Contacts of the strand formed by residues 230 - 237 (chain A) in PDB entry 6D6Q
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 GLU 230 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A HIS* 5.1 3.8 - - - +
225A MET* 3.9 4.8 - - - +
226A ASN* 3.7 27.4 + - - +
228A HIS* 3.8 21.5 + - - +
229A ARG* 1.3 82.7 - - - +
231A ILE* 1.3 65.8 + - - +
232A CYS* 3.2 14.6 + - - -
203B ARG* 3.2 38.0 + - + -
204B LEU 3.0 15.9 - - - +
205B HIS* 4.4 6.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ILE* 4.2 11.0 - - + -
224A ALA 3.7 5.6 - - - +
225A MET* 3.2 25.1 - - - -
229A ARG 4.1 0.2 - - - -
230A GLU* 1.3 69.9 - - - +
232A CYS* 1.3 62.1 + - - +
233A THR 4.1 4.3 - - - +
234A ILE* 4.0 16.4 - - + -
251A SER* 4.1 13.7 - - - +
200B MET* 3.4 34.5 - - + -
202B ALA 3.0 6.2 - - - +
203B ARG* 3.1 2.1 - - - -
204B LEU* 2.7 42.9 + - + +
205B HIS 4.3 9.2 - - - +
206B GLU* 4.5 10.1 - - - -
209B LEU* 4.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A CYS 4.3 5.8 - - - +
113A SER* 2.8 39.1 + - - +
191A PRO* 4.2 11.9 - - + -
224A ALA* 3.3 19.6 + - + -
226A ASN* 3.5 18.2 - - - -
230A GLU 3.2 15.1 + - - -
231A ILE* 1.3 74.7 - - - +
233A THR* 1.3 71.4 + - + +
201B ASP 4.2 0.2 - - - -
202B ALA* 3.3 29.5 + - - +
203B ARG* 4.6 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A LEU* 4.1 10.7 - - - +
108A ARG* 3.6 35.7 - - + +
109A CYS* 3.7 30.2 - - - +
112A ASN* 6.3 0.4 - - + -
193A CYS* 5.1 0.7 - - - -
222A VAL* 5.4 0.7 - - - +
224A ALA* 2.9 36.3 + - - +
231A ILE* 3.8 3.3 - - - +
232A CYS* 1.3 89.9 - - - +
234A ILE* 1.3 74.3 + - - +
200B MET* 3.7 14.4 - - - +
201B ASP* 4.5 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 4.1 2.0 + - - -
221A LEU* 5.2 2.7 - - + -
222A VAL* 3.1 8.5 - - - +
223A ILE* 3.5 33.2 - - + -
231A ILE* 4.0 15.7 - - + -
233A THR* 1.3 86.9 - - - +
235A GLN* 1.3 63.3 + - - +
184B LEU* 4.9 1.1 - - + -
198B LEU* 3.2 49.7 - - + +
199B GLU* 3.8 0.5 - - - -
200B MET* 3.2 49.0 + - + +
209B LEU* 5.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 4.9 17.2 + - - +
105A LEU* 3.3 38.7 - - + +
108A ARG* 3.4 16.9 + - - +
220A LEU 3.6 1.0 - - - +
221A LEU* 3.3 9.1 - - - +
222A VAL* 2.9 38.8 + - + +
234A ILE* 1.3 75.3 - - - +
236A SER* 1.3 65.3 + - - +
237A SER* 4.2 10.3 - - - -
97B GLU* 4.1 15.8 + - - +
101B GLN* 4.5 4.2 - - - +
198B LEU 3.4 5.2 - - - -
199B GLU* 3.2 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU 3.4 4.7 - - - -
221A LEU* 4.4 10.3 - - - -
235A GLN* 1.3 77.8 + - - +
237A SER* 1.3 61.0 + - - +
240A ILE* 4.8 9.2 - - - -
242A LEU* 4.6 14.8 - - - -
101B GLN* 6.0 0.2 - - - +
104B GLN* 3.9 4.6 + - - -
196B ALA 4.5 2.6 + - - -
197B LEU* 3.5 24.9 - - - +
198B LEU* 2.9 40.9 + - - -
199B GLU* 4.1 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A LYS* 3.3 31.4 + - - -
219A GLY* 3.4 3.5 - - - -
220A LEU* 2.9 53.1 + - - +
222A VAL* 5.9 0.3 - - - +
235A GLN* 5.1 10.1 - - - -
236A SER* 1.3 75.6 - - - +
238A GLY* 1.3 61.6 + - - +
239A GLY 3.5 2.0 - - - -
240A ILE* 4.0 4.5 - - - +
104B GLN* 3.9 9.2 - - - -
----------------------------------------------------------
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