Contacts of the strand formed by residues 198 - 205 (chain A) in PDB entry 3RCL
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.4 27.8 - - + -
53A ASP 3.3 4.7 - - - +
54A ALA* 4.8 1.3 - - + -
59A LEU* 5.1 1.3 - - + -
94A THR* 3.1 10.3 - - - -
95A PHE* 2.9 46.3 + - + +
98A VAL* 4.2 3.6 - - + -
184A ILE* 3.7 38.1 - - + +
187A PHE* 4.1 22.0 - - + -
194A THR* 3.8 25.5 + - + -
196A LYS* 3.4 13.8 + - + +
197A LYS* 1.3 73.4 - - - +
199A VAL* 1.3 59.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.3 4.4 - - - -
53A ASP* 2.8 42.4 + - + -
92A GLY* 3.8 15.5 - - - +
93A SER 3.5 10.5 - - - +
94A THR* 4.2 6.3 - - + -
197A LYS* 3.8 37.9 - - + +
198A ILE* 1.3 77.4 - - - +
200A ILE* 1.3 73.3 + - - +
201A THR* 3.2 17.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.2 15.3 - - + -
51A ASP 3.4 6.7 - - - +
52A VAL* 4.6 5.4 - - + +
90A TYR* 4.0 15.7 - - + +
92A GLY* 2.7 34.1 + - - -
93A SER* 2.8 30.1 + - - +
95A PHE* 3.9 30.5 - - + -
106A ALA* 4.4 8.3 - - + -
154A PHE* 4.3 20.4 - - + -
199A VAL* 1.3 69.1 - - - +
201A THR* 1.3 55.9 + - - +
202A ASP 3.4 21.8 - - - +
203A CYS* 4.0 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASP* 2.9 20.0 + - - +
53A ASP* 3.3 46.5 + - + +
91A LYS* 2.9 26.5 + - - +
92A GLY* 4.5 2.6 + - - +
199A VAL* 3.8 15.0 - - + +
200A ILE* 1.3 73.3 - - - +
202A ASP* 1.3 79.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 4.2 7.6 - - + +
51A ASP* 2.8 43.8 + - - +
91A LYS* 2.8 25.7 + - - +
200A ILE* 3.4 5.2 - - - +
201A THR* 1.3 103.6 + - - +
203A CYS* 1.3 66.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TYR* 3.1 33.4 + - - +
50A LEU* 3.8 14.6 - - + -
81A LEU 4.5 0.4 - - - -
82A CYS* 3.1 33.5 - - - +
83A THR* 4.9 1.2 - - - +
90A TYR* 3.9 13.7 - - - -
91A LYS* 3.4 41.5 - - - +
200A ILE* 4.0 2.5 - - + -
202A ASP* 1.3 77.6 - - - +
204A GLY* 1.3 58.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A VAL* 3.2 7.6 - - - +
49A TYR* 2.9 41.3 + - - -
82A CYS* 3.4 21.0 + - - +
83A THR* 4.2 4.0 - - - -
203A CYS* 1.3 79.4 - - - +
205A GLN* 1.3 60.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PRO* 3.9 7.9 - - - +
47A LEU 3.6 5.8 - - - +
48A VAL* 4.1 6.7 - - + -
49A TYR* 3.9 3.8 - - - -
79A ARG* 3.0 47.6 + - - +
83A THR* 3.8 16.1 - - + +
204A GLY* 1.3 73.2 - - - -
206A LEU* 1.3 64.8 + - - +
207A SER* 2.9 38.7 + - - +
----------------------------------------------------------
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