Contacts of the helix formed by residues 227 - 236 (chain B) in PDB entry 1ML3
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 GLY 227 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B THR* 1.3 73.9 + - - +
228B ALA* 1.3 55.7 + - - +
229B ALA 3.2 2.9 - - - -
230B LYS* 2.9 13.9 + - - +
231B ALA* 2.6 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B SER* 4.1 5.3 + - - +
167B THR* 3.3 42.6 - - + -
168B THR* 3.1 23.3 + - - +
190B MET* 4.0 5.2 - - + -
226B THR* 3.2 11.4 + - + +
227B GLY* 1.3 75.4 - - - +
229B ALA* 1.3 63.4 + - - +
231B ALA* 3.2 1.0 + - - -
232B VAL* 3.0 27.3 + - - +
1166B CYX 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 3.9 15.3 - - + -
190B MET* 3.8 17.1 - - + +
226B THR* 4.8 3.2 + - + +
227B GLY 3.0 1.0 + - - -
228B ALA* 1.3 78.1 - - - +
230B LYS* 1.3 64.6 + - - +
232B VAL* 3.0 21.1 + - - +
233B GLY 3.9 1.4 + - - -
243B LEU* 4.0 13.8 - - + +
244B THR* 3.2 39.5 - - - +
245B GLY* 3.4 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A PRO* 6.5 1.8 - - + -
226B THR 5.3 4.7 + - - +
227B GLY* 2.9 13.8 + - - +
229B ALA* 1.3 77.7 - - - +
231B ALA* 1.3 58.3 + - - +
233B GLY* 2.8 22.9 + - - +
234B MET* 4.1 2.9 + - - +
240B GLN* 5.8 1.9 + - - -
243B LEU 3.7 19.3 - - - +
244B THR* 4.0 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PRO* 6.1 7.6 - - + -
143B THR* 5.5 2.4 - - + +
164B ALA* 6.0 2.7 - - + -
168B THR* 3.5 17.4 - - + +
227B GLY 2.6 23.5 + - - +
228B ALA 3.4 6.5 - - - +
230B LYS* 1.3 72.2 - - - +
232B VAL* 1.3 62.5 + - - +
233B GLY 3.0 0.2 - - - -
234B MET* 3.1 36.3 + - - +
235B VAL* 3.7 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B THR* 4.0 17.3 - - + -
171B LEU* 3.5 28.0 - - + -
172B ALA* 4.3 13.7 - - + +
175B VAL* 4.5 4.5 - - + -
228B ALA 3.0 17.5 + - - +
229B ALA 3.0 11.8 + - - +
231B ALA* 1.3 76.7 - - - +
233B GLY* 1.3 55.9 + - - +
234B MET 3.0 0.6 + - - -
235B VAL* 3.2 4.0 + - + +
236B ILE* 2.8 52.8 + - + +
239B THR* 3.9 3.8 - - - +
243B LEU* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ALA 3.9 1.4 + - - -
230B LYS* 2.8 14.5 + - - -
232B VAL* 1.3 79.5 - - - +
234B MET* 1.3 60.0 + - - +
236B ILE 3.9 2.5 - - - -
237B PRO* 3.3 19.9 - - - +
239B THR* 3.5 15.6 + - - -
240B GLN* 3.4 34.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ALA 5.0 9.2 - - - +
141B ALA 4.4 9.9 - - - +
142B LYS* 5.5 3.1 + - - -
143B THR* 3.1 37.5 - - - +
149B ASN* 4.9 2.6 + - - -
152B GLU* 5.3 1.9 - - - +
230B LYS 4.9 1.3 - - - +
231B ALA* 3.1 27.2 + - - +
232B VAL 3.0 0.6 - - - -
233B GLY* 1.3 79.1 - - - +
235B VAL* 1.3 68.4 + - + +
237B PRO* 3.6 14.7 - - - +
240B GLN* 5.2 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B THR* 4.1 20.9 - - + +
145B VAL* 3.6 26.2 - - + -
148B VAL* 3.0 36.9 - - + +
149B ASN* 3.6 37.7 + - - +
152B GLU* 4.7 3.6 - - - +
168B THR* 4.7 7.4 - - + -
172B ALA* 4.8 4.0 - - + -
231B ALA 4.2 8.7 - - - +
232B VAL* 3.2 7.3 + - - +
234B MET* 1.3 78.0 - - - +
236B ILE* 1.3 59.2 + - + +
237B PRO* 3.3 8.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 4.0 14.4 - - + -
172B ALA 3.9 8.1 - - - +
175B VAL* 3.8 14.6 - - + -
176B HIS* 3.6 42.8 - - + +
179B VAL* 4.6 13.7 - - + -
232B VAL* 2.8 23.2 + - + +
233B GLY 3.8 1.4 - - - +
235B VAL* 1.3 78.1 - - + +
237B PRO* 1.3 65.0 - - + +
238B SER* 3.6 18.2 - - - +
239B THR* 2.6 40.1 + - + +
----------------------------------------------------------
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