2 4.0 - - - -
51J TYR* 4.0 2.9 - - - -
52J ILE* 1.3 81.9 - - - +
54J ASN* 1.3 64.3 + - - +
55J VAL* 3.1 13.4 + - - +
56J GLY 3.3 8.0 + - - -
57J ASP* 3.1 37.4 + - - +
72J ARG* 3.2 15.2 + - - -
----------------------------------------------------------
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