Contacts of the strand formed by residues 69 - 74 (chain H) in PDB entry 1UB6
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 PHE 69 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40H ARG* 4.1 0.9 - - - -
50H VAL* 3.6 25.6 - - + +
61H TYR* 3.2 22.1 - - + -
65H VAL* 3.1 43.1 + - + +
66H ALA 4.5 4.3 - - - +
67H GLY 5.0 0.9 - - - -
68H ARG* 1.3 109.1 + - + +
70H THR* 1.3 66.0 + - - +
82H LEU* 4.4 10.1 - - + -
83H GLN 3.3 3.1 - - - +
84H MET* 3.7 42.0 - - + -
85H SER 4.2 2.2 - - - -
87H LEU* 4.1 5.2 - - + -
91H ASP* 3.8 24.7 - - - -
95H TYR* 4.0 12.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61H TYR* 3.4 7.4 + - - +
68H ARG 4.9 2.1 + - - -
69H PHE* 1.3 77.1 + - - +
71H ILE* 1.3 71.4 + - - +
72H SER* 3.9 9.0 + - - -
81H TYR* 4.3 0.3 - - - +
82H LEU* 3.6 3.5 + - - -
83H GLN* 2.7 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 71 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H MET 3.8 23.1 - - - +
37H SER* 4.4 1.1 - - - -
38H TRP* 3.4 25.1 - - + +
51H ALA* 4.0 11.7 - - + +
52H SER* 3.7 30.3 - - - +
53H ILE* 3.8 13.8 - - + +
59H THR* 3.8 20.0 - - + +
61H TYR* 2.9 30.4 + - + +
70H THR* 1.3 77.1 - - - +
72H SER* 1.3 65.4 + - - +
80H LEU* 4.0 9.9 - - + -
81H TYR 3.4 13.7 - - - +
82H LEU* 4.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 72 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53H ILE* 4.3 9.2 - - - -
70H THR* 3.9 9.2 + - - -
71H ILE* 1.3 76.4 - - - +
73H ARG* 1.3 60.2 + - - +
80H LEU* 3.1 9.6 - - - +
81H TYR* 2.8 54.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H PHE* 3.0 31.9 + - + -
30H SER* 3.6 20.1 + - - +
34H TYR 3.1 16.4 + - - -
36H MET* 3.9 6.2 - - - +
53H ILE* 3.9 29.0 + - + +
54H SER 2.4 27.6 + - - -
55H SER 3.3 15.4 + - - -
57H GLY* 3.8 7.9 - - - +
72H SER* 1.3 79.6 - - - +
74H ASP* 1.3 62.2 + - - +
75H ASN* 2.9 39.5 + - - +
79H ILE 3.4 10.5 - - - +
80H LEU* 4.2 7.6 - - + -
81H TYR* 4.8 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 74 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H ARG* 1.3 71.4 - - - +
75H ASN* 1.3 53.6 + - - +
76H VAL* 2.9 21.5 + - - +
77H ARG* 2.8 51.1 + - - +
78H ASN* 2.8 32.6 + - - -
79H ILE* 2.8 24.0 + - + +
81H TYR* 4.1 21.1 + - + -
----------------------------------------------------------
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