Contacts of the strand formed by residues 230 - 238 (chain A) in PDB entry 6BAA
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 VAL 230 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS* 3.7 31.2 - - - -
223A THR 3.7 4.9 - - - +
224A THR* 4.3 15.3 - - + -
228A GLY 3.6 11.2 + - - +
229A GLU* 1.3 88.2 - - - +
231A VAL* 1.3 69.5 + - - +
232A PRO* 4.0 2.1 - - + +
317B PRO* 3.8 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS* 3.2 9.9 - - - +
223A THR 2.9 38.0 + - - +
229A GLU* 5.6 7.0 - - + -
230A VAL* 1.3 79.6 - - - +
232A PRO* 1.3 65.9 - - + +
233A LEU 3.5 4.7 - - - +
234A HIS* 3.1 55.4 - - + +
192B ARG* 4.7 14.4 - - - +
256B ILE* 5.9 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A LYS* 3.5 31.2 + - + +
230A VAL* 4.0 7.6 - - + +
231A VAL* 1.3 88.9 - - + +
233A LEU* 1.3 72.5 + - + +
234A HIS 3.9 0.4 - - - -
317B PRO* 4.4 16.8 - - + -
318B ILE 5.2 0.9 - - - +
319B VAL* 3.7 47.3 - - + +
326B TYR* 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE* 3.8 29.8 - - + -
44A VAL* 5.8 0.4 - - + -
220A VAL* 3.6 29.6 - - + -
221A ARG 4.5 0.7 - - - -
231A VAL* 3.5 4.2 - - - +
232A PRO* 1.3 91.8 - - + +
234A HIS* 1.3 63.1 + - - +
235A GLN* 3.5 15.3 + - + +
253B ALA* 4.4 8.5 - - + -
255B LEU* 5.1 5.2 - - - +
319B VAL* 3.7 37.7 - - + -
326B TYR* 3.6 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A VAL 2.9 14.0 - - - +
220A VAL* 3.4 2.1 - - - -
221A ARG* 3.0 32.4 + - + +
223A THR* 4.2 16.8 + - + +
231A VAL* 3.1 32.5 - - + +
233A LEU* 1.3 73.8 - - - +
235A GLN* 1.3 78.8 + - - +
236A VAL* 3.6 18.8 - - + +
192B ARG* 3.8 25.2 + - - -
193B HIS* 6.0 2.2 + - - -
258B TYR* 5.1 7.9 + + - -
----------------------------------------------------------
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
----------------------------------------------------------
35A PHE* 3.9 28.7 - - - -
218A GLN* 2.8 37.6 + - + +
219A VAL 3.4 4.0 - - - -
220A VAL* 4.8 10.5 - - + +
233A LEU* 3.5 13.6 + - - +
234A HIS* 1.3 91.1 + - - +
236A VAL* 1.3 59.9 + - - +
237A ASP* 4.2 4.8 + - - +
284A ILE* 6.1 0.2 - - - +
249B ILE* 3.9 12.1 - - + +
250B PHE* 3.1 22.2 + - - +
252B VAL 5.1 1.4 - - - +
253B ALA* 5.4 2.0 - - - +
255B LEU* 3.7 25.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A GLN* 3.1 10.3 - - - -
219A VAL* 2.9 45.2 + - + +
221A ARG* 5.7 7.4 - - + +
223A THR* 5.9 0.9 - - - +
234A HIS* 3.6 26.0 - - + +
235A GLN* 1.3 72.7 - - - +
237A ASP* 1.3 76.2 + - - +
238A ILE* 3.6 1.2 + - - +
264A ASN 5.7 1.8 - - - +
266A PRO* 4.0 32.8 - - + -
243B GLY* 5.9 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A MET 3.9 2.9 - - - -
218A GLN* 4.5 15.5 - - - +
235A GLN 5.2 3.6 - - - +
236A VAL* 1.3 81.4 - - - +
238A ILE* 1.3 66.5 + - - +
239A PRO* 3.9 5.7 - - - +
266A PRO* 5.2 0.9 - - - +
241B GLU 4.8 0.2 - - - +
242B ASN* 3.0 38.0 + - - +
243B GLY* 2.6 37.2 + - - +
244B VAL* 3.8 11.2 - - + +
248B SER 4.6 3.5 - - - +
249B ILE* 5.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A HIS* 5.6 0.3 - - - -
217A MET* 2.8 48.2 + - + +
219A VAL* 3.5 35.2 - - + -
236A VAL 3.8 2.7 - - - +
237A ASP* 1.3 84.1 - - - +
239A PRO* 1.3 64.6 - - + +
240A MET* 3.6 11.1 + - - +
247A ASN* 5.6 0.9 - - - +
259A HIS* 3.3 47.1 - - + +
265A SER* 4.8 0.2 - - - +
266A PRO* 3.6 26.5 - - + -
267A LEU* 5.4 1.6 - - + -
244B VAL* 3.6 5.5 - - - +
----------------------------------------------------------
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