Contacts of the strand formed by residues 227 - 235 (chain B) in PDB entry 1ITB
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 ILE 227 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 4.5 4.5 - - - -
221B VAL* 3.8 30.3 - - + -
225B SER* 4.7 3.4 - - - +
226B GLN* 1.3 83.7 + - - +
228B GLN* 1.3 62.5 + - - +
229B LEU* 3.5 26.5 - - + -
279B LEU 3.9 0.3 - - - +
280B ASN* 3.8 2.6 - - - +
281B ILE* 3.0 46.1 + - + +
284B ILE* 3.9 17.5 - - + -
310B LEU* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 5.4 3.6 - - - +
226B GLN* 6.0 2.7 - - - +
227B ILE* 1.3 76.6 - - - +
229B LEU* 1.3 67.0 + - - +
230B ILE* 4.1 17.4 + - + +
278B VAL* 3.7 22.0 - - + +
279B LEU 3.3 2.5 - - - -
280B ASN* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 4.0 24.0 - - + -
227B ILE* 3.5 28.7 - - + -
228B GLN* 1.3 76.1 - - - +
230B ILE* 1.3 61.7 + - - +
243B TRP* 3.9 12.7 + - + -
277B THR 3.7 1.6 - - - +
278B VAL* 3.7 0.5 - - - -
279B LEU* 2.8 68.4 + - + +
281B ILE* 4.2 6.7 - - + +
293B PHE* 3.9 30.1 - - + -
308B ILE* 4.5 20.9 - - + -
310B LEU* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B SER* 4.1 9.5 + - - -
214B PRO* 3.7 11.8 - - - +
228B GLN* 4.1 21.7 + - + +
229B LEU* 1.3 78.5 - - - +
231B CYS* 1.3 66.7 + - - +
232B ASN* 3.8 4.0 + - + +
243B TRP* 3.9 4.0 - - - -
276B ILE* 3.9 31.9 - - + -
277B THR 3.7 3.1 - - - +
278B VAL* 4.1 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ILE* 4.1 9.2 - - - -
214B PRO* 3.6 16.2 - - - -
230B ILE* 1.3 74.2 - - - +
232B ASN* 1.3 60.3 + - - +
233B VAL* 4.1 11.8 - - - +
241B ALA* 4.8 1.1 - - + +
243B TRP* 3.7 18.0 - - + +
275B LEU 3.5 1.7 - - - +
276B ILE* 3.5 6.9 - - - -
277B THR* 3.0 36.6 + - - +
295B CYS* 2.0 49.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ILE* 3.6 3.3 - - - +
212B VAL* 2.6 52.6 + - - +
213B SER* 3.5 20.2 + - - +
214B PRO* 3.9 4.0 - - - +
230B ILE* 3.8 5.5 + - + +
231B CYS* 1.3 74.5 - - - +
233B VAL* 1.3 68.8 + - - +
234B THR* 4.4 0.7 + - - -
274B THR* 3.9 12.5 - - - +
275B LEU 3.6 2.9 - - - -
276B ILE* 3.8 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PRO* 3.7 29.2 - - + -
210B VAL 3.3 9.2 - - - +
211B ILE* 4.2 6.1 - - + -
231B CYS* 4.1 13.7 - - - -
232B ASN* 1.3 82.1 + - - +
234B THR* 1.3 67.7 + - - +
241B ALA* 3.8 23.6 - - + -
273B SER 3.6 0.2 - - - +
274B THR* 3.1 7.3 - - - -
275B LEU* 2.9 53.7 + - + -
297B ALA* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG 5.1 0.2 - - - +
209B PRO* 3.9 1.2 - - - +
210B VAL* 2.8 46.8 + - + +
212B VAL* 3.4 19.7 - - - +
232B ASN* 4.4 1.0 + - - -
233B VAL* 1.3 72.2 + - - +
235B GLY* 1.3 59.5 + - - +
271B ARG 4.8 0.5 - - - +
272B ARG* 4.1 33.9 - - + +
273B SER 3.4 5.2 - - - +
274B THR* 4.3 11.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PRO* 4.6 7.2 - - - -
233B VAL* 3.9 4.1 - - - +
234B THR* 1.3 76.4 - - - +
236B GLN* 1.3 67.4 + - - +
239B ASP* 3.5 9.9 - - - -
271B ARG 3.6 17.0 - - - -
273B SER* 2.7 32.6 + - - +
275B LEU* 5.2 1.4 - - - +
----------------------------------------------------------
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