Contacts of the helix formed by residues 83 - 98 (chain F) in PDB entry 1YFJ
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 83 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F LYS 3.7 13.7 - - - -
79F LEU* 3.9 3.6 - - - -
80F SER* 2.8 41.6 + - - -
82F THR* 1.3 75.0 - - - +
84F LYS* 1.3 53.6 + - - +
85F GLU* 2.4 23.9 + - - +
86F GLU* 2.9 14.0 + - - +
87F PHE* 3.0 10.4 + - - +
127F PHE* 4.0 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F THR 3.2 8.7 + - - +
83F SER* 1.3 74.4 - - - +
85F GLU* 1.3 63.5 + - - +
87F PHE* 3.9 2.0 - - - +
88F LEU* 3.3 20.4 + - - +
127F PHE* 3.5 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F THR 4.8 0.2 + - - -
83F SER* 2.4 10.5 + - - +
84F LYS* 1.3 78.0 - - - +
86F GLU* 1.3 69.7 + - - +
87F PHE 3.0 0.3 + - - -
88F LEU* 3.2 13.8 + - - +
89F LYS* 3.7 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F TYR* 2.8 33.6 - - + +
78F LYS* 3.3 19.5 - - + +
79F LEU* 4.4 3.1 - - - +
83F SER* 2.9 8.7 + - - +
85F GLU* 1.3 77.8 - - - +
87F PHE* 1.3 62.8 + - - +
89F LYS* 3.1 12.7 + - - +
90F LEU* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F LEU* 5.7 5.0 - - + +
83F SER* 3.0 15.6 + - - +
84F LYS 3.9 2.7 - - - +
85F GLU 3.0 1.0 + - - -
86F GLU* 1.3 71.9 - - - +
88F LEU* 1.3 70.6 - - + +
89F LYS 2.9 2.0 - - - -
90F LEU* 2.7 26.5 + - + +
91F ARG* 3.1 29.6 + - + +
106F LEU* 3.8 31.6 - - + -
109F HIS* 3.9 23.1 - + + -
110F GLY* 4.4 5.4 - - - -
125F THR* 3.6 18.8 - - - -
126F PRO 4.3 1.8 - - - -
127F PHE* 3.3 57.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F LYS 3.3 9.6 + - - +
85F GLU* 3.2 11.8 + - - +
87F PHE* 1.3 80.0 - - + +
89F LYS* 1.3 60.4 + - - +
91F ARG* 3.6 32.4 + - - +
92F GLU* 3.4 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F GLU 3.7 3.4 + - - +
86F GLU* 3.1 14.1 + - - +
87F PHE 2.8 1.2 + - - -
88F LEU* 1.3 76.2 - - - +
90F LEU* 1.3 52.3 + - - +
91F ARG 3.1 1.3 - - - -
92F GLU* 2.7 30.1 + - - +
93F ASP* 2.7 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F TYR* 4.9 14.4 - - + -
86F GLU 3.1 8.2 + - - +
87F PHE* 2.7 23.9 + - + +
89F LYS* 1.3 74.7 - - - +
91F ARG* 1.3 60.4 + - - +
93F ASP* 3.1 15.0 + - - +
94F TYR* 3.0 27.7 + - - +
102F LEU* 5.4 1.1 - - + +
106F LEU* 5.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9079 G 2.9 40.2 + - - -
87F PHE* 3.1 26.2 + - + +
88F LEU* 3.7 32.2 + - - +
90F LEU* 1.3 77.0 - - - +
92F GLU* 1.3 51.3 + - - +
94F TYR* 5.1 2.7 - - - -
95F ASN* 2.7 49.2 + - - +
106F LEU* 5.7 5.8 - - + +
123F PHE* 2.6 43.2 + - + +
124F THR* 4.2 1.6 - - - +
125F THR 3.5 23.2 + - - +
126F PRO* 4.4 3.8 - - - +
127F PHE 5.3 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88F LEU 3.4 8.3 + - - +
89F LYS* 2.7 23.1 + - - +
91F ARG* 1.3 73.7 - - - +
93F ASP* 1.3 65.8 + - - +
95F ASN* 3.7 5.0 - - - +
96F LYS* 3.3 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F TYR* 5.8 2.6 - - - +
89F LYS* 2.7 26.5 + - - +
90F LEU* 3.1 18.6 + - - +
92F GLU* 1.3 81.7 - - - +
94F TYR* 1.3 52.3 + - - +
96F LYS* 2.9 2.1 + - - +
97F THR* 2.6 37.9 + - - -
102F LEU* 6.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F LEU 3.0 11.9 + - - +
91F ARG* 4.6 2.5 - - - +
93F ASP* 1.3 74.2 - - - +
95F ASN* 1.3 63.8 + - - +
97F THR* 3.6 10.7 - - - -
98F ARG* 2.3 35.9 + - - +
99F ASP 4.5 3.6 - - - +
102F LEU* 3.3 32.5 - - + +
103F LEU* 4.3 12.3 - - + +
106F LEU* 6.0 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F ARG* 2.7 27.6 + - - +
92F GLU* 3.7 7.0 - - - +
94F TYR* 1.3 76.2 - - - +
96F LYS* 1.3 56.9 + - + +
98F ARG* 2.6 42.4 + - - +
122F ASN* 2.4 45.7 - - - +
123F PHE* 2.7 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92F GLU 3.3 11.8 + - - +
93F ASP 2.9 3.5 + - - +
95F ASN* 1.3 77.2 - - + +
97F THR* 1.3 64.5 + - - +
98F ARG* 4.3 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 97 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ASP* 2.6 25.0 + - - -
94F TYR* 3.6 8.3 - - - -
96F LYS* 1.3 75.8 - - - +
98F ARG* 1.3 71.9 + - - +
99F ASP* 3.4 13.6 - - - -
102F LEU* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 98 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F TYR* 2.3 26.3 + - - -
95F ASN* 2.6 32.8 + - - +
96F LYS* 4.3 4.7 - - - +
97F THR* 1.3 74.3 - - - +
99F ASP* 1.3 52.9 + - - +
100F PRO* 2.8 22.1 - - - +
103F LEU* 6.2 0.9 - - - -
120F LYS 3.5 15.4 + - - -
121F GLY* 2.8 32.0 + - - -
----------------------------------------------------------
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