Contacts of the strand formed by residues 198 - 205 (chain X) in PDB entry 3RCI
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 ILE 198 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X VAL* 3.4 28.3 - - + -
53X ASP 3.3 4.5 - - - +
54X ALA* 4.8 3.1 - - + -
59X LEU* 4.9 1.1 - - + -
94X THR* 3.1 9.0 - - - -
95X PHE* 2.9 50.9 + - + +
98X VAL* 4.1 2.7 - - + -
184X ILE* 3.7 38.8 - - + +
187X PHE* 4.1 19.3 - - + -
194X THR* 3.6 30.5 + - + -
196X LYS 3.4 12.4 + - - +
197X LYS* 1.3 72.6 - - - +
199X VAL* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52X VAL* 3.2 4.7 - - - -
53X ASP* 2.8 40.9 + - + +
92X GLY* 4.0 14.1 - - - +
93X SER 3.5 9.9 - - - +
94X THR* 4.2 6.1 - - + -
197X LYS* 3.9 40.6 - - + +
198X ILE* 1.3 76.6 - - - +
200X ILE* 1.3 74.4 + - - +
201X THR* 3.2 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 200 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50X LEU* 4.2 15.7 - - + -
51X ASP 3.3 6.3 - - - +
52X VAL* 4.6 5.4 - - + -
90X TYR* 4.0 20.9 - - + +
91X LYS 3.8 0.2 - - - -
92X GLY* 2.8 30.3 + - - -
93X SER* 2.8 24.5 + - - +
94X THR 5.1 0.2 - - - +
95X PHE* 3.8 31.6 - - + -
106X ALA* 4.4 7.9 - - + -
154X PHE* 4.3 19.7 - - + -
199X VAL* 1.3 69.4 - - - +
201X THR* 1.3 59.2 + - - +
202X ASP 3.4 21.8 - - - +
203X CYS* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X ASP* 2.8 23.1 + - - +
53X ASP* 3.2 46.9 + - + +
91X LYS* 3.4 23.0 - - - +
92X GLY* 4.7 2.1 + - - +
199X VAL* 3.2 15.5 + - + +
200X ILE* 1.3 73.7 - - - +
202X ASP* 1.3 62.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X TYR* 3.0 24.2 + - - -
51X ASP* 2.8 42.1 + - + +
61X ARG* 5.1 0.9 + - - -
91X LYS* 2.9 31.8 + - - +
200X ILE* 3.3 5.7 - - - +
201X THR* 1.3 83.0 + - - +
203X CYS* 1.3 82.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 203 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49X TYR* 3.1 30.1 + - - +
50X LEU* 3.8 15.0 - - + -
81X LEU 4.5 0.7 - - - -
82X CYS* 3.2 30.7 - - - +
83X THR* 4.9 1.2 - - - +
90X TYR* 3.9 13.5 - - - -
91X LYS* 3.4 37.6 - - - +
200X ILE* 4.0 1.8 - - + -
202X ASP* 1.3 89.5 + - - +
204X GLY* 1.3 58.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X VAL* 3.2 8.3 - - - +
49X TYR* 2.9 42.5 + - - -
82X CYS* 3.4 19.6 + - - +
83X THR* 4.4 3.6 - - - -
203X CYS* 1.3 80.0 - - - +
205X GLN* 1.3 59.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X PRO* 3.8 8.7 - - - +
47X LEU 3.5 5.6 - - - +
48X VAL* 4.1 6.3 - - + -
49X TYR* 3.9 3.4 - - - -
79X ARG* 3.0 46.9 + - - +
83X THR* 3.8 16.3 - - + +
204X GLY* 1.3 74.1 - - - -
206X LEU* 1.3 66.2 + - - +
207X SER* 2.9 38.0 + - - +
----------------------------------------------------------
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