Contacts of the helix formed by residues 224 - 234 (chain B) in PDB entry 1ZDT
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 PRO 224 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASN 4.1 3.8 - - - +
223B VAL* 1.3 90.6 - - + +
225B GLU* 1.3 66.9 + - - +
226B LEU* 3.1 2.5 - - + +
227B ILE* 2.9 20.3 + - + +
228B LEU* 3.1 9.4 + - - +
400B ALA* 3.6 42.8 - - + +
403B ASP* 3.9 19.1 - - + +
404B TYR* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL 3.5 2.6 + - - -
224B PRO* 1.3 69.4 - - - +
226B LEU* 1.3 64.2 + - - +
228B LEU* 3.1 22.9 + - - +
229B GLN* 2.8 56.3 + - - +
232B GLN* 5.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PRO* 3.0 1.4 + - + +
225B GLU* 1.3 76.7 - - - +
227B ILE* 1.3 58.4 + - - +
229B GLN* 3.2 13.9 + - - +
230B LEU* 2.8 49.5 + - + +
284B MET* 3.4 33.2 - - + -
370B CYS* 4.7 2.2 - - - -
373B PHE* 4.3 13.5 - - + -
396B LYS* 4.7 22.9 - - + +
397B ALA* 3.6 39.3 - - + +
400B ALA* 4.1 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL* 3.8 15.9 - - + -
224B PRO* 2.9 13.1 + - + +
226B LEU* 1.3 77.2 - - - +
228B LEU* 1.3 57.0 + - - +
230B LEU* 3.1 9.4 + - + +
231B LEU* 2.9 32.0 + - + +
366B GLN* 3.9 38.1 - - + +
369B VAL* 4.4 1.6 - - + -
370B CYS* 4.1 26.2 - - + -
400B ALA* 3.7 21.5 - - + +
401B LEU* 4.5 1.3 - - + +
404B TYR* 3.6 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL* 3.3 48.0 - - + +
224B PRO 3.1 4.5 + - - +
225B GLU* 3.1 26.4 + - - +
227B ILE* 1.3 75.6 - - - +
229B GLN* 1.3 59.3 + - - +
231B LEU* 3.5 18.2 + - + +
232B GLN* 3.2 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLU* 2.8 49.5 + - - +
226B LEU* 3.3 29.9 - - - +
228B LEU* 1.3 76.3 - - - +
230B LEU* 1.3 62.2 + - - +
232B GLN* 3.2 23.7 + - - +
233B LEU* 3.2 20.8 + - - +
284B MET* 3.6 35.0 - - - +
396B LYS* 6.1 1.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 2.8 34.6 + - + +
227B ILE* 3.1 9.8 + - - +
229B GLN* 1.3 74.4 - - - +
231B LEU* 1.3 63.2 + - - +
233B LEU* 3.4 4.6 + - + +
234B GLU* 3.1 24.9 + - - +
279B TRP* 4.5 9.7 + - + +
283B CYS* 4.1 13.7 - - - -
284B MET* 3.8 14.8 - - + -
369B VAL* 3.6 36.5 - - + +
370B CYS* 3.9 12.1 - - + +
373B PHE* 3.5 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B VAL* 5.4 0.7 - - + -
227B ILE* 2.9 19.9 + - + +
228B LEU* 3.6 25.1 - - + +
230B LEU* 1.3 76.7 - - - +
232B GLN* 1.3 62.5 + - + +
233B LEU 3.4 0.3 + - - -
234B GLU* 3.5 16.3 + - - +
365B ARG* 3.8 44.6 + - + +
366B GLN* 3.9 28.7 - - + +
369B VAL* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLU* 5.0 4.8 + - - -
228B LEU* 3.2 28.5 + - - +
229B GLN* 3.2 20.0 + - - +
231B LEU* 1.3 78.8 - - + +
233B LEU* 1.3 66.5 + - + +
234B GLU 3.9 2.5 + - - +
282B ARG* 4.6 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B GLN* 3.2 12.5 + - + +
230B LEU* 3.8 6.3 - - - +
231B LEU 3.2 0.8 - - - -
232B GLN* 1.3 84.7 - - + +
234B GLU* 1.3 61.5 + - - +
235B PRO* 3.3 9.9 - - - +
279B TRP* 3.5 21.6 - - + +
282B ARG* 3.3 66.9 + - + +
283B CYS* 3.7 14.1 - - - -
284B MET* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU 3.1 14.0 + - - +
231B LEU* 3.8 11.7 - - - +
232B GLN 3.5 3.8 - - - +
233B LEU* 1.3 75.4 - - - +
235B PRO* 1.3 85.3 - - - +
236B ASP* 3.4 2.4 + - - -
279B TRP* 3.9 5.7 + - - -
365B ARG* 3.2 36.1 + - - +
368B PHE* 3.7 16.7 - - + -
369B VAL* 3.8 22.3 - - + +
372B LYS* 3.3 32.4 + - - -
----------------------------------------------------------
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