Contacts of the strand formed by residues 189 - 195 (chain A) in PDB entry 2OZL
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 CYS 189 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A GLY 4.3 1.3 - - - -
146A ALA* 4.1 16.2 - - - -
149A ALA* 3.7 14.6 - - + -
161A CYS 3.6 4.0 - - - -
163A THR* 3.4 27.8 - - - -
182A ALA* 4.9 1.1 - - + -
187A LEU* 2.7 18.4 + - + +
188A PRO* 1.3 71.8 - - - +
190A ILE* 1.3 63.1 + - - +
191A PHE* 3.7 36.7 + - + -
244A CYS* 4.0 1.8 - - - -
250A PRO* 3.2 24.7 - - + +
251A ILE 3.3 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A VAL* 4.4 5.2 - - + -
161A CYS 2.9 14.9 + - - +
162A LEU* 3.6 25.9 - - + -
163A THR 2.8 27.3 + - - -
188A PRO 5.0 1.1 - - - +
189A CYS* 1.3 72.8 - - - +
191A PHE* 1.3 61.6 + - - +
192A ILE* 3.4 24.0 + - + +
237A THR* 4.9 3.8 - - + +
240A ALA* 3.8 15.9 - - + -
241A ALA* 3.7 36.3 - - + +
244A CYS* 3.6 21.3 - - + -
251A ILE* 3.5 13.2 - - + +
253A MET* 4.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A VAL* 3.6 34.3 - - + -
146A ALA* 4.9 2.7 - - + -
163A THR* 3.5 7.2 - - - -
165A TYR* 4.1 12.1 - + + -
178A ALA* 4.0 15.3 - - + -
179A TYR* 4.0 22.9 - + + -
182A ALA* 3.7 31.2 - - + -
189A CYS* 3.8 26.2 - - - -
190A ILE* 1.3 71.8 - - - +
192A ILE* 1.3 61.3 + - - +
193A CYS 4.2 0.2 - - - -
220A ILE* 4.2 3.1 - - + -
250A PRO* 3.8 13.7 - - + -
251A ILE 3.0 8.4 + - - +
252A LEU* 3.3 31.1 - - + +
253A MET* 2.8 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.0 10.1 - - + -
162A LEU* 4.0 22.0 - - + -
163A THR 2.7 10.5 + - - +
164A LEU* 3.3 35.4 - - + +
165A TYR* 2.9 32.5 + - - +
190A ILE* 3.6 16.2 - - + +
191A PHE* 1.3 78.4 - - - +
193A CYS* 1.3 62.5 + - - +
194A GLU* 3.7 2.1 + - + +
253A MET* 3.2 33.2 - - + +
255A LEU* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 3.1 28.4 + - + +
166A GLY 3.9 4.9 - - - -
167A ASP* 3.9 30.3 - - - -
191A PHE 4.2 0.4 - - - -
192A ILE* 1.3 72.6 - - - +
194A GLU* 1.3 65.0 + - - +
195A ASN* 3.2 7.7 + - - -
213A TYR* 3.8 32.3 - - + +
253A MET 2.9 11.4 + - - +
254A GLU* 3.5 5.8 - - + +
255A LEU 2.9 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A GLN* 4.0 17.9 - - - +
71A CYS* 3.8 23.5 - - - +
87A THR* 4.3 11.4 + - - -
90A ARG* 5.2 7.6 - - - +
94A PHE* 3.9 16.9 - - - -
164A LEU* 4.0 24.9 - - + +
165A TYR 2.8 15.8 + - - +
166A GLY* 3.4 7.5 + - - -
167A ASP* 3.3 20.6 + - - +
192A ILE* 4.7 5.4 - - + -
193A CYS* 1.3 69.7 - - - +
195A ASN* 1.3 59.8 + - - +
196A ASN* 3.6 6.6 + - - +
255A LEU* 3.8 13.5 - - + -
257A THR* 4.8 7.6 - - + -
2330A TPP 5.1 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASP* 3.6 11.1 - - + +
193A CYS* 3.2 5.6 + - - +
194A GLU* 1.3 71.4 - - - +
196A ASN* 1.3 56.0 + - - +
197A ARG* 2.9 27.5 + - - +
204A VAL* 3.7 8.7 - - - +
211A THR 4.9 1.4 + - - -
213A TYR* 3.7 19.8 - - - -
254A GLU* 3.0 34.0 + - + +
255A LEU 2.8 15.6 + - - +
256A GLN* 3.6 12.5 - - - +
257A THR* 2.9 26.6 + - - +
----------------------------------------------------------
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