Contacts of the strand formed by residues 108 - 113 (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 LYS 108 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU 5.3 0.4 + - - -
84C SER* 4.1 23.0 + - - +
85C LYS 3.6 25.7 + - - +
86C LEU* 3.9 9.1 - - + +
87C LEU* 2.8 34.8 + - - +
106C GLU 4.1 0.9 + - - +
107C ASN* 1.3 70.8 - - - +
109C ILE* 1.3 59.4 + - - +
130C ASN* 4.3 1.1 - - - -
132C ASN* 3.7 25.6 - - + +
133C VAL* 4.0 13.2 - - + -
134C ASN* 4.5 9.3 - - - +
137C ASP* 3.4 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU* 3.4 21.5 - - + +
89C SER* 5.4 0.9 - - - -
96C ILE* 5.2 7.1 - - + +
99C LEU* 3.8 33.4 - - + -
100C GLU* 3.7 19.7 - - + +
103C VAL* 3.7 14.4 - - + -
104C GLY 3.5 24.7 - - - +
107C ASN* 3.4 12.7 + - + +
108C LYS* 1.3 78.1 - - - +
110C VAL* 1.3 65.3 + - - +
111C TRP 4.4 0.4 - - - +
129C SER* 3.6 0.2 - - - -
130C ASN* 3.0 52.2 + - + +
133C VAL* 3.4 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 3.5 22.7 - - + -
87C LEU 2.9 16.4 + - - +
88C ILE* 3.3 14.8 - - + -
89C SER* 2.9 25.8 + - - -
109C ILE* 1.3 78.4 - - - +
111C TRP* 1.3 60.3 + - - +
112C VAL* 3.7 10.8 + - + -
127C TYR* 3.3 35.7 - - + -
128C CYS 3.3 10.8 - - - +
129C SER* 3.9 10.3 - - - -
133C VAL* 4.5 4.7 - - + -
141C VAL* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C SER* 3.1 23.3 - - - -
91C CYS 2.8 21.5 + - - -
93C GLY 3.7 34.5 - - - -
94C LEU 3.4 19.4 + - - -
95C ASN* 3.6 25.8 - - + -
96C ILE* 4.4 6.1 - - + +
99C LEU* 4.3 10.8 - - + -
110C VAL* 1.3 71.0 - - - +
112C VAL* 1.3 62.9 + - - +
113C MSE 4.0 12.5 - - + +
127C TYR* 3.1 4.3 - - - -
128C CYS* 2.7 47.7 + - - +
156C GLU* 4.4 5.4 - - + -
159C MSE 3.3 52.8 - - + +
160C ASP* 4.3 13.9 - - - -
163C THR* 4.8 2.9 - - - -
257C SER* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ILE* 3.9 24.9 - - + -
89C SER 2.9 17.4 + - - +
90C ILE* 3.1 18.9 - - + -
110C VAL* 4.0 18.4 - - + +
111C TRP* 1.3 78.6 - - - +
113C MSE 1.3 63.3 + - - +
114C PRO* 3.4 2.9 - - + +
125C PHE* 4.4 12.1 - - + -
126C ILE 3.5 7.6 - - - +
127C TYR* 3.7 12.6 - - + -
141C VAL* 4.5 3.1 - - + -
145C PHE* 4.0 34.8 - - + -
151C ILE* 4.2 12.8 - - + -
159C MSE 4.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ILE 3.5 20.4 - - - +
91C CYS 3.8 5.4 - - - +
92C GLY* 3.7 24.2 - - - -
111C TRP* 4.0 10.5 - - + +
112C VAL* 1.3 72.3 - - - +
114C PRO* 1.3 62.1 - - - +
124C SER 3.4 3.5 - - - +
125C PHE* 3.4 6.5 - - - -
126C ILE* 2.8 54.8 + - + +
159C MSE 3.8 9.6 - - + +
163C THR* 3.3 41.1 - - + +
166C SER* 4.6 0.3 + - - -
167C GLY* 4.3 5.4 - - - -
264C NAP 3.5 32.1 - - + -
----------------------------------------------------------
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