Contacts of the helix formed by residues 250 - 265 (chain A) in PDB entry 1WOH
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 THR 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.5 4.8 - - - -
234A ASP* 5.3 1.6 - - + -
237A VAL* 4.7 12.6 - - + -
248A GLY 4.9 2.9 - - - +
249A LEU* 1.3 78.5 - - - +
251A TYR* 1.3 64.9 + - - +
252A ALA* 3.4 8.3 + - - +
253A GLN* 2.9 44.3 + - + +
254A GLY 3.1 15.9 + - - -
247B ASP* 4.1 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PHE* 3.8 15.1 - + + -
237A VAL* 4.6 15.6 - - + +
238A ILE* 5.9 1.8 - - + -
250A THR* 1.3 74.3 - - - +
252A ALA* 1.3 59.5 + - - +
254A GLY* 3.3 0.7 + - - -
255A MET* 2.9 35.1 + - + +
288A LEU* 3.4 32.8 - - + -
289A MET* 6.1 1.8 - - - -
291A ARG* 3.0 21.7 + - - +
292A LEU* 3.3 39.2 + - + +
295A GLU* 2.8 28.3 + - - +
246B PRO* 3.5 33.2 - - + -
247B ASP* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR* 3.2 6.0 - - - +
251A TYR* 1.3 82.1 - - - +
253A GLN* 1.3 57.9 + - + +
255A MET* 3.4 4.4 + - - +
256A LYS* 2.9 53.1 + - - +
247B ASP* 3.1 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A MET* 3.6 15.1 - - - +
207A VAL* 4.0 25.3 + - + +
208A THR* 4.8 6.3 + - - +
211A LEU* 5.0 9.7 - - + +
248A GLY 4.0 0.9 - - - +
249A LEU* 3.4 16.8 - - + -
250A THR* 2.9 43.5 + - - +
252A ALA* 1.3 74.3 - - + +
254A GLY* 1.3 67.8 + - - +
256A LYS* 3.2 10.8 + - + +
257A ILE* 3.1 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 4.0 4.3 - - - +
233A PHE* 3.8 20.2 - - - -
249A LEU* 4.1 16.7 - - - +
250A THR 3.1 8.9 + - - -
251A TYR 3.8 2.0 - - - -
253A GLN* 1.3 77.7 - - - +
255A MET* 1.3 56.7 + - - +
257A ILE* 3.3 6.5 + - - +
258A LEU* 3.1 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A TYR* 2.9 26.5 + - + +
252A ALA* 3.7 5.4 - - - +
254A GLY* 1.3 74.1 - - - +
256A LYS* 1.3 60.1 + - + +
258A LEU* 4.0 9.9 - - + -
259A ALA* 2.8 34.1 + - + +
292A LEU* 3.6 22.9 - - + +
295A GLU* 3.4 41.5 - - + +
296A THR* 3.4 36.8 - - - +
299A GLU* 4.0 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 4.6 26.0 - - + -
215A LEU* 4.0 7.6 - - + +
252A ALA* 2.9 43.9 + - - +
253A GLN* 3.2 9.5 + - + +
255A MET* 1.3 75.9 - - + +
257A ILE* 1.3 58.9 + - - +
259A ALA* 3.8 5.8 - - - +
260A ALA* 3.0 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 4.8 7.9 - - + -
142A LEU* 3.9 23.3 - - + -
179A VAL* 3.7 29.6 - - + -
207A VAL* 4.8 1.8 - - + -
211A LEU* 4.4 12.8 - - + -
214A VAL* 4.9 3.6 - - + -
215A LEU* 3.9 19.1 - - + -
218A LEU* 3.5 29.1 - - + +
249A LEU* 4.0 19.1 - - + -
253A GLN 3.1 16.0 + - - +
254A GLY* 3.5 7.0 - - - +
255A MET 3.2 0.2 - - - -
256A LYS* 1.3 77.4 - - - +
258A LEU* 1.3 63.1 + - - +
