Contacts of the strand formed by residues 45 - 51 (chain N) in PDB entry 6XOX
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 45 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A GLU* 5.1 6.4 - - - +
37N VAL* 3.8 10.3 - - + -
38N ARG 3.3 6.3 - - - +
39N GLN* 3.4 38.6 - - + +
44N GLY* 1.3 73.5 - - - -
46N GLU* 1.3 59.3 + - - +
95N TYR* 3.7 20.2 - - + -
110N VAL* 3.3 28.3 - - + +
111N THR 4.2 12.3 - - - +
112N SER* 5.6 0.7 - - - -
113N THR* 4.3 16.4 - - - +
118N ARG* 3.5 36.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A THR 3.2 25.5 + - - +
264A ASN* 4.0 17.7 + - - +
268A GLU* 6.4 3.1 - - + -
37N VAL* 3.3 2.3 - - - +
38N ARG* 2.5 89.2 + - + +
39N GLN* 5.8 0.2 - - - -
40N ALA* 5.9 2.9 - - - +
44N GLY 3.5 4.7 + - - +
45N LEU* 1.3 74.6 - - - +
47N TRP* 1.3 67.5 + - - +
61N THR* 6.2 1.7 - - - +
110N VAL* 3.7 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLN* 3.3 35.3 - - + +
268A GLU* 6.1 1.7 - - - +
271A ASN* 3.2 38.8 - - - +
35N ASN* 4.3 9.6 - - + -
36N TRP 3.9 7.0 - - - -
37N VAL* 4.5 6.3 - - + +
46N GLU* 1.3 83.2 - - - +
48N VAL* 1.3 66.8 + - - +
49N SER* 3.3 17.4 - - - -
50N ASP* 2.4 54.8 + - - -
59N SER* 4.0 7.6 - - - -
60N TYR* 3.3 23.6 - - - -
61N THR* 3.5 38.6 + - - +
109N ASP* 5.5 3.6 - - - -
110N VAL* 3.8 15.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 48 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N TRP* 2.8 24.6 + - + +
37N VAL 4.4 1.1 - - - -
38N ARG* 3.7 45.8 - - + +
47N TRP* 1.3 84.7 - - - +
49N SER* 1.3 68.7 + - - +
60N TYR* 3.5 0.7 - - - +
61N THR* 2.8 35.1 + - + -
64N VAL* 4.3 9.6 - - + -
68N PHE* 4.0 31.6 - - + -
81N LEU* 4.7 4.7 - - + -
94N TYR* 5.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N ASN* 2.9 11.1 - - - +
36N TRP* 2.9 32.6 + - - -
47N TRP* 3.3 10.1 - - - +
48N VAL* 1.3 88.8 - - - +
50N ASP* 1.3 56.4 + - - +
59N SER 2.7 20.0 + - - -
60N TYR* 3.4 14.8 - - - -
70N ILE* 3.3 34.1 - - - +
81N LEU* 4.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 50 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A ASN* 4.9 0.2 - - - +
274A LYS* 4.0 20.8 + - - -
33N LYS* 4.2 20.2 + - - +
34N MET 3.4 3.8 - - - -
35N ASN* 2.3 31.0 + - - +
47N TRP* 2.4 37.3 + - - -
49N SER* 1.3 78.3 + - - +
51N ILE* 1.3 64.0 + - - +
58N ILE* 3.6 5.0 - - - +
59N SER* 2.9 43.9 + - - +
70N ILE* 4.1 0.9 - - - -
107N CYS* 5.7 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N LYS* 3.2 5.1 - - - +
34N MET* 2.9 41.2 + - + -
50N ASP* 1.3 75.6 - - - +
52N SER* 1.3 66.0 + - - +
55N GLY* 3.7 26.7 - - - +
57N SER 3.8 5.8 - - - +
58N ILE* 4.7 6.7 - - + +
70N ILE* 3.7 28.0 - - + +
71N SER* 3.8 12.6 - - - +
72N ARG* 3.7 39.3 - - + +
79N LEU* 3.7 19.7 - - + -
----------------------------------------------------------
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