Contacts of the strand formed by residues 51 - 58 (chain H) in PDB entry 1LNU
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 ARG 51 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ILE* 4.4 25.9 - - - +
41H CYS* 3.1 1.6 - - - -
42H TYR* 2.7 58.1 + - + +
49H ARG* 5.3 3.1 - - + +
50H ILE* 1.3 78.6 - - - +
52H TYR* 1.3 60.0 + - - +
53H VAL* 4.1 13.2 - - + +
67H ASP* 2.7 40.3 + - - +
68H SER* 4.4 4.5 - - - -
69H ASP* 3.5 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 52 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H ALA* 3.1 22.2 - - + +
39H GLY 3.7 19.3 - - - -
40H GLU 4.2 0.2 - - - -
41H CYS* 3.1 26.7 - - + -
50H ILE 4.3 0.2 - - - -
51H ARG* 1.3 69.9 - - - +
53H VAL* 1.3 64.4 + - - +
54H THR* 3.3 23.6 - - + +
66H TYR* 3.6 14.2 - + + +
67H ASP 3.7 0.2 - - - -
68H SER* 2.9 40.5 + - - +
97H THR* 4.1 10.5 - - + -
100H GLU* 2.5 59.5 + - + +
101H LEU* 4.1 25.2 - - + +
104H VAL* 4.1 11.9 - - + -
105H CYS* 4.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 53 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ILE* 5.9 1.3 - - + -
38H MET 3.7 0.7 - - - +
40H GLU* 2.8 46.1 + - + +
42H TYR* 4.3 10.1 - - + -
51H ARG* 4.1 17.3 - - + +
52H TYR* 1.3 81.6 - - - +
54H THR* 1.3 61.9 + - - +
55H ARG* 3.5 37.5 + - + +
65H ARG* 3.8 19.7 - - + -
66H TYR 3.2 13.5 - - - +
67H ASP* 3.8 23.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H LYS 5.0 0.4 - - - +
37H PHE* 3.7 30.3 - - + -
38H MET 3.6 3.1 - - - -
39H GLY* 4.1 5.8 - - - -
52H TYR* 3.3 38.1 - - + +
53H VAL* 1.3 69.4 - - - +
55H ARG* 1.3 64.0 + - - +
56H TYR* 4.0 10.9 + - - +
65H ARG* 3.4 5.0 - - - +
66H TYR* 3.0 57.5 + - - +
97H THR* 4.3 5.1 - - + +
100H GLU* 3.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 55 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G ILE* 4.3 16.6 - - - +
144G TYR* 3.6 22.2 + - - -
36H GLN 3.6 1.6 - - - +
37H PHE* 3.4 18.2 - - - -
38H MET* 3.4 22.7 + - + +
40H GLU* 2.3 36.4 + - - -
42H TYR* 4.1 5.3 + - - -
53H VAL* 3.5 30.4 - - + +
54H THR* 1.3 80.1 - - - +
56H TYR* 1.3 65.2 + - - +
57H ILE* 3.9 13.7 - - + -
62H GLU* 2.6 44.0 + - + +
64H VAL 4.0 3.4 - - - -
65H ARG* 3.7 10.9 - - + +
67H ASP* 5.6 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ASN* 4.4 3.8 - - - -
7H LYS 4.2 4.0 + - - -
8H ALA* 4.2 2.7 - - + -
9H ASN* 3.8 35.2 + - - -
35H TYR* 3.0 27.6 - + - +
36H GLN 3.4 4.5 - - - -
37H PHE* 3.3 38.6 - + - -
54H THR* 4.0 21.3 + - - +
55H ARG* 1.3 76.9 - - - +
57H ILE* 1.3 63.0 + - - +
62H GLU* 3.4 2.8 - - - -
63H TYR* 3.0 36.2 + - + -
64H VAL* 3.2 26.2 + - + +
65H ARG* 4.9 2.7 - - - -
73H HIS* 4.7 4.5 - - - -
87H TRP* 3.6 32.0 - + - -
97H THR* 5.5 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G TYR* 3.3 43.7 - - + -
34H VAL 3.9 0.5 - - - +
35H TYR* 3.6 8.2 - - - -
36H GLN* 2.8 56.4 + - + +
38H MET* 4.6 2.5 - - - -
55H ARG* 3.9 19.3 - - + +
56H TYR* 1.3 77.2 - - - +
58H TYR* 1.3 59.2 + - - +
59H ASN 3.9 4.2 - - - +
60H ARG* 3.2 16.4 - - - +
61H GLU 3.1 31.9 - - - +
62H GLU* 3.4 18.2 - - - +
63H TYR* 4.2 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G LEU* 3.9 24.2 - - + -
74G LEU* 3.6 48.0 - - + -
75G THR* 3.7 16.9 - - - -
78G SER* 3.6 25.6 - - - -
81G THR* 3.1 20.6 + - - -
33H PHE* 3.8 9.8 - + + -
34H VAL 4.0 1.3 - - - -
35H TYR* 4.7 3.1 - + - -
57H ILE* 1.3 70.9 - - - +
59H ASN* 1.3 96.6 + - - +
60H ARG 2.5 18.7 + - - -
61H GLU* 2.7 29.7 + - + +
63H TYR* 3.9 9.0 - - + -
79H LEU* 4.6 9.0 - - + -
----------------------------------------------------------
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