Contacts of the strand formed by residues 86 - 89 (chain C) in PDB entry 2RCY
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 LEU 86 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C ASP 3.2 7.4 + - - +
61C ILE* 3.4 27.5 - - + +
62C ILE* 2.9 28.3 + - - +
85C LYS* 1.3 70.2 - - - +
87C LEU* 1.3 64.5 + - - +
88C ILE* 3.7 12.1 - - + -
108C LYS* 3.9 14.3 - - + +
110C VAL* 3.5 32.5 - - + -
133C VAL* 5.1 3.6 - - + -
137C ASP* 3.4 52.5 - - + +
140C TYR* 4.7 8.1 - - + -
141C VAL* 4.5 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C MSE 4.5 3.6 - - + -
62C ILE* 3.6 24.7 - - + +
64C CYS* 4.9 1.8 - - + -
75C LEU* 3.9 30.3 - - + -
78C ILE* 4.2 1.1 - - + -
82C LEU* 4.1 31.0 - - + -
85C LYS 3.5 1.9 + - - +
86C LEU* 1.3 71.9 - - - +
88C ILE* 1.3 67.6 + - - +
89C SER* 4.2 4.9 + - - +
99C LEU* 5.7 1.8 - - + -
103C VAL* 3.9 27.8 - - + -
107C ASN* 5.4 1.8 - - + -
108C LYS 2.8 17.6 + - - +
109C ILE* 3.4 18.8 - - + +
110C VAL* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 5.1 0.2 - - + -
61C ILE* 3.7 21.8 - - + -
62C ILE 2.8 7.4 + - - +
63C VAL* 3.3 26.3 - - + -
64C CYS* 2.9 25.3 + - - +
86C LEU* 3.7 12.1 - - + -
87C LEU* 1.3 79.8 - - - +
89C SER* 1.3 59.8 + - - +
90C ILE* 3.6 28.9 - - + -
110C VAL* 3.3 23.8 - - + -
112C VAL* 3.9 11.4 - - + -
141C VAL* 5.2 4.9 - - + -
144C ILE* 6.4 0.4 - - + -
145C PHE* 3.8 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C CYS* 4.1 11.6 - - - +
75C LEU* 5.9 0.2 - - - -
87C LEU* 4.2 4.2 + - - -
88C ILE* 1.3 74.7 - - - +
90C ILE* 1.3 63.5 + - - +
91C CYS* 3.4 22.6 + - - +
94C LEU 5.1 0.2 + - - -
99C LEU* 3.5 42.6 - - - +
109C ILE* 5.4 2.5 - - - -
110C VAL 2.9 8.1 + - - -
111C TRP* 3.1 7.9 - - - -
112C VAL 2.9 27.4 + - - +
----------------------------------------------------------
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