Contacts of the strand formed by residues 227 - 234 (chain H) in PDB entry 1B6C
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 227 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175H THR 4.5 1.4 - - - +
176H THR* 3.2 22.9 - - + +
177H LEU* 2.9 51.6 + - + +
178H LYS 4.7 0.9 + - - -
223H LYS* 3.1 3.8 - - - -
224H TRP* 2.8 51.2 + - + +
225H ARG 3.2 4.3 + - - +
226H GLY* 1.3 69.8 - - - -
228H GLU* 1.3 74.0 + - - +
229H VAL* 3.6 1.0 + - - +
263H ILE* 5.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 228 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H ARG* 2.6 44.0 + - + +
222H GLY 3.4 5.6 - - - +
223H LYS* 4.4 10.5 - - + +
226H GLY 3.5 2.8 + - - +
227H GLU* 1.3 86.6 - - - +
229H VAL* 1.3 62.2 + - - +
281H ASP* 5.6 0.7 - - - -
282H TYR* 3.9 37.5 + - + +
284H GLU* 5.4 2.6 - - - +
343H LYS* 5.3 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177H LEU* 4.4 12.3 - - + -
205H ILE* 4.0 24.9 - - + -
221H ARG* 3.7 4.9 - - - +
222H GLY* 2.5 51.1 + - - +
223H LYS* 4.2 2.7 - - - +
224H TRP* 5.2 1.1 - - + +
227H GLU* 4.4 3.6 - - - +
228H GLU* 1.3 78.5 - - - +
230H ALA* 1.3 57.6 + - - +
231H VAL* 4.1 7.2 - - + -
263H ILE* 3.2 24.0 - - + -
279H VAL* 3.2 12.6 - - + -
280H SER 3.2 22.2 - - - +
281H ASP* 5.2 0.4 - - - -
282H TYR* 3.8 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211H ILE* 5.7 0.7 - - + -
219H VAL* 4.9 10.8 - - + -
220H TRP 3.6 5.4 - - - +
229H VAL* 1.3 74.5 - - - +
231H VAL* 1.3 62.7 + - - +
232H LYS 5.7 0.2 - - - +
278H LEU 3.5 0.9 - - - +
279H VAL* 3.2 6.2 - - - +
280H SER* 2.8 43.3 + - - +
281H ASP 3.2 24.2 - - - +
282H TYR* 4.1 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205H ILE* 4.2 17.0 - - + -
207H LEU* 4.0 22.9 - - + -
218H GLU 3.7 0.2 - - - +
219H VAL* 3.4 3.3 - - - +
220H TRP* 2.8 42.9 + - + +
222H GLY* 4.8 1.3 - - - -
229H VAL* 4.1 18.6 - - + -
230H ALA* 1.3 78.6 - - - +
232H LYS* 1.3 61.9 + - - +
233H ILE* 3.6 14.7 + - + +
277H TRP* 3.4 39.0 - - + -
278H LEU 3.4 6.1 - - - +
279H VAL* 4.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 232 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H PHE* 4.0 17.0 - - + +
217H GLY 4.9 0.7 - - - +
218H GLU 3.4 10.1 - - - +
219H VAL* 3.8 23.1 - - + +
230H ALA 4.1 0.6 - - - -
231H VAL* 1.3 73.2 - - - +
233H ILE* 1.3 60.9 + - - +
234H PHE* 3.3 40.9 - - + -
245H GLU* 4.1 6.6 + - - -
276H LEU 3.5 4.2 - - - +
277H TRP* 3.5 1.6 - - - -
278H LEU* 2.7 45.2 + - + +
351H ASP* 2.9 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 233 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207H LEU* 4.1 18.8 - - + -
217H GLY* 3.3 4.4 - - - -
218H GLU* 2.7 36.2 + - + +
220H TRP* 3.8 26.9 - - + +
231H VAL* 3.9 13.9 - - + +
232H LYS* 1.3 75.3 - - - +
234H PHE* 1.3 67.6 + - - +
275H GLN* 3.6 36.6 - - + +
276H LEU 3.3 6.7 - - - +
277H TRP* 3.7 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 234 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H PHE* 4.0 15.9 - - + -
232H LYS* 3.3 47.6 - - + -
233H ILE* 1.3 81.4 - - - +
235H SER* 1.3 66.0 + - - +
236H SER 4.2 0.2 + - - -
238H GLU* 3.7 24.0 - - + +
241H SER* 4.1 11.2 - - - -
242H TRP* 3.7 43.7 - + + -
245H GLU* 4.1 13.5 - - - -
275H GLN* 5.1 1.6 - - - +
276H LEU* 2.9 36.4 + - + +
278H LEU* 3.8 21.1 - - + -
351H ASP* 5.7 1.3 - - - -
353H GLY* 6.3 0.2 - - - -
372H ARG* 5.2 2.0 - - - -
----------------------------------------------------------
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