Contacts of the strand formed by residues 190 - 196 (chain A) in PDB entry 3RIE
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 TYR 190 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN* 3.5 40.6 - - - +
120A VAL 3.7 3.4 - - - -
121A LEU* 3.5 49.6 - - + -
144A ASP* 2.5 31.3 + - + +
182A PHE* 3.6 14.0 - - - -
186A VAL* 3.8 28.2 - - + +
188A ASN* 4.2 6.2 - - + +
189A THR* 1.4 76.0 - - - +
191A ASP* 1.3 60.7 + - - +
192A VAL 3.7 13.2 - - - +
193A ILE* 4.0 9.6 - - + -
219A ALA* 2.8 21.8 + - + +
220A LEU* 3.3 7.1 - - - +
221A LYS* 2.7 27.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 4.0 8.8 + - - +
116A GLU 4.6 3.1 - - - -
117A PRO* 3.9 20.2 - - + -
118A LYS* 2.7 31.0 + - - +
119A ASN* 3.0 20.4 + - - +
190A TYR* 1.3 73.4 - - - +
192A VAL* 1.3 65.5 + - - +
220A LEU* 4.4 0.2 - - - -
221A LYS* 3.2 32.0 - - - +
223A ASN* 5.1 3.6 + - - +
224A GLY* 3.3 6.4 - - - -
225A TYR* 3.1 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 4.0 26.7 - - + +
111A MET* 3.9 16.8 - - - -
114A SER* 3.8 25.4 - - - +
117A PRO* 4.5 1.1 - - + -
119A ASN 3.7 1.6 + - - -
120A VAL* 3.4 17.3 - - + +
121A LEU 3.1 23.0 + - - -
190A TYR* 3.3 2.0 - - - +
191A ASP* 1.3 88.6 - - + +
193A ILE* 1.3 68.1 + - - +
194A ILE* 3.7 27.1 - - + -
220A LEU* 4.3 0.2 - - - -
225A TYR* 3.2 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.4 28.9 - - + +
123A VAL* 4.1 9.4 - - + -
183A LEU* 4.7 0.2 - - + -
190A TYR* 4.0 12.3 - - + -
192A VAL* 1.3 77.6 - - - +
194A ILE* 1.3 64.1 + - - +
195A VAL* 4.0 5.8 - - + -
216A ILE* 3.7 41.7 - - + +
219A ALA* 3.9 21.8 - - + +
220A LEU* 3.6 30.7 - - + -
225A TYR 3.0 6.8 + - - +
226A CYS* 3.1 9.8 - - + -
227A VAL 3.1 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET* 3.9 36.1 - - + +
107A THR* 4.0 10.3 - - + +
110A PRO* 4.3 1.6 - - + -
111A MET* 5.1 0.2 - - + -
120A VAL* 4.4 4.3 - - + -
121A LEU 2.9 9.5 + - - +
122A VAL* 3.4 4.1 - - + +
123A VAL 2.9 25.3 + - - +
130A ILE* 3.6 44.9 - - + -
134A LEU* 4.3 14.1 - - + -
192A VAL* 3.7 21.3 - - + -
193A ILE* 1.3 77.5 - - - +
195A VAL* 1.4 60.6 + - - +
196A ASP 3.4 2.9 + - - +
227A VAL* 3.5 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A MET* 3.4 4.5 - - - +
123A VAL* 4.0 17.0 - - + -
193A ILE* 4.2 4.3 - - + -
194A ILE* 1.4 69.1 - - - +
196A ASP* 1.3 57.8 + - - +
197A SER* 3.6 20.3 + - - +
207A LEU* 4.6 4.7 - - + +
212A PHE* 4.0 26.2 - - + -
213A TYR* 5.4 0.4 - - - +
216A ILE* 4.0 19.3 - - + -
226A CYS* 3.9 24.9 - - - -
227A VAL 2.9 8.9 + - - -
228A ALA* 3.7 16.6 - - + -
229A GLN* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TYR* 2.8 35.2 + - - +
103A HIS* 4.4 0.2 - - - -
106A MET* 4.3 4.9 - - + -
122A VAL* 4.5 3.1 - - + -
123A VAL 2.8 16.9 + - - +
125A GLY* 2.9 37.1 + - - +
127A ASP* 4.8 0.2 - - - +
130A ILE* 3.5 25.7 - - + +
194A ILE* 3.4 1.7 + - + +
195A VAL* 1.3 70.4 - - - +
197A SER* 1.3 57.6 + - - +
401A MTA 3.3 5.4 - - - +
501A JFQ 2.9 32.8 + - - -
----------------------------------------------------------
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