Contacts of the strand formed by residues 96 - 100 (chain C) in PDB entry 5FDK
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 96 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 3.7 9.6 + - - +
92C ILE* 4.0 3.2 - - - +
93C TYR 3.1 27.3 + - - +
94C LYS* 3.2 5.1 - - + +
95C GLY* 1.3 81.8 - - - +
97C TYR* 1.3 64.4 + - - +
98C ILE* 3.2 5.7 + - - +
131C ASP* 2.6 58.5 + - - +
132C GLY 4.3 2.0 + - - -
133C ILE* 3.4 39.0 - - + +
197C TYR* 4.5 22.8 - - - +
198C PHE* 5.6 15.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL 5.7 0.4 - - - -
91A GLY* 3.1 40.8 - - - +
92A ILE* 4.1 16.2 - - + -
95A GLY 3.5 10.6 + - - +
96A ARG 4.1 15.9 - - - +
97A TYR* 3.7 21.6 - + - +
90C ASN* 3.5 26.9 + - + +
91C GLY 3.5 5.4 - - - -
96C ARG* 1.3 72.0 - - - +
98C ILE* 1.3 67.2 + - - +
99C ASP* 3.0 39.9 + - + -
123C HIS* 4.6 7.2 + + - -
127C VAL* 4.3 17.7 - - + -
131C ASP 5.6 0.2 + - - -
132C GLY* 3.9 3.7 - - - -
133C ILE 3.1 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C ILE* 3.5 29.4 - - + -
90C ASN* 3.4 2.8 - - - -
91C GLY 2.9 30.8 + - - +
93C TYR* 4.3 25.4 - - + +
96C ARG 3.2 14.1 + - - +
97C TYR* 1.3 81.1 - - - +
99C ASP* 1.3 67.6 + - - +
100C PHE* 4.0 22.0 - - + -
133C ILE* 3.4 46.0 - - + -
189C TYR* 5.7 1.8 - - + -
190C ILE* 6.1 2.2 - - + -
193C ILE* 5.3 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C THR* 3.8 12.6 - - - +
89C TYR 3.4 16.9 - - - +
90C ASN* 4.3 0.9 - - - +
97C TYR* 3.0 31.2 + - + -
98C ILE* 1.3 76.1 - - - +
100C PHE* 1.3 91.8 + - - +
123C HIS* 3.2 25.1 - - - -
127C VAL* 4.0 10.6 - - + +
133C ILE* 2.8 11.4 + - - +
134C CYS* 3.2 13.4 - - - -
135C PHE 2.9 24.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 4.3 9.0 - - + -
54C ILE* 4.3 9.2 - - + -
87C THR* 4.0 2.9 - - - -
88C ASN 3.9 1.0 + - - -
89C TYR* 3.0 64.3 + + + -
90C ASN 5.7 0.2 - - - -
98C ILE* 4.0 19.7 - - + -
99C ASP* 1.3 92.9 + - - +
101C GLU* 1.3 74.8 + - - +
124C MET* 6.2 0.9 - - - -
134C CYS* 5.2 1.6 - - - -
135C PHE* 3.4 38.6 - - + +
136C VAL* 4.1 0.9 - - - +
137C ILE* 4.1 15.7 - - + +
189C TYR* 3.6 44.6 - + - -
----------------------------------------------------------
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