Contacts of the strand formed by residues 184 - 189 (chain A) in PDB entry 6C90
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 ARG 184 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ALA* 4.6 0.8 - - - +
183A GLN* 1.3 76.5 - - - +
185A VAL* 1.3 69.9 + - - +
186A ILE* 4.9 1.6 - - + -
220A PRO 3.8 2.6 + - - -
221A THR* 2.8 31.1 + - - +
222A ALA 2.6 29.4 + - - -
223A SER* 3.2 11.5 - - - +
225A LEU* 4.0 10.8 - - + +
242A VAL* 3.4 49.8 + - - +
245A GLU* 3.0 29.7 + - + +
246A VAL* 3.3 13.0 - - + -
247A ALA* 2.8 28.8 + - - +
248A TRP 3.7 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ILE* 4.1 18.4 - - + +
178A ALA* 3.7 21.8 - - + -
179A LEU* 4.1 8.1 - - + -
184A ARG* 1.3 76.0 - - - +
186A ILE* 1.3 69.6 + - - +
223A SER 3.0 4.4 + - - +
224A CYS* 3.4 25.4 - - + +
225A LEU 3.0 24.6 + - - -
246A VAL* 4.7 0.4 - - - -
248A TRP* 3.3 28.5 - - + +
250A ILE* 4.0 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A ARG* 4.9 2.2 - - + -
185A VAL* 1.3 80.4 - - - +
187A PHE* 1.3 56.6 + - - +
188A THR* 3.5 25.4 - - + -
224A CYS* 5.7 0.2 - - - -
225A LEU* 3.3 10.1 - - + +
227A MET* 3.7 31.4 - - + -
232A LEU* 4.2 5.8 - - + -
242A VAL* 5.6 0.4 - - + +
243A MET* 3.4 42.2 - - + -
246A VAL* 3.8 21.8 - - + -
248A TRP 3.0 9.2 + - - +
249A VAL* 3.4 10.4 - - + -
250A ILE* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A THR* 5.6 3.4 - - + -
171A ALA* 3.9 14.8 - - + -
175A ILE* 4.6 8.1 - - + -
186A ILE* 1.3 72.7 - - - +
188A THR* 1.3 61.7 + - - +
189A SER* 3.6 22.0 - - - -
198A LYS* 3.6 28.9 - - + -
202A MET* 5.2 9.0 - - + -
224A CYS* 4.9 9.4 - - - -
225A LEU 3.0 9.2 + - - +
226A VAL* 3.2 24.2 - - + +
227A MET 3.0 23.6 + - - +
250A ILE* 3.5 40.2 - - + -
252A ASP* 3.5 31.9 - - + -
282A LEU* 4.8 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ILE* 3.5 25.8 - - + -
187A PHE* 1.3 72.5 - - - +
189A SER* 1.3 62.1 + - - +
227A MET* 3.2 13.9 - - + -
229A THR* 3.8 17.0 - - - +
232A LEU* 3.8 24.2 - - + -
249A VAL* 4.2 6.1 - - + -
250A ILE 2.8 15.8 + - - +
251A PHE* 3.3 24.6 - - - -
252A ASP* 3.0 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PHE* 3.6 20.1 - - - -
188A THR* 1.3 74.8 - - - +
190A PRO* 1.3 77.0 - - - +
191A ILE 3.5 7.1 + - - -
194A LEU* 4.2 6.6 - - - +
195A SER* 3.5 24.1 + - - -
198A LYS* 4.1 10.7 - - - +
226A VAL* 5.0 0.7 - - - +
227A MET 3.2 5.9 + - - -
228A THR* 3.6 5.4 - - - -
229A THR* 3.5 24.4 + - - +
252A ASP* 4.4 6.0 + - - +
257A MET* 5.2 0.4 - - - -
----------------------------------------------------------
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