Contacts of the strand formed by residues 64 - 69 (chain F) in PDB entry 3QAZ
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 THR 64 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F TRP* 5.3 1.1 - - - -
62F ASN* 4.1 9.4 - - + +
63F LEU* 1.3 76.1 - - - +
65F LEU* 1.3 59.7 + - - +
66F HIS* 3.2 20.7 + - - +
83F TYR* 3.3 15.0 - - + +
109F GLN 3.4 1.0 - - - +
110F LEU* 3.6 1.8 - - - +
111F GLN* 2.7 61.9 + - - +
113F PRO* 4.5 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38F VAL* 4.6 6.7 - - + -
50F CYS* 4.3 18.2 - - + +
52F TRP* 3.6 35.9 - - + -
63F LEU 4.2 0.4 + - - -
64F THR* 1.3 72.1 - - - +
66F HIS* 1.3 86.0 + - - +
67F TYR* 4.1 20.4 - - + +
80F CYS* 3.2 35.2 + - + +
83F TYR* 3.2 9.4 + - + +
93F CYS* 3.9 19.3 - - + -
95F LEU* 5.9 0.4 - - + -
106F PHE* 6.2 0.2 - - + -
108F VAL* 4.8 8.7 - - + -
109F GLN 3.3 12.6 - - - +
110F LEU* 4.8 3.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F THR* 3.2 33.8 + - - +
65F LEU* 1.3 79.7 + - - +
67F TYR* 1.3 58.8 + - - +
68F TRP* 4.5 1.9 - - - -
77F VAL* 4.9 10.7 - - + +
78F GLN 3.4 8.5 - - - +
79F LYS* 3.3 46.7 + - + +
80F CYS 4.7 0.9 - - - -
83F TYR* 5.3 1.6 - - - -
108F VAL 3.5 0.3 - - - -
109F GLN* 2.6 64.5 + - + +
111F GLN* 4.6 9.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F LEU* 4.3 16.2 - - + -
66F HIS* 1.3 74.0 - - - +
68F TRP* 1.3 73.7 + - - +
69F TYR* 5.4 8.7 - + - -
78F GLN* 3.1 56.7 + - + +
79F LYS 4.6 9.9 + - - -
80F CYS* 5.2 4.9 - - - -
81F SER 6.1 0.2 - - - -
95F LEU* 3.2 44.9 - - + -
99F GLU* 2.7 42.3 + - + +
106F PHE* 3.9 18.8 - + + -
107F VAL 3.0 17.3 - - - +
108F VAL* 4.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F HIS 4.5 1.1 - - - -
67F TYR* 1.3 91.6 - - - +
69F TYR* 1.3 65.1 + - - +
70F LYS* 4.3 21.3 - - + +
75F ASP* 4.7 12.6 - - - +
76F LYS 4.4 6.7 - - - +
77F VAL* 3.3 42.8 - - + -
78F GLN* 5.7 0.7 - - - -
106F PHE* 5.3 0.2 - - - -
107F VAL* 2.8 67.6 + - + +
109F GLN* 2.7 57.4 - - + -
121F THR* 4.5 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F TYR* 5.4 8.1 - + - -
68F TRP* 1.3 77.5 - - - +
70F LYS* 1.3 66.1 + - - +
72F SER* 3.8 20.4 + - - +
73F ASP 4.8 3.4 - - - +
74F ASN* 4.2 26.7 + - + +
75F ASP* 3.7 11.5 + - - +
76F LYS 5.6 0.2 + - - -
99F GLU 2.5 25.5 + - - -
100F ILE* 3.4 3.1 - - - +
101F HIS* 2.8 58.3 + + + -
104F GLN* 4.3 11.0 - - + +
105F THR 3.1 18.2 - - - +
106F PHE* 3.3 38.7 - + + -
126F LEU* 5.0 2.2 - - + +
----------------------------------------------------------
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