260A ALA 3.4 0.2 + - - -
261A ALA* 3.1 19.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 5.0 4.5 - - + +
142A LEU* 3.9 29.4 - - + -
226A PHE* 3.7 38.8 - - + -
228A VAL* 4.2 13.9 - - + -
254A GLY 3.1 18.1 + - - +
255A MET* 3.9 11.4 - - + +
257A ILE* 1.3 75.7 - - - +
259A ALA* 1.3 57.8 + - - +
261A ALA 3.3 0.9 + - - -
262A ALA* 2.9 31.5 + - - +
270A LEU* 5.5 0.7 - - + -
292A LEU* 4.0 24.5 - - + -
296A THR* 3.5 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A MET* 2.8 25.6 + - + +
256A LYS* 3.8 6.7 - - - +
258A LEU* 1.3 71.5 - - - +
260A ALA* 1.3 63.8 + - - +
262A ALA* 3.3 2.8 + - - +
263A ALA* 3.1 24.6 + - - +
299A GLU* 3.8 42.4 - - + +
303A HIS* 5.5 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LEU* 4.0 22.2 - - + +
218A LEU* 4.0 14.4 - - + -
256A LYS 3.0 17.7 + - - +
257A ILE 3.6 4.5 - - - +
259A ALA* 1.3 76.9 - - - +
261A ALA* 1.3 62.8 + - - +
263A ALA* 3.3 9.2 + - - +
264A ASN* 3.0 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 4.5 13.7 - - + -
218A LEU* 4.1 15.6 - - + +
219A PRO* 5.2 0.7 - - + -
224A VAL* 5.3 1.1 - - + -
226A PHE* 3.4 28.5 - - + -
257A ILE 3.1 13.3 + - - +
260A ALA* 1.3 79.5 - - - +
262A ALA* 1.3 62.6 + - - +
264A ASN 3.4 0.3 + - - -
265A ASN* 2.9 42.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PHE* 3.8 4.9 - - + -
258A LEU 2.9 18.4 + - - +
259A ALA 3.3 4.7 + - - +
261A ALA* 1.3 76.0 - - - +
263A ALA* 1.3 61.3 + - - +
264A ASN 3.6 0.2 + - - -
265A ASN 3.7 12.5 - - - +
267A VAL* 4.0 13.6 - - - +
296A THR* 4.9 0.9 - - + +
299A GLU* 4.2 10.4 - - + +
300A VAL* 4.0 38.9 - - + +
303A HIS* 3.7 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ALA 3.1 16.9 + - - +
260A ALA* 3.7 7.2 - - - +
261A ALA 3.2 0.4 - - - -
262A ALA* 1.3 78.6 - - - +
264A ASN* 1.3 67.8 + - - +
265A ASN 3.7 0.4 - - - -
303A HIS* 3.6 47.7 + - + +
305A LEU* 5.6 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PRO 4.5 0.7 - - - +
220A ARG* 4.5 26.5 - - + +
221A GLY* 2.7 34.1 + - - -
260A ALA* 3.0 25.4 + - - +
261A ALA 3.4 2.4 + - - -
263A ALA* 1.3 88.2 - - - +
265A ASN* 1.3 61.0 + - - +
305A LEU* 6.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PRO* 2.7 26.9 + - - +
220A ARG* 3.3 9.0 + - - -
221A GLY* 3.1 9.2 + - - +
222A GLN* 2.9 34.8 + - - +
224A VAL* 3.7 21.4 - - + +
261A ALA* 2.9 32.8 + - - +
262A ALA 3.7 13.9 - - - +
263A ALA 3.7 0.6 - - - -
264A ASN* 1.3 82.7 - - - +
266A THR* 1.3 64.5 + - - +
267A VAL* 3.6 5.7 + - + +
303A HIS 5.1 4.5 - - - +
304A VAL* 5.9 1.6 - - - -
305A LEU* 5.1 8.9 - - - +
----------------------------------------------------------
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