Contacts of the strand formed by residues 194 - 200 (chain A) in PDB entry 3ONW
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 LEU 194 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 3.5 24.9 - - - +
34A VAL* 4.2 17.7 - - + -
189A PHE 3.6 0.2 - - - +
190A THR* 3.2 26.0 - - - +
191A PHE 2.8 16.7 + - - +
192A LYS 3.7 10.5 - - - +
193A ASP* 1.3 81.5 - - - +
195A HIS* 1.3 61.9 + - - +
196A PHE* 3.5 30.9 + - + -
340A THR* 4.3 7.4 - - + -
343A ILE* 4.8 7.4 - - + -
344A ILE* 3.9 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 2.8 48.5 + - + +
33A GLU* 3.5 32.4 + - - +
34A VAL* 2.8 29.5 + - - +
189A PHE 4.0 3.1 + - - -
190A THR* 3.8 22.6 + - + +
193A ASP 5.6 0.4 - - - -
194A LEU* 1.3 73.2 - - - +
196A PHE* 1.3 61.0 + - - +
197A LYS* 5.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 3.4 25.6 - - + -
36A LEU* 3.5 30.7 - - + -
188A HIS* 3.3 10.9 - - - +
189A PHE* 3.0 65.1 + + + +
191A PHE* 3.9 28.9 - + + -
194A LEU* 3.5 32.3 + - + -
195A HIS* 1.3 72.2 - - - +
197A LYS* 1.3 62.2 + - - +
198A MET 4.0 0.9 - - - +
336A PHE* 3.9 7.6 - + - -
340A THR* 3.7 22.7 - - + -
343A ILE* 4.2 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 3.3 32.7 + - - +
34A VAL 2.8 14.6 + - - +
35A LYS* 3.7 6.4 - - + -
36A LEU* 2.7 35.0 + - - +
186A GLU* 3.6 23.3 - - - +
187A THR 4.0 3.4 - - - -
188A HIS* 4.7 7.9 - - + -
195A HIS* 4.9 3.4 - - - +
196A PHE* 1.3 76.5 - - - +
198A MET* 1.3 56.0 + - - +
199A PHE* 3.7 20.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.3 25.4 - - + +
38A LEU* 3.7 33.9 - - + -
49A ILE* 4.2 7.9 - - + -
50A VAL* 4.5 12.7 - - + +
53A MET* 3.7 27.6 - - + -
185A VAL 3.6 1.4 - - - +
186A GLU* 3.3 22.3 - - - +
187A THR* 3.1 24.2 + - - +
189A PHE* 4.7 8.3 - - + -
196A PHE 4.0 0.8 - - - -
197A LYS* 1.3 71.6 - - - +
199A PHE* 1.3 62.0 + - - +
200A ASP 4.0 0.5 + - - -
222A ILE* 4.5 11.0 - - + -
336A PHE* 3.7 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LYS* 3.9 33.0 - - + -
36A LEU 2.7 14.9 + - - +
37A LEU* 3.6 16.7 - - + +
38A LEU* 2.8 32.7 + - - +
184A ILE* 3.8 24.9 - - + -
185A VAL 3.4 3.4 - - - -
186A GLU* 3.3 37.5 - - + -
197A LYS* 3.7 31.6 - - + -
198A MET* 1.3 73.5 - - - +
200A ASP* 1.3 57.2 + - - +
201A VAL* 4.0 1.8 - - + -
214A CYS* 5.6 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.1 9.1 - - + +
46A LYS* 3.3 31.3 - - - +
47A SER* 3.7 27.5 + - - -
50A VAL* 4.0 21.2 - - + +
183A GLY 4.5 0.3 - - - +
184A ILE* 3.8 1.5 - - - -
185A VAL* 3.0 44.5 + - + +
198A MET 4.0 1.0 + - - -
199A PHE* 1.3 71.6 - - - +
201A VAL* 1.3 62.7 + - - +
202A GLY* 3.1 18.3 + - - -
401A GDP 4.6 1.6 + - - -
----------------------------------------------------------
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