Contacts of the helix formed by residues 66 - 76 (chain A) in PDB entry 1YFL
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 SER 66 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 5.1 0.4 - - - -
65A VAL* 1.3 75.4 - - - +
67A TRP* 1.3 67.0 + - - +
68A ASP* 3.3 9.9 + - - +
69A ASP* 2.7 43.5 + - - +
70A VAL* 2.9 11.8 + - - +
72A LYS* 5.4 0.2 + - - -
140A PHE* 3.8 7.4 - - - -
144A LYS* 5.2 1.3 - - - +
68E ASP* 4.2 10.5 - - - -
71E LEU* 5.6 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 1.3 74.4 - - - +
68A ASP* 1.3 56.9 + - - +
70A VAL* 3.1 27.8 - - + +
71A LEU* 2.8 67.4 + - + +
104A TYR* 4.4 5.4 - + - -
108A PHE* 4.6 1.3 - + - -
132A ILE* 4.4 12.6 - - + -
136A SER* 3.9 16.2 - - - -
137A GLU* 2.8 58.6 + - + -
140A PHE* 3.4 46.5 - + + -
68E ASP* 3.5 26.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 2.9 9.2 + - - +
67A TRP* 1.3 74.9 - - - +
69A ASP* 1.3 68.9 + - - +
70A VAL 2.9 1.2 + - - -
71A LEU* 2.9 14.5 + - - +
72A LYS* 2.7 50.0 + - - +
68E ASP* 5.0 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASN 3.8 3.5 - - - +
65A VAL* 2.9 23.2 - - + +
66A SER* 2.7 46.5 + - - +
68A ASP* 1.3 72.6 - - - +
70A VAL* 1.3 65.8 + - - +
72A LYS* 3.2 35.1 + - - +
73A VAL* 3.3 14.7 + - - +
101A LEU* 4.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 4.5 7.6 - - + -
66A SER 2.9 11.2 + - - +
67A TRP* 3.1 42.8 - - + +
68A ASP 2.9 0.4 + - - -
69A ASP* 1.3 73.7 - - - +
71A LEU* 1.3 68.9 + - - +
72A LYS 3.0 1.0 + - - -
73A VAL* 3.1 17.9 + - - +
74A ILE* 3.3 25.3 + - + +
101A LEU* 4.7 7.9 - - + -
104A TYR* 3.9 30.3 - - + -
105A VAL* 4.7 5.1 - - + +
108A PHE* 4.6 5.2 - - + -
140A PHE* 4.0 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TRP* 2.8 75.3 + - + +
68A ASP* 2.9 14.8 + - - +
70A VAL* 1.3 72.9 - - + +
72A LYS* 1.3 67.5 + - - +
74A ILE* 3.0 10.5 + - - +
75A LYS* 2.9 20.3 + - - +
132A ILE* 4.1 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 2.7 52.7 + - - +
69A ASP* 3.2 26.3 + - - +
71A LEU* 1.3 69.6 - - - +
73A VAL* 1.3 57.8 + - + +
74A ILE 2.7 12.1 + - - -
75A LYS* 2.8 19.1 + - - +
76A GLN* 2.8 14.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ASP 3.4 12.6 - - - +
70A VAL 3.1 6.4 + - - +
72A LYS* 1.3 75.7 - - + +
74A ILE* 1.3 59.5 + - - +
76A GLN* 3.7 16.5 + - - +
77A TYR* 3.1 33.8 + - + +
79A LEU* 4.8 0.7 - - - +
90A LEU* 5.1 0.2 - - + -
101A LEU* 3.3 27.6 - - + -
102A LEU* 3.6 28.9 - - + -
105A VAL* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 3.4 24.2 - - + +
71A LEU* 3.2 11.9 - - - +
72A LYS 2.7 4.8 + - - -
73A VAL* 1.3 71.2 - - - +
75A LYS* 1.3 67.5 + - - +
77A TYR* 2.7 5.2 + - - +
78A LYS 2.7 19.4 + - - -
79A LEU* 3.4 41.7 + - + +
105A VAL* 4.3 18.4 - - + -
108A PHE* 5.5 0.9 - - + -
109A HIS* 5.0 0.9 - - - +
131A THR* 4.7 7.9 - - - +
132A ILE* 3.4 45.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU 2.9 10.6 + - - +
72A LYS* 2.8 15.0 + - - +
74A ILE* 1.3 70.8 - - - +
76A GLN* 1.3 56.4 + - - +
78A LYS* 2.7 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS 2.8 18.4 + - - +
73A VAL* 3.7 17.6 - - - +
75A LYS* 1.3 71.6 - - - +
77A TYR* 1.3 86.4 + - - +
102A LEU* 5.8 0.4 - - - +
----------------------------------------------------------
